#################### # Tab completion file to allow for easy use of this tool with the command-line using Bash. #################### #################################################################################################### # High-level caller/dispatch script information: CALLER_SCRIPT_NAME="gatk" # A description of these variables is below in the main completion function (_masterCompletionFunction) CS_PREFIX_OPTIONS_ALL_LEGAL_ARGUMENTS=(--help --list --dry-run --java-options FixCallSetSampleOrdering ClippingRankSumTest CleanSam BedToIntervalList CreateSomaticPanelOfNormals GatherVcfsCloud FlagStat ParallelCopyGCSDirectoryIntoHDFSSpark CompareSAMs PairedReadFilter StrandBiasBySample SecondOfPairReadFilter DetermineGermlineContigPloidy FastaAlternateReferenceMaker FastaReferenceMaker MeanQualityByCycleSpark PileupSpark HaplotypeCaller GatherBamFiles EstimateLibraryComplexity LiftoverVcf MergeVcfs NonChimericOriginalAlignmentReadFilter LeftAlignAndTrimVariants ASEReadCounter ValidAlignmentEndReadFilter FindBadGenomicKmersSpark CNNVariantWriteTensors SortVcf ReferenceBases ClusterCrosscheckMetrics AnnotateVcfWithBamDepth AS_BaseQualityRankSumTest CreateReadCountPanelOfNormals AS_InbreedingCoeff CollectInsertSizeMetricsSpark MappingQuality ReadLengthReadFilter CollectMultipleMetricsSpark MergeSamFiles CountBasesInReference CountFalsePositives PrintVariantsSpark MarkDuplicatesSpark AccumulateVariantCallingMetrics FilterVcf FisherStrand ChromosomeCounts QualityScoreDistributionSpark GatherVcfs MatchingBasesAndQualsReadFilter PathSeqBwaSpark RenameSampleInVcf CountVariants DownsampleSam CollectHiSeqXPfFailMetrics RMSMappingQuality MappingQualityReadFilter MappingQualityZero IntervalListToBed CollectJumpingLibraryMetrics CNNVariantTrain ExtractSequences ReadLengthEqualsCigarLengthReadFilter FirstOfPairReadFilter CollectReadCounts ReplaceSamHeader Mutect2 CollectQualityYieldMetricsSpark Concordance EvaluateInfoFieldConcordance AS_FisherStrand ScatterIntervalsByNs AS_ReadPosRankSumTest VariantAnnotator MergeBamAlignment SamToFastq AddCommentsToBam CreateSequenceDictionary WellformedReadFilter CollectIlluminaBasecallingMetrics ReadStrandFilter SampleReadFilter MateDifferentStrandReadFilter ApplyBQSR AnnotatePairOrientation RevertBaseQualityScores ViewSam IlluminaBasecallsToSam DiscoverVariantsFromContigAlignmentsSAMSpark AS_MappingQualityRankSumTest NonNFastaSize ReblockGVCF LikelihoodRankSumTest MappedReadFilter SplitNCigarReads SvDiscoverFromLocalAssemblyContigAlignmentsSpark QualByDepth MappingQualityRankSumTest BaitDesigner CollectIndependentReplicateMetrics ReadPosRankSumTest ReadsPipelineSpark AnnotateVcfWithExpectedAlleleFraction CpxVariantReInterpreterSpark ExcessHet ReadGroupReadFilter TandemRepeat ModelSegments CallCopyRatioSegments SetNmMdAndUqTags CountReadsSpark CollectQualityYieldMetrics AllowAllReadsReadFilter AnnotateIntervals CollectInsertSizeMetrics CNNScoreVariants LibraryReadFilter FifoBuffer UpdateVcfSequenceDictionary IntervalListTools PossibleDeNovo CollectWgsMetricsWithNonZeroCoverage GermlineCNVCaller AS_StrandOddsRatio CollectVariantCallingMetrics CountBasesSpark ConvertHeaderlessHadoopBamShardToBam FastqToSam MarkIlluminaAdapters CollectIlluminaLaneMetrics GenotypeGVCFs HaplotypeCallerSpark SimpleMarkDuplicatesWithMateCigar UnmarkDuplicates CountVariantsSpark DepthPerSampleHC MappingQualityNotZeroReadFilter FindMendelianViolations SamFormatConverter SplitSamByLibrary CompareMetrics CollectSequencingArtifactMetrics MarkDuplicates SampleList CollectMultipleMetrics ExtractSVEvidenceSpark NotDuplicateReadFilter IlluminaBasecallsToFastq ReadPosition IndexFeatureFile AS_QualByDepth FixVcfHeader PostprocessGermlineCNVCalls StrandArtifact Coverage ReadNameReadFilter PathSeqFilterSpark BwaSpark FilterSamReads RevertSamSpark PositionBasedDownsampleSam SeqIsStoredReadFilter CollectAlignmentSummaryMetrics CollectWgsMetrics BamToBfq CheckIlluminaDirectory NotSecondaryAlignmentReadFilter CigarContainsNoNOperator CheckFingerprint AddOrReplaceReadGroups VcfToIntervalList CalculateMixingFractions Pileup SplitReads ApplyVQSR PlotDenoisedCopyRatios ReorderSam PathSeqScoreSpark ProperlyPairedReadFilter ConvertSequencingArtifactToOxoG FixMateInformation DenoiseReadCounts GenomicsDBImport FuncotatorDataSourceDownloader CheckPileup UmiAwareMarkDuplicatesWithMateCigar ClipReads ReadGroupBlackListReadFilter GetPileupSummaries BuildBamIndex AlignmentAgreesWithHeaderReadFilter NotSupplementaryAlignmentReadFilter ExtractOriginalAlignmentRecordsByNameSpark AS_RMSMappingQuality BQSRPipelineSpark FilterFuncotations UpdateVCFSequenceDictionary BaseRecalibratorSpark CollectRawWgsMetrics DepthPerAlleleBySample SelectVariants AnalyzeCovariates PathSeqBuildReferenceTaxonomy FilterAlignmentArtifacts PrintReads CalculateReadGroupChecksum CollectRnaSeqMetrics GetSampleName CompareBaseQualities BamIndexStats CollectOxoGMetrics VariantEval MarkDuplicatesWithMateCigar GatherBQSRReports GenotypeConcordance CompareDuplicatesSpark BaseQualityRankSumTest CountNs MateOnSameContigOrNoMappedMateReadFilter BaseRecalibrator PlatformUnitReadFilter SortSamSpark SetNmAndUqTags OxoGReadCounts VariantRecalibrator ValidateBasicSomaticShortMutations OverclippedReadFilter FragmentLength CountBases PlatformReadFilter LiftOverIntervalList PassesVendorQualityCheckReadFilter PrimaryLineReadFilter CollectBaseDistributionByCycle PrintReadsSpark PathSeqBuildKmers VariantFiltration InbreedingCoeff MetricsReadFilter FilterIntervals RevertSam CountReads UniqueAltReadCount MeanQualityByCycle VcfFormatConverter FilterByOrientationBias VariantsToTable CollectRrbsMetrics CheckTerminatorBlock GatherTranches AlleleFraction QualityScoreDistribution FlagStatSpark NormalizeFasta ValidAlignmentStartReadFilter HasReadGroupReadFilter MakeSitesOnlyVcf BaseQuality SplitSamByNumberOfReads ExtractIlluminaBarcodes FindBreakpointEvidenceSpark CalculateContamination CombineGVCFs FixMisencodedBaseQualityReads RevertOriginalBaseQualitiesAndAddMateCigar BwaAndMarkDuplicatesPipelineSpark AddOATag Funcotator MappingQualityAvailableReadFilter PathSeqPipelineSpark CollectHsMetrics ValidateVariants FilterMutectCalls CrosscheckFingerprints SplitIntervals FragmentLengthReadFilter AmbiguousBaseReadFilter ApplyBQSRSpark CalcMetadataSpark SortSam OriginalAlignment StructuralVariationDiscoveryPipelineSpark NonZeroReferenceLengthAlignmentReadFilter ValidateSamFile CollectGcBiasMetrics SplitVcfs LeftAlignIndels CreateHadoopBamSplittingIndex CrosscheckReadGroupFingerprints CollectBaseDistributionByCycleSpark FilterVariantTranches CalculateGenotypePosteriors NonZeroFragmentLengthReadFilter GenotypeSummaries CollectTargetedPcrMetrics CollectAllelicCounts StrandOddsRatio BwaMemIndexImageCreator PlotModeledSegments RemoveNearbyIndels PreprocessIntervals GoodCigarReadFilter PolymorphicNuMT ) CS_PREFIX_OPTIONS_NORMAL_COMPLETION_ARGUMENTS=(--help --list --dry-run --java-options FixCallSetSampleOrdering ClippingRankSumTest CleanSam BedToIntervalList CreateSomaticPanelOfNormals GatherVcfsCloud FlagStat ParallelCopyGCSDirectoryIntoHDFSSpark CompareSAMs PairedReadFilter StrandBiasBySample SecondOfPairReadFilter DetermineGermlineContigPloidy FastaAlternateReferenceMaker FastaReferenceMaker MeanQualityByCycleSpark PileupSpark HaplotypeCaller GatherBamFiles EstimateLibraryComplexity LiftoverVcf MergeVcfs NonChimericOriginalAlignmentReadFilter LeftAlignAndTrimVariants ASEReadCounter ValidAlignmentEndReadFilter FindBadGenomicKmersSpark CNNVariantWriteTensors SortVcf ReferenceBases ClusterCrosscheckMetrics AnnotateVcfWithBamDepth AS_BaseQualityRankSumTest CreateReadCountPanelOfNormals AS_InbreedingCoeff CollectInsertSizeMetricsSpark MappingQuality ReadLengthReadFilter CollectMultipleMetricsSpark MergeSamFiles CountBasesInReference CountFalsePositives PrintVariantsSpark MarkDuplicatesSpark AccumulateVariantCallingMetrics FilterVcf FisherStrand ChromosomeCounts QualityScoreDistributionSpark GatherVcfs MatchingBasesAndQualsReadFilter PathSeqBwaSpark RenameSampleInVcf CountVariants DownsampleSam CollectHiSeqXPfFailMetrics RMSMappingQuality MappingQualityReadFilter MappingQualityZero IntervalListToBed CollectJumpingLibraryMetrics CNNVariantTrain ExtractSequences ReadLengthEqualsCigarLengthReadFilter FirstOfPairReadFilter CollectReadCounts ReplaceSamHeader Mutect2 CollectQualityYieldMetricsSpark Concordance EvaluateInfoFieldConcordance AS_FisherStrand ScatterIntervalsByNs AS_ReadPosRankSumTest VariantAnnotator MergeBamAlignment SamToFastq AddCommentsToBam CreateSequenceDictionary WellformedReadFilter CollectIlluminaBasecallingMetrics ReadStrandFilter SampleReadFilter MateDifferentStrandReadFilter ApplyBQSR AnnotatePairOrientation RevertBaseQualityScores ViewSam IlluminaBasecallsToSam DiscoverVariantsFromContigAlignmentsSAMSpark AS_MappingQualityRankSumTest NonNFastaSize ReblockGVCF LikelihoodRankSumTest MappedReadFilter SplitNCigarReads SvDiscoverFromLocalAssemblyContigAlignmentsSpark QualByDepth MappingQualityRankSumTest BaitDesigner CollectIndependentReplicateMetrics ReadPosRankSumTest ReadsPipelineSpark AnnotateVcfWithExpectedAlleleFraction CpxVariantReInterpreterSpark ExcessHet ReadGroupReadFilter TandemRepeat ModelSegments CallCopyRatioSegments SetNmMdAndUqTags CountReadsSpark CollectQualityYieldMetrics AllowAllReadsReadFilter AnnotateIntervals CollectInsertSizeMetrics CNNScoreVariants LibraryReadFilter FifoBuffer UpdateVcfSequenceDictionary IntervalListTools PossibleDeNovo CollectWgsMetricsWithNonZeroCoverage GermlineCNVCaller AS_StrandOddsRatio CollectVariantCallingMetrics CountBasesSpark ConvertHeaderlessHadoopBamShardToBam FastqToSam MarkIlluminaAdapters CollectIlluminaLaneMetrics GenotypeGVCFs HaplotypeCallerSpark SimpleMarkDuplicatesWithMateCigar UnmarkDuplicates CountVariantsSpark DepthPerSampleHC MappingQualityNotZeroReadFilter FindMendelianViolations SamFormatConverter SplitSamByLibrary CompareMetrics CollectSequencingArtifactMetrics MarkDuplicates SampleList CollectMultipleMetrics ExtractSVEvidenceSpark NotDuplicateReadFilter IlluminaBasecallsToFastq ReadPosition IndexFeatureFile AS_QualByDepth FixVcfHeader PostprocessGermlineCNVCalls StrandArtifact Coverage ReadNameReadFilter PathSeqFilterSpark BwaSpark FilterSamReads RevertSamSpark PositionBasedDownsampleSam SeqIsStoredReadFilter CollectAlignmentSummaryMetrics CollectWgsMetrics BamToBfq CheckIlluminaDirectory NotSecondaryAlignmentReadFilter CigarContainsNoNOperator CheckFingerprint AddOrReplaceReadGroups VcfToIntervalList CalculateMixingFractions Pileup SplitReads ApplyVQSR PlotDenoisedCopyRatios ReorderSam PathSeqScoreSpark ProperlyPairedReadFilter ConvertSequencingArtifactToOxoG FixMateInformation DenoiseReadCounts GenomicsDBImport FuncotatorDataSourceDownloader CheckPileup UmiAwareMarkDuplicatesWithMateCigar ClipReads ReadGroupBlackListReadFilter GetPileupSummaries BuildBamIndex AlignmentAgreesWithHeaderReadFilter NotSupplementaryAlignmentReadFilter ExtractOriginalAlignmentRecordsByNameSpark AS_RMSMappingQuality BQSRPipelineSpark FilterFuncotations UpdateVCFSequenceDictionary BaseRecalibratorSpark CollectRawWgsMetrics DepthPerAlleleBySample SelectVariants AnalyzeCovariates PathSeqBuildReferenceTaxonomy FilterAlignmentArtifacts PrintReads CalculateReadGroupChecksum CollectRnaSeqMetrics GetSampleName CompareBaseQualities BamIndexStats CollectOxoGMetrics VariantEval MarkDuplicatesWithMateCigar GatherBQSRReports GenotypeConcordance CompareDuplicatesSpark BaseQualityRankSumTest CountNs MateOnSameContigOrNoMappedMateReadFilter BaseRecalibrator PlatformUnitReadFilter SortSamSpark SetNmAndUqTags OxoGReadCounts VariantRecalibrator ValidateBasicSomaticShortMutations OverclippedReadFilter FragmentLength CountBases PlatformReadFilter LiftOverIntervalList PassesVendorQualityCheckReadFilter PrimaryLineReadFilter CollectBaseDistributionByCycle PrintReadsSpark PathSeqBuildKmers VariantFiltration InbreedingCoeff MetricsReadFilter FilterIntervals RevertSam CountReads UniqueAltReadCount MeanQualityByCycle VcfFormatConverter FilterByOrientationBias VariantsToTable CollectRrbsMetrics CheckTerminatorBlock GatherTranches AlleleFraction QualityScoreDistribution FlagStatSpark NormalizeFasta ValidAlignmentStartReadFilter HasReadGroupReadFilter MakeSitesOnlyVcf BaseQuality SplitSamByNumberOfReads ExtractIlluminaBarcodes FindBreakpointEvidenceSpark CalculateContamination CombineGVCFs FixMisencodedBaseQualityReads RevertOriginalBaseQualitiesAndAddMateCigar BwaAndMarkDuplicatesPipelineSpark AddOATag Funcotator MappingQualityAvailableReadFilter PathSeqPipelineSpark CollectHsMetrics ValidateVariants FilterMutectCalls CrosscheckFingerprints SplitIntervals FragmentLengthReadFilter AmbiguousBaseReadFilter ApplyBQSRSpark CalcMetadataSpark SortSam OriginalAlignment StructuralVariationDiscoveryPipelineSpark NonZeroReferenceLengthAlignmentReadFilter ValidateSamFile CollectGcBiasMetrics SplitVcfs LeftAlignIndels CreateHadoopBamSplittingIndex CrosscheckReadGroupFingerprints CollectBaseDistributionByCycleSpark FilterVariantTranches CalculateGenotypePosteriors NonZeroFragmentLengthReadFilter GenotypeSummaries CollectTargetedPcrMetrics CollectAllelicCounts StrandOddsRatio BwaMemIndexImageCreator PlotModeledSegments RemoveNearbyIndels PreprocessIntervals GoodCigarReadFilter PolymorphicNuMT ) CS_PREFIX_OPTIONS_ALL_ARGUMENT_VALUE_TYPES=("null" "null" "null" "String" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" "null" ) CS_PREFIX_OPTIONS_MUTUALLY_EXCLUSIVE_ARGS=("--help;list,dry-run,java-options" "--list;help,dry-run,java-options") CS_PREFIX_OPTIONS_SYNONYMOUS_ARGS=("--help;-h") CS_PREFIX_OPTIONS_MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) CS_PREFIX_OPTIONS_MAX_OCCURRENCES=(1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 ) CS_POSTFIX_OPTIONS_ALL_LEGAL_ARGUMENTS=(--spark-runner --spark-master --cluster --dry-run --java-options --conf --driver-memory --driver-cores --executor-memory --executor-cores --num-executors) CS_POSTFIX_OPTIONS_NORMAL_COMPLETION_ARGUMENTS=(--spark-runner --spark-master --cluster --dry-run --java-options --conf --driver-memory --driver-cores --executor-memory --executor-cores --num-executors) CS_POSTFIX_OPTIONS_ALL_ARGUMENT_VALUE_TYPES=("String" "String" "String" "null" "String" "file" "int" "int" "int" "int" "int") CS_POSTFIX_OPTIONS_MUTUALLY_EXCLUSIVE_ARGS=("") CS_POSTFIX_OPTIONS_SYNONYMOUS_ARGS=("") CS_POSTFIX_OPTIONS_MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0) CS_POSTFIX_OPTIONS_MAX_OCCURRENCES=(1 1 1 1 1 1 1 1 1 1) # Whether we have to worry about these extra script options at all. HAS_POSTFIX_OPTIONS="true" # All the tool names we are able to complete: ALL_TOOLS=(FixCallSetSampleOrdering ClippingRankSumTest CleanSam BedToIntervalList CreateSomaticPanelOfNormals GatherVcfsCloud FlagStat ParallelCopyGCSDirectoryIntoHDFSSpark CompareSAMs PairedReadFilter StrandBiasBySample SecondOfPairReadFilter DetermineGermlineContigPloidy FastaAlternateReferenceMaker FastaReferenceMaker MeanQualityByCycleSpark PileupSpark HaplotypeCaller GatherBamFiles EstimateLibraryComplexity LiftoverVcf MergeVcfs NonChimericOriginalAlignmentReadFilter LeftAlignAndTrimVariants ASEReadCounter ValidAlignmentEndReadFilter FindBadGenomicKmersSpark CNNVariantWriteTensors SortVcf ReferenceBases ClusterCrosscheckMetrics AnnotateVcfWithBamDepth AS_BaseQualityRankSumTest CreateReadCountPanelOfNormals AS_InbreedingCoeff CollectInsertSizeMetricsSpark MappingQuality ReadLengthReadFilter CollectMultipleMetricsSpark MergeSamFiles CountBasesInReference CountFalsePositives PrintVariantsSpark MarkDuplicatesSpark AccumulateVariantCallingMetrics FilterVcf FisherStrand ChromosomeCounts QualityScoreDistributionSpark GatherVcfs MatchingBasesAndQualsReadFilter PathSeqBwaSpark RenameSampleInVcf CountVariants DownsampleSam CollectHiSeqXPfFailMetrics RMSMappingQuality MappingQualityReadFilter MappingQualityZero IntervalListToBed CollectJumpingLibraryMetrics CNNVariantTrain ExtractSequences ReadLengthEqualsCigarLengthReadFilter FirstOfPairReadFilter CollectReadCounts ReplaceSamHeader Mutect2 CollectQualityYieldMetricsSpark Concordance EvaluateInfoFieldConcordance AS_FisherStrand ScatterIntervalsByNs AS_ReadPosRankSumTest VariantAnnotator MergeBamAlignment SamToFastq AddCommentsToBam CreateSequenceDictionary WellformedReadFilter CollectIlluminaBasecallingMetrics ReadStrandFilter SampleReadFilter MateDifferentStrandReadFilter ApplyBQSR AnnotatePairOrientation RevertBaseQualityScores ViewSam IlluminaBasecallsToSam DiscoverVariantsFromContigAlignmentsSAMSpark AS_MappingQualityRankSumTest NonNFastaSize ReblockGVCF LikelihoodRankSumTest MappedReadFilter SplitNCigarReads SvDiscoverFromLocalAssemblyContigAlignmentsSpark QualByDepth MappingQualityRankSumTest BaitDesigner CollectIndependentReplicateMetrics ReadPosRankSumTest ReadsPipelineSpark AnnotateVcfWithExpectedAlleleFraction CpxVariantReInterpreterSpark ExcessHet ReadGroupReadFilter TandemRepeat ModelSegments CallCopyRatioSegments SetNmMdAndUqTags CountReadsSpark CollectQualityYieldMetrics AllowAllReadsReadFilter AnnotateIntervals CollectInsertSizeMetrics CNNScoreVariants LibraryReadFilter FifoBuffer UpdateVcfSequenceDictionary IntervalListTools PossibleDeNovo CollectWgsMetricsWithNonZeroCoverage GermlineCNVCaller AS_StrandOddsRatio CollectVariantCallingMetrics CountBasesSpark ConvertHeaderlessHadoopBamShardToBam FastqToSam MarkIlluminaAdapters CollectIlluminaLaneMetrics GenotypeGVCFs HaplotypeCallerSpark SimpleMarkDuplicatesWithMateCigar UnmarkDuplicates CountVariantsSpark DepthPerSampleHC MappingQualityNotZeroReadFilter FindMendelianViolations SamFormatConverter SplitSamByLibrary CompareMetrics CollectSequencingArtifactMetrics MarkDuplicates SampleList CollectMultipleMetrics ExtractSVEvidenceSpark NotDuplicateReadFilter IlluminaBasecallsToFastq ReadPosition IndexFeatureFile AS_QualByDepth FixVcfHeader PostprocessGermlineCNVCalls StrandArtifact Coverage ReadNameReadFilter PathSeqFilterSpark BwaSpark FilterSamReads RevertSamSpark PositionBasedDownsampleSam SeqIsStoredReadFilter CollectAlignmentSummaryMetrics CollectWgsMetrics BamToBfq CheckIlluminaDirectory NotSecondaryAlignmentReadFilter CigarContainsNoNOperator CheckFingerprint AddOrReplaceReadGroups VcfToIntervalList CalculateMixingFractions Pileup SplitReads ApplyVQSR PlotDenoisedCopyRatios ReorderSam PathSeqScoreSpark ProperlyPairedReadFilter ConvertSequencingArtifactToOxoG FixMateInformation DenoiseReadCounts GenomicsDBImport FuncotatorDataSourceDownloader CheckPileup UmiAwareMarkDuplicatesWithMateCigar ClipReads ReadGroupBlackListReadFilter GetPileupSummaries BuildBamIndex AlignmentAgreesWithHeaderReadFilter NotSupplementaryAlignmentReadFilter ExtractOriginalAlignmentRecordsByNameSpark AS_RMSMappingQuality BQSRPipelineSpark FilterFuncotations UpdateVCFSequenceDictionary BaseRecalibratorSpark CollectRawWgsMetrics DepthPerAlleleBySample SelectVariants AnalyzeCovariates PathSeqBuildReferenceTaxonomy FilterAlignmentArtifacts PrintReads CalculateReadGroupChecksum CollectRnaSeqMetrics GetSampleName CompareBaseQualities BamIndexStats CollectOxoGMetrics VariantEval MarkDuplicatesWithMateCigar GatherBQSRReports GenotypeConcordance CompareDuplicatesSpark BaseQualityRankSumTest CountNs MateOnSameContigOrNoMappedMateReadFilter BaseRecalibrator PlatformUnitReadFilter SortSamSpark SetNmAndUqTags OxoGReadCounts VariantRecalibrator ValidateBasicSomaticShortMutations OverclippedReadFilter FragmentLength CountBases PlatformReadFilter LiftOverIntervalList PassesVendorQualityCheckReadFilter PrimaryLineReadFilter CollectBaseDistributionByCycle PrintReadsSpark PathSeqBuildKmers VariantFiltration InbreedingCoeff MetricsReadFilter FilterIntervals RevertSam CountReads UniqueAltReadCount MeanQualityByCycle VcfFormatConverter FilterByOrientationBias VariantsToTable CollectRrbsMetrics CheckTerminatorBlock GatherTranches AlleleFraction QualityScoreDistribution FlagStatSpark NormalizeFasta ValidAlignmentStartReadFilter HasReadGroupReadFilter MakeSitesOnlyVcf BaseQuality SplitSamByNumberOfReads ExtractIlluminaBarcodes FindBreakpointEvidenceSpark CalculateContamination CombineGVCFs FixMisencodedBaseQualityReads RevertOriginalBaseQualitiesAndAddMateCigar BwaAndMarkDuplicatesPipelineSpark AddOATag Funcotator MappingQualityAvailableReadFilter PathSeqPipelineSpark CollectHsMetrics ValidateVariants FilterMutectCalls CrosscheckFingerprints SplitIntervals FragmentLengthReadFilter AmbiguousBaseReadFilter ApplyBQSRSpark CalcMetadataSpark SortSam OriginalAlignment StructuralVariationDiscoveryPipelineSpark NonZeroReferenceLengthAlignmentReadFilter ValidateSamFile CollectGcBiasMetrics SplitVcfs LeftAlignIndels CreateHadoopBamSplittingIndex CrosscheckReadGroupFingerprints CollectBaseDistributionByCycleSpark FilterVariantTranches CalculateGenotypePosteriors NonZeroFragmentLengthReadFilter GenotypeSummaries CollectTargetedPcrMetrics CollectAllelicCounts StrandOddsRatio BwaMemIndexImageCreator PlotModeledSegments RemoveNearbyIndels PreprocessIntervals GoodCigarReadFilter PolymorphicNuMT ) #################################################################################################### # Get the name of the tool that we're currently trying to call _gatk_getToolName() { # Naively go through each word in the line until we find one that is in our list of tools: for word in ${COMP_WORDS[@]} ; do if ( echo " ${ALL_TOOLS[@]} " | grep -q " ${word} " ) ; then echo "${word}" break fi done } # Get the index of the toolname inside COMP_WORDS _gatk_getToolNameIndex() { # Naively go through each word in the line until we find one that is in our list of tools: local ctr=0 for word in ${COMP_WORDS[@]} ; do if ( echo " ${ALL_TOOLS[@]} " | grep -q " ${word} " ) ; then echo $ctr break fi let ctr=$ctr+1 done } # Get all possible tool names for the current command line if the current command is a # complete command on its own already. # If there is no complete command yet, then this prints nothing. _gatk_getAllPossibleToolNames() { # We want to return a list of possible tool names if and only if # the current word is a valid complete tool name # AND # the current word is also a substring in more than one tool name local tool count matches toolList let count=0 matches=false toolList=() # Go through tool names and get what matches and partial matches we have: for tool in ${ALL_TOOLS[@]} ; do if [[ "${COMP_WORDS[COMP_CWORD]}" == "${tool}" ]] ; then matches=true let count=$count+1 toolList+=($tool) elif [[ "${tool}" == "${COMP_WORDS[COMP_CWORD]}"* ]] ; then toolList+=($tool) fi done # If we have a complete match, then we print out our partial matches as a space separated string. # That way we have a list of all possible full completions for this match. # For instance, if there was a tool named "read" and another named "readBetter" this would get both. if $matches ; then echo "${toolList[@]}" fi } # Gets how many dependent arguments we have left to fill _gatk_getDependentArgumentCount() { local depArgCount=0 for word in ${COMP_LINE} ; do for depArg in ${DEPENDENT_ARGUMENTS[@]} ; do if [[ "${word}" == "${depArg}" ]] ; then $((depArgCount++)) fi done done echo $depArgCount } # Resolves the given argument name to its long (normal) name _gatk_resolveVarName() { local argName=$1 if [[ "${SYNONYMOUS_ARGS[@]}" == *"${argName}"* ]] ; then echo "${SYNONYMOUS_ARGS[@]}" | sed -e "s#.* \\([a-zA-Z0-9;,_\\-]*${argName}[a-zA-Z0-9,;_\\-]*\\).*#\\1#g" -e 's#;.*##g' else echo "${argName}" fi } # Checks if we need to complete the VALUE for an argument. # Prints the index in the given argument list of the corresponding argument whose value we must complete. # Takes as input 1 positional argument: the name of the last argument given to this script # Otherwise prints -1 _gatk_needToCompleteArgValue() { if [[ "${prev}" != "--" ]] ; then local resolved=$( _gatk_resolveVarName ${prev} ) for (( i=0 ; i < ${#ALL_LEGAL_ARGUMENTS[@]} ; i++ )) ; do if [[ "${resolved}" == "${ALL_LEGAL_ARGUMENTS[i]}" ]] ; then # Make sure the argument isn't one that takes no additional value # such as a flag. if [[ "${ALL_ARGUMENT_VALUE_TYPES[i]}" != "null" ]] ; then echo "$i" else echo "-1" fi return 0 fi done fi echo "-1" } # Get the completion word list for the given argument type. # Prints the completion string to the screen _gatk_getCompletionWordList() { # Normalize the type string so it's easier to deal with: local argType=$( echo $1 | tr '[A-Z]' '[a-z]') local isNumeric=false local isFloating=false local completionType="" [[ "${argType}" == *"file"* ]] && completionType='-A file' [[ "${argType}" == *"folder"* ]] && completionType='-A directory' [[ "${argType}" == *"directory"* ]] && completionType='-A directory' [[ "${argType}" == *"boolean"* ]] && completionType='-W true false' [[ "${argType}" == "int" ]] && completionType='-W 0 1 2 3 4 5 6 7 8 9' && isNumeric=true [[ "${argType}" == *"[int]"* ]] && completionType='-W 0 1 2 3 4 5 6 7 8 9' && isNumeric=true [[ "${argType}" == "long" ]] && completionType='-W 0 1 2 3 4 5 6 7 8 9' && isNumeric=true [[ "${argType}" == *"[long]"* ]] && completionType='-W 0 1 2 3 4 5 6 7 8 9' && isNumeric=true [[ "${argType}" == "double" ]] && completionType='-W . 0 1 2 3 4 5 6 7 8 9' && isNumeric=true && isFloating=true [[ "${argType}" == *"[double]"* ]] && completionType='-W . 0 1 2 3 4 5 6 7 8 9' && isNumeric=true && isFloating=true [[ "${argType}" == "float" ]] && completionType='-W . 0 1 2 3 4 5 6 7 8 9' && isNumeric=true && isFloating=true [[ "${argType}" == *"[float]"* ]] && completionType='-W . 0 1 2 3 4 5 6 7 8 9' && isNumeric=true && isFloating=true # If we have a number, we need to prepend the current completion to it so that we can continue to tab complete: if $isNumeric ; then completionType=$( echo ${completionType} | sed -e "s#\([0-9]\)#$cur\1#g" ) # If we're floating point, we need to make sure we don't complete a `.` character # if one already exists in our number: if $isFloating ; then echo "$cur" | grep -o '\.' &> /dev/null local r=$? [[ $r -eq 0 ]] && completionType=$( echo ${completionType} | awk '{$2="" ; print}' ) fi fi echo "${completionType}" } # Function to handle the completion tasks once we have populated our arg variables # When passed an argument handles the case for the caller script. _gatk_handleArgs() { # Argument offset index is used in the special case where we are past the " -- " delimiter. local argOffsetIndex=0 # We handle the beginning differently if this function was called with an argument if [[ $# -eq 0 ]] ; then # Get the number of arguments we have input so far: local toolNameIndex=$(_gatk_getToolNameIndex) local numArgs=$((COMP_CWORD-toolNameIndex-1)) # Now we check to see what kind of argument we are on right now # We handle each type separately by order of precedence: if [[ ${numArgs} -lt ${NUM_POSITIONAL_ARGUMENTS} ]] ; then # We must complete a positional argument. # Assume that positional arguments are all FILES: COMPREPLY=( $(compgen -A file -- $cur) ) return 0 fi # Dependent arguments must come right after positional arguments # We must check to see how many dependent arguments we've gotten so far: local numDepArgs=$( _gatk_getDependentArgumentCount ) if [[ $numDepArgs -lt ${#DEPENDENT_ARGUMENTS[@]} ]] ; then # We must complete a dependent argument next. COMPREPLY=( $(compgen -W '${DEPENDENT_ARGUMENTS[@]}' -- $cur) ) return 0 fi elif [[ "${1}" == "POSTFIX_OPTIONS" ]] ; then # Get the index of the special delimiter. # we ignore everything up to and including it. for (( i=0; i < COMP_CWORD ; i++ )) ; do if [[ "${COMP_WORDS[i]}" == "--" ]] ; then let argOffsetIndex=$i+1 fi done fi # NOTE: We don't need to worry about the prefix options case. # The caller will specify it and it skips the two special cases above. # First we must resolve all arguments to their full names # This is necessary to save time later because of short argument names / synonyms local resolvedArgList=() for (( i=argOffsetIndex ; i < COMP_CWORD ; i++ )) ; do prevArg=${COMP_WORDS[i]} # Skip the current word to be completed: [[ "${prevArg}" == "${cur}" ]] && continue # Check if this has synonyms: if [[ "${SYNONYMOUS_ARGS[@]}" == *"${prevArg}"* ]] ; then local resolvedArg=$( _gatk_resolveVarName "${prevArg}" ) resolvedArgList+=($resolvedArg) # Make sure this is an argument: elif [[ "${ALL_LEGAL_ARGUMENTS[@]}" == *"${prevArg}"* ]] ; then resolvedArgList+=($prevArg) fi done # Check to see if the last thing we typed was a complete argument. # If so, we must complete the VALUE for the argument, not the # argument itself: # Note: This is shorthand for last element in the array: local argToComplete=$( _gatk_needToCompleteArgValue ) if [[ $argToComplete -ne -1 ]] ; then # We must complete the VALUE for an argument. # Get the argument type. local valueType=${ALL_ARGUMENT_VALUE_TYPES[argToComplete]} # Get the correct completion string for the type: local completionString=$( _gatk_getCompletionWordList "${valueType}" ) if [[ ${#completionString} -eq 0 ]] ; then # We don't have any information on the type to complete. # We use the default SHELL behavior: COMPREPLY=() else # We have a completion option. Let's plug it in: local compOperator=$( echo "${completionString}" | awk '{print $1}' ) local compOptions=$( echo "${completionString}" | awk '{$1="" ; print}' ) case ${compOperator} in -A) COMPREPLY=( $(compgen -A ${compOptions} -- $cur) ) ;; -W) COMPREPLY=( $(compgen -W '${compOptions}' -- $cur) ) ;; *) COMPREPLY=() ;; esac fi return 0 fi # We must create a list of the valid remaining arguments: # Create a list of all arguments that are # mutually exclusive with arguments we have already specified local mutex_list="" for prevArg in ${resolvedArgList[@]} ; do if [[ "${MUTUALLY_EXCLUSIVE_ARGS[@]}" == *"${prevArg};"* ]] ; then local mutexArgs=$( echo "${MUTUALLY_EXCLUSIVE_ARGS[@]}" | sed -e "s#.*${prevArg};\([a-zA-Z0-9_,\-]*\) .*#\1#g" -e "s#,# --#g" -e "s#^#--#g" ) mutex_list="${mutex_list}${mutexArgs}" fi done local remaining_legal_arguments=() for (( i=0; i < ${#NORMAL_COMPLETION_ARGUMENTS[@]} ; i++ )) ; do local legalArg=${NORMAL_COMPLETION_ARGUMENTS[i]} local okToAdd=true # Get the number of times this has occurred in the arguments already: local numPrevOccurred=$( grep -o -- "${legalArg}" <<< "${resolvedArgList[@]}" | wc -l | awk '{print $1}' ) if [[ $numPrevOccurred -lt "${MAX_OCCURRENCES[i]}" ]] ; then # Make sure this arg isn't mutually exclusive to another argument that we've already had: if [[ "${mutex_list}" == "${legalArg} "* ]] || [[ "${mutex_list}" == *" ${legalArg} "* ]] || [[ "${mutex_list}" == *" ${legalArg}" ]] ; then okToAdd=false fi # Check if we're still good to add in the argument: if $okToAdd ; then # Add in the argument: remaining_legal_arguments+=($legalArg) # Add in the synonyms of the argument: if [[ "${SYNONYMOUS_ARGS[@]}" == *"${legalArg}"* ]] ; then local synonymString=$( echo "${SYNONYMOUS_ARGS[@]}" | sed -e "s#.*${legalArg};\([a-zA-Z0-9_,\-]*\).*#\1#g" -e "s#,# #g" ) remaining_legal_arguments+=($synonymString) fi fi fi done # Add in the special option "--" which separates tool options from meta-options if they're necessary: if $HAS_POSTFIX_OPTIONS ; then if [[ $# -eq 0 ]] || [[ "${1}" == "PREFIX_OPTIONS" ]] ; then remaining_legal_arguments+=("--") fi fi COMPREPLY=( $(compgen -W '${remaining_legal_arguments[@]}' -- $cur) ) return 0 } #################################################################################################### _gatk_masterCompletionFunction() { # Set up global variables for the functions that do completion: prev=${COMP_WORDS[COMP_CWORD-1]} cur=${COMP_WORDS[COMP_CWORD]} # How many positional arguments a tool will have. # These positional arguments must come directly after a tool name. NUM_POSITIONAL_ARGUMENTS=0 # The types of the positional arguments, in the order in which they must be specified # on the command-line. POSITIONAL_ARGUMENT_TYPE=() # The set of legal arguments that aren't dependent arguments. # (A dependent argument is an argument that must occur immediately after # all positional arguments.) NORMAL_COMPLETION_ARGUMENTS=() # The set of ALL legal arguments # Corresponds by index to the type of those arguments in ALL_ARGUMENT_VALUE_TYPES ALL_LEGAL_ARGUMENTS=() # The types of ALL legal arguments # Corresponds by index to the names of those arguments in ALL_LEGAL_ARGUMENTS ALL_ARGUMENT_VALUE_TYPES=() # Arguments that are mutually exclusive. # These are listed here as arguments concatenated together with delimiters: #
;[,,...] MUTUALLY_EXCLUSIVE_ARGS=() # Alternate names of arguments. # These are listed here as arguments concatenated together with delimiters. #
;[,,...] SYNONYMOUS_ARGS=() # The minimum number of times an argument can occur. MIN_OCCURRENCES=() # The maximum number of times an argument can occur. MAX_OCCURRENCES=() # Set up locals for this function: local toolName=$( _gatk_getToolName ) # Get possible tool matches: local possibleToolMatches=$( _gatk_getAllPossibleToolNames ) # Check if we have postfix options # and if we now need to go through them: if $HAS_POSTFIX_OPTIONS && [[ "${COMP_WORDS[@]}" == *" -- "* ]] ; then NUM_POSITIONAL_ARGUMENTS=0 POSITIONAL_ARGUMENT_TYPE=() DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=("${CS_POSTFIX_OPTIONS_NORMAL_COMPLETION_ARGUMENTS[@]}") MUTUALLY_EXCLUSIVE_ARGS=("${CS_POSTFIX_OPTIONS_MUTUALLY_EXCLUSIVE_ARGS[@]}") SYNONYMOUS_ARGS=("${CS_POSTFIX_OPTIONS_SYNONYMOUS_ARGS[@]}") MIN_OCCURRENCES=("${CS_POSTFIX_OPTIONS_MIN_OCCURRENCES[@]}") MAX_OCCURRENCES=("${CS_POSTFIX_OPTIONS_MAX_OCCURRENCES[@]}") ALL_LEGAL_ARGUMENTS=("${CS_POSTFIX_OPTIONS_ALL_LEGAL_ARGUMENTS[@]}") ALL_ARGUMENT_VALUE_TYPES=("${CS_POSTFIX_OPTIONS_ALL_ARGUMENT_VALUE_TYPES[@]}") # Complete the arguments for the base script: # Strictly speaking, what the argument to this function is doesn't matter. _gatk_handleArgs POSTFIX_OPTIONS # Check if we have a complete tool match that may match more than one tool: elif [[ ${#possibleToolMatches} -ne 0 ]] ; then # Set our reply as a list of the possible tool matches: COMPREPLY=( $(compgen -W '${possibleToolMatches[@]}' -- $cur) ) elif [[ ${toolName} == "FixCallSetSampleOrdering" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--batch-size --output --reader-threads --sample-name-map --variant --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --gvcf-to-header-sample-map-file --help --interval-merging-rule --intervals --reference --sites-only-vcf-output --skipPrompt --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--output;-O" "--variant;-V" "--add-output-sam-program-record;-add-output-sam-program-record" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-bam-md5;-OBM" "--create-output-variant-index;-OVI" "--create-output-variant-md5;-OVM" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--input;-I" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--lenient;-LE" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--seconds-between-progress-updates;-seconds-between-progress-updates" "--sequence-dictionary;-sequence-dictionary" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--cloud-index-prefetch-buffer;-CIPB" "--cloud-prefetch-buffer;-CPB" "--disable-bam-index-caching;-DBIC" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--reference;-R" "--skipPrompt;-Y" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--batch-size --output --reader-threads --sample-name-map --variant --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --gvcf-to-header-sample-map-file --help --interval-merging-rule --intervals --reference --sites-only-vcf-output --skipPrompt --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("Integer" "File" "Integer" "String" "String" "boolean" "boolean" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "List[String]" "int" "int" "IntervalSetRule" "boolean" "Boolean" "List[String]" "List[String]" "ValidationStringency" "double" "String" "String" "boolean" "boolean" "LogLevel" "List[File]" "int" "int" "boolean" "boolean" "int" "String" "String" "boolean" "IntervalMergingRule" "List[String]" "String" "boolean" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "ClippingRankSumTest" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=() MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=() MAX_OCCURRENCES=() ALL_LEGAL_ARGUMENTS=() ALL_ARGUMENT_VALUE_TYPES=() # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "CleanSam" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--INPUT --OUTPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--INPUT;-I" "--OUTPUT;-O" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--help;-h" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--INPUT --OUTPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "File" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "List[File]" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "BedToIntervalList" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--INPUT --OUTPUT --SEQUENCE_DICTIONARY --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --SORT --UNIQUE --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--INPUT;-I" "--OUTPUT;-O" "--SEQUENCE_DICTIONARY;-SD" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--help;-h" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--INPUT --OUTPUT --SEQUENCE_DICTIONARY --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --SORT --UNIQUE --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "File" "File" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "List[File]" "boolean" "boolean" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "CreateSomaticPanelOfNormals" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--output --vcfs --gatk-config-file --QUIET --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --duplicate-sample-strategy --gcs-max-retries --gcs-project-for-requester-pays --help --min-sample-count --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--output;-O" "--vcfs;-vcfs" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--gcs-max-retries;-gcs-retries" "--help;-h" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--output --vcfs --gatk-config-file --QUIET --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --duplicate-sample-strategy --gcs-max-retries --gcs-project-for-requester-pays --help --min-sample-count --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "Set[File]" "String" "Boolean" "String" "boolean" "boolean" "LogLevel" "List[File]" "DuplicateSampleStrategy" "int" "String" "boolean" "int" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "GatherVcfsCloud" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--input --output --gatk-config-file --QUIET --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-prefetch-buffer --create-output-variant-index --gather-type --gcs-max-retries --gcs-project-for-requester-pays --help --version --disable-contig-ordering-check --ignore-safety-checks --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--input;-I" "--output;-O" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--cloud-prefetch-buffer;-CPB" "--create-output-variant-index;-OVI" "--gcs-max-retries;-gcs-retries" "--help;-h" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--input --output --gatk-config-file --QUIET --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-prefetch-buffer --create-output-variant-index --gather-type --gcs-max-retries --gcs-project-for-requester-pays --help --version --disable-contig-ordering-check --ignore-safety-checks --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("List[String]" "File" "String" "Boolean" "String" "boolean" "boolean" "LogLevel" "List[File]" "int" "boolean" "GatherType" "int" "String" "boolean" "boolean" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "FlagStat" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--input --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --reference --sites-only-vcf-output --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--input;-I" "--add-output-sam-program-record;-add-output-sam-program-record" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-bam-md5;-OBM" "--create-output-variant-index;-OVI" "--create-output-variant-md5;-OVM" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--lenient;-LE" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--seconds-between-progress-updates;-seconds-between-progress-updates" "--sequence-dictionary;-sequence-dictionary" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--cloud-index-prefetch-buffer;-CIPB" "--cloud-prefetch-buffer;-CPB" "--disable-bam-index-caching;-DBIC" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--reference;-R" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--input --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --reference --sites-only-vcf-output --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("List[String]" "boolean" "boolean" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "int" "int" "IntervalSetRule" "boolean" "Boolean" "List[String]" "List[String]" "ValidationStringency" "double" "String" "String" "boolean" "boolean" "LogLevel" "List[File]" "int" "int" "boolean" "boolean" "int" "String" "boolean" "IntervalMergingRule" "List[String]" "String" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "ParallelCopyGCSDirectoryIntoHDFSSpark" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--input-gcs-path --output-hdfs-directory --add-output-vcf-command-line --create-output-bam-index --create-output-bam-splitting-index --create-output-variant-index --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --read-filter --read-index --read-validation-stringency --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --bam-partition-size --conf --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --input-file-glob --interval-merging-rule --intervals --num-reducers --output-shard-tmp-dir --program-name --reference --sharded-output --spark-master --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=("--output-shard-tmp-dir;sharded-output" "--sharded-output;output-shard-tmp-dir" ) SYNONYMOUS_ARGS=("--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-variant-index;-OVI" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--input;-I" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--conf;-conf" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--reference;-R" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--input-gcs-path --output-hdfs-directory --add-output-vcf-command-line --create-output-bam-index --create-output-bam-splitting-index --create-output-variant-index --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --read-filter --read-index --read-validation-stringency --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --bam-partition-size --conf --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --input-file-glob --interval-merging-rule --intervals --num-reducers --output-shard-tmp-dir --program-name --reference --sharded-output --spark-master --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("String" "String" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "List[String]" "int" "int" "IntervalSetRule" "Boolean" "List[String]" "List[String]" "ValidationStringency" "String" "boolean" "boolean" "LogLevel" "List[File]" "long" "List[String]" "boolean" "int" "String" "boolean" "String" "IntervalMergingRule" "List[String]" "int" "String" "String" "String" "boolean" "String" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "CompareSAMs" ]] ; then # Set up the completion information for this tool: NUM_POSITIONAL_ARGUMENTS=2 POSITIONAL_ARGUMENT_TYPE=("List[File]") DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--help;-h" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "List[File]" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "PairedReadFilter" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=() MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=() MAX_OCCURRENCES=() ALL_LEGAL_ARGUMENTS=() ALL_ARGUMENT_VALUE_TYPES=() # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "StrandBiasBySample" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=() MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=() MAX_OCCURRENCES=() ALL_LEGAL_ARGUMENTS=() ALL_ARGUMENT_VALUE_TYPES=() # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "SecondOfPairReadFilter" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=() MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=() MAX_OCCURRENCES=() ALL_LEGAL_ARGUMENTS=() ALL_ARGUMENT_VALUE_TYPES=() # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "DetermineGermlineContigPloidy" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--input --output --output-prefix --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --adamax-beta-1 --adamax-beta-2 --arguments_file --caller-external-admixing-rate --caller-internal-admixing-rate --caller-update-convergence-threshold --contig-ploidy-priors --convergence-snr-averaging-window --convergence-snr-countdown-window --convergence-snr-trigger-threshold --disable-annealing --disable-caller --disable-sampler --gcs-max-retries --gcs-project-for-requester-pays --global-psi-scale --help --initial-temperature --interval-merging-rule --intervals --learning-rate --log-emission-samples-per-round --log-emission-sampling-median-rel-error --log-emission-sampling-rounds --mapping-error-rate --max-advi-iter-first-epoch --max-advi-iter-subsequent-epochs --max-calling-iters --max-training-epochs --mean-bias-standard-deviation --min-training-epochs --model --num-thermal-advi-iters --sample-psi-scale --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--input;-I" "--output;-O" "--exclude-intervals;-XL" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--input --output --output-prefix --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --adamax-beta-1 --adamax-beta-2 --arguments_file --caller-external-admixing-rate --caller-internal-admixing-rate --caller-update-convergence-threshold --contig-ploidy-priors --convergence-snr-averaging-window --convergence-snr-countdown-window --convergence-snr-trigger-threshold --disable-annealing --disable-caller --disable-sampler --gcs-max-retries --gcs-project-for-requester-pays --global-psi-scale --help --initial-temperature --interval-merging-rule --intervals --learning-rate --log-emission-samples-per-round --log-emission-sampling-median-rel-error --log-emission-sampling-rounds --mapping-error-rate --max-advi-iter-first-epoch --max-advi-iter-subsequent-epochs --max-calling-iters --max-training-epochs --mean-bias-standard-deviation --min-training-epochs --model --num-thermal-advi-iters --sample-psi-scale --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("List[File]" "String" "String" "List[String]" "String" "int" "int" "IntervalSetRule" "Boolean" "String" "boolean" "boolean" "LogLevel" "double" "double" "List[File]" "double" "double" "double" "File" "int" "int" "double" "boolean" "boolean" "boolean" "int" "String" "double" "boolean" "double" "IntervalMergingRule" "List[String]" "double" "int" "double" "int" "double" "int" "int" "int" "int" "double" "int" "String" "int" "double" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "FastaAlternateReferenceMaker" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--output --reference --variant --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --line-width --sites-only-vcf-output --snp-mask --snp-mask-priority --use-iupac-sample --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--output;-O" "--reference;-R" "--variant;-V" "--add-output-sam-program-record;-add-output-sam-program-record" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-bam-md5;-OBM" "--create-output-variant-index;-OVI" "--create-output-variant-md5;-OVM" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--input;-I" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--lenient;-LE" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--seconds-between-progress-updates;-seconds-between-progress-updates" "--sequence-dictionary;-sequence-dictionary" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--cloud-index-prefetch-buffer;-CIPB" "--cloud-prefetch-buffer;-CPB" "--disable-bam-index-caching;-DBIC" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--output --reference --variant --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --line-width --sites-only-vcf-output --snp-mask --snp-mask-priority --use-iupac-sample --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("String" "String" "FeatureInput[VariantContext]" "boolean" "boolean" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "List[String]" "int" "int" "IntervalSetRule" "boolean" "Boolean" "List[String]" "List[String]" "ValidationStringency" "double" "String" "String" "boolean" "boolean" "LogLevel" "List[File]" "int" "int" "boolean" "boolean" "int" "String" "boolean" "IntervalMergingRule" "List[String]" "int" "boolean" "FeatureInput[VariantContext]" "boolean" "String" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "FastaReferenceMaker" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--output --reference --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --line-width --sites-only-vcf-output --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--output;-O" "--reference;-R" "--add-output-sam-program-record;-add-output-sam-program-record" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-bam-md5;-OBM" "--create-output-variant-index;-OVI" "--create-output-variant-md5;-OVM" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--input;-I" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--lenient;-LE" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--seconds-between-progress-updates;-seconds-between-progress-updates" "--sequence-dictionary;-sequence-dictionary" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--cloud-index-prefetch-buffer;-CIPB" "--cloud-prefetch-buffer;-CPB" "--disable-bam-index-caching;-DBIC" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--output --reference --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --line-width --sites-only-vcf-output --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("String" "String" "boolean" "boolean" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "List[String]" "int" "int" "IntervalSetRule" "boolean" "Boolean" "List[String]" "List[String]" "ValidationStringency" "double" "String" "String" "boolean" "boolean" "LogLevel" "List[File]" "int" "int" "boolean" "boolean" "int" "String" "boolean" "IntervalMergingRule" "List[String]" "int" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "MeanQualityByCycleSpark" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--add-output-vcf-command-line --create-output-bam-index --create-output-bam-splitting-index --create-output-variant-index --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --read-filter --read-index --read-validation-stringency --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --alignedReadsOnly --arguments_file --bam-partition-size --chart --conf --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --num-reducers --output --output-shard-tmp-dir --pfReadsOnly --program-name --reference --sharded-output --spark-master --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=("--output-shard-tmp-dir;sharded-output" "--sharded-output;output-shard-tmp-dir" ) SYNONYMOUS_ARGS=("--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-variant-index;-OVI" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--input;-I" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--alignedReadsOnly;-A" "--chart;-C" "--conf;-conf" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--output;-O" "--pfReadsOnly;-F" "--reference;-R" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--add-output-vcf-command-line --create-output-bam-index --create-output-bam-splitting-index --create-output-variant-index --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --read-filter --read-index --read-validation-stringency --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --alignedReadsOnly --arguments_file --bam-partition-size --chart --conf --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --num-reducers --output --output-shard-tmp-dir --pfReadsOnly --program-name --reference --sharded-output --spark-master --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "List[String]" "int" "int" "IntervalSetRule" "Boolean" "List[String]" "List[String]" "ValidationStringency" "String" "boolean" "boolean" "LogLevel" "boolean" "List[File]" "long" "File" "List[String]" "boolean" "int" "String" "boolean" "IntervalMergingRule" "List[String]" "int" "String" "String" "boolean" "String" "String" "boolean" "String" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "PileupSpark" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--input --output --add-output-vcf-command-line --create-output-bam-index --create-output-bam-splitting-index --create-output-variant-index --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --read-filter --read-index --read-validation-stringency --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --bam-partition-size --conf --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --maxDepthPerSample --metadata --num-reducers --output-insert-length --output-shard-tmp-dir --program-name --readShardSize --reference --sharded-output --show-verbose --shuffle --spark-master --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=("--output-shard-tmp-dir;sharded-output" "--sharded-output;output-shard-tmp-dir" ) SYNONYMOUS_ARGS=("--input;-I" "--output;-O" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-variant-index;-OVI" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--conf;-conf" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--maxDepthPerSample;-maxDepthPerSample" "--metadata;-metadata" "--output-insert-length;-output-insert-length" "--readShardSize;-readShardSize" "--reference;-R" "--show-verbose;-verbose" "--shuffle;-shuffle" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--input --output --add-output-vcf-command-line --create-output-bam-index --create-output-bam-splitting-index --create-output-variant-index --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --read-filter --read-index --read-validation-stringency --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --bam-partition-size --conf --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --maxDepthPerSample --metadata --num-reducers --output-insert-length --output-shard-tmp-dir --program-name --readShardSize --reference --sharded-output --show-verbose --shuffle --spark-master --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("List[String]" "String" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "int" "int" "IntervalSetRule" "Boolean" "List[String]" "List[String]" "ValidationStringency" "String" "boolean" "boolean" "LogLevel" "List[File]" "long" "List[String]" "boolean" "int" "String" "boolean" "IntervalMergingRule" "List[String]" "int" "List[FeatureInput[Feature]]" "int" "boolean" "String" "String" "int" "String" "boolean" "boolean" "boolean" "String" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "HaplotypeCaller" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--input --output --reference --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --activity-profile-out --alleles --annotate-with-num-discovered-alleles --annotation --annotation-group --annotations-to-exclude --arguments_file --assembly-region-out --base-quality-score-threshold --cloud-index-prefetch-buffer --cloud-prefetch-buffer --contamination-fraction-to-filter --correct-overlapping-quality --dbsnp --disable-bam-index-caching --disable-sequence-dictionary-validation --founder-id --gcs-max-retries --gcs-project-for-requester-pays --genotyping-mode --graph-output --help --heterozygosity --heterozygosity-stdev --indel-heterozygosity --interval-merging-rule --intervals --max-reads-per-alignment-start --min-base-quality-score --native-pair-hmm-threads --native-pair-hmm-use-double-precision --num-reference-samples-if-no-call --output-mode --pedigree --population-callset --sample-name --sample-ploidy --sites-only-vcf-output --standard-min-confidence-threshold-for-calling --use-old-qual-calculator --version --active-probability-threshold --adaptive-pruning --adaptive-pruning-initial-error-rate --allow-non-unique-kmers-in-ref --all-site-pls --assembly-region-padding --bam-output --bam-writer-type --comp --consensus --contamination-fraction-per-sample-file --debug --disable-optimizations --disable-tool-default-annotations --do-not-run-physical-phasing --dont-increase-kmer-sizes-for-cycles --dont-trim-active-regions --dont-use-soft-clipped-bases --emit-ref-confidence --enable-all-annotations --genotype-filtered-alleles --gvcf-gq-bands --indel-size-to-eliminate-in-ref-model --input-prior --kmer-size --max-alternate-alleles --max-assembly-region-size --max-genotype-count --max-mnp-distance --max-num-haplotypes-in-population --max-prob-propagation-distance --max-unpruned-variants --min-assembly-region-size --min-dangling-branch-length --min-pruning --num-pruning-samples --pair-hmm-gap-continuation-penalty --pair-hmm-implementation --pcr-indel-model --phred-scaled-global-read-mismapping-rate --pruning-lod-threshold --showHidden --smith-waterman --use-alleles-trigger --use-filtered-reads-for-annotations --recover-dangling-heads --use-new-qual-calculator ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--input;-I" "--output;-O" "--reference;-R" "--add-output-sam-program-record;-add-output-sam-program-record" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-bam-md5;-OBM" "--create-output-variant-index;-OVI" "--create-output-variant-md5;-OVM" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--lenient;-LE" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--seconds-between-progress-updates;-seconds-between-progress-updates" "--sequence-dictionary;-sequence-dictionary" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--annotation;-A" "--annotation-group;-G" "--annotations-to-exclude;-AX" "--cloud-index-prefetch-buffer;-CIPB" "--cloud-prefetch-buffer;-CPB" "--contamination-fraction-to-filter;-contamination" "--dbsnp;-D" "--disable-bam-index-caching;-DBIC" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--founder-id;-founder-id" "--gcs-max-retries;-gcs-retries" "--graph-output;-graph" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--min-base-quality-score;-mbq" "--pedigree;-ped" "--population-callset;-population" "--sample-name;-ALIAS" "--sample-ploidy;-ploidy" "--standard-min-confidence-threshold-for-calling;-stand-call-conf" "--use-old-qual-calculator;-old-qual" "--bam-output;-bamout" "--comp;-comp" "--contamination-fraction-per-sample-file;-contamination-file" "--debug;-debug" "--disable-tool-default-annotations;-disable-tool-default-annotations" "--emit-ref-confidence;-ERC" "--gvcf-gq-bands;-GQB" "--max-mnp-distance;-mnp-dist" "--pair-hmm-implementation;-pairHMM" "--showHidden;-showHidden" "--use-new-qual-calculator;-new-qual" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--input --output --reference --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --activity-profile-out --alleles --annotate-with-num-discovered-alleles --annotation --annotation-group --annotations-to-exclude --arguments_file --assembly-region-out --base-quality-score-threshold --cloud-index-prefetch-buffer --cloud-prefetch-buffer --contamination-fraction-to-filter --correct-overlapping-quality --dbsnp --disable-bam-index-caching --disable-sequence-dictionary-validation --founder-id --gcs-max-retries --gcs-project-for-requester-pays --genotyping-mode --graph-output --help --heterozygosity --heterozygosity-stdev --indel-heterozygosity --interval-merging-rule --intervals --max-reads-per-alignment-start --min-base-quality-score --native-pair-hmm-threads --native-pair-hmm-use-double-precision --num-reference-samples-if-no-call --output-mode --pedigree --population-callset --sample-name --sample-ploidy --sites-only-vcf-output --standard-min-confidence-threshold-for-calling --use-old-qual-calculator --version --active-probability-threshold --adaptive-pruning --adaptive-pruning-initial-error-rate --allow-non-unique-kmers-in-ref --all-site-pls --assembly-region-padding --bam-output --bam-writer-type --comp --consensus --contamination-fraction-per-sample-file --debug --disable-optimizations --disable-tool-default-annotations --do-not-run-physical-phasing --dont-increase-kmer-sizes-for-cycles --dont-trim-active-regions --dont-use-soft-clipped-bases --emit-ref-confidence --enable-all-annotations --genotype-filtered-alleles --gvcf-gq-bands --indel-size-to-eliminate-in-ref-model --input-prior --kmer-size --max-alternate-alleles --max-assembly-region-size --max-genotype-count --max-mnp-distance --max-num-haplotypes-in-population --max-prob-propagation-distance --max-unpruned-variants --min-assembly-region-size --min-dangling-branch-length --min-pruning --num-pruning-samples --pair-hmm-gap-continuation-penalty --pair-hmm-implementation --pcr-indel-model --phred-scaled-global-read-mismapping-rate --pruning-lod-threshold --showHidden --smith-waterman --use-alleles-trigger --use-filtered-reads-for-annotations --recover-dangling-heads --use-new-qual-calculator ) ALL_ARGUMENT_VALUE_TYPES=("List[String]" "String" "String" "boolean" "boolean" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "int" "int" "IntervalSetRule" "boolean" "Boolean" "List[String]" "List[String]" "ValidationStringency" "double" "String" "String" "boolean" "boolean" "LogLevel" "String" "FeatureInput[VariantContext]" "boolean" "List[String]" "List[String]" "List[String]" "List[File]" "String" "byte" "int" "int" "double" "boolean" "FeatureInput[VariantContext]" "boolean" "boolean" "List[String]" "int" "String" "GenotypingOutputMode" "String" "boolean" "Double" "double" "double" "IntervalMergingRule" "List[String]" "int" "byte" "int" "boolean" "int" "OutputMode" "File" "FeatureInput[VariantContext]" "String" "int" "boolean" "double" "boolean" "boolean" "double" "boolean" "double" "boolean" "boolean" "int" "String" "WriterType" "List[FeatureInput[VariantContext]]" "boolean" "File" "boolean" "boolean" "boolean" "boolean" "boolean" "boolean" "boolean" "ReferenceConfidenceMode" "boolean" "boolean" "List[Integer]" "int" "List[Double]" "List[Integer]" "int" "int" "int" "int" "int" "int" "int" "int" "int" "int" "int" "int" "Implementation" "PCRErrorModel" "int" "double" "boolean" "Implementation" "boolean" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "GatherBamFiles" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--INPUT --OUTPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--INPUT;-I" "--OUTPUT;-O" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--help;-h" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--INPUT --OUTPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("List[File]" "File" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "List[File]" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "EstimateLibraryComplexity" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--INPUT --OUTPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --BARCODE_TAG --help --MAX_DIFF_RATE --MAX_GROUP_RATIO --MAX_OPTICAL_DUPLICATE_SET_SIZE --MAX_READ_LENGTH --MIN_GROUP_COUNT --MIN_IDENTICAL_BASES --MIN_MEAN_QUALITY --OPTICAL_DUPLICATE_PIXEL_DISTANCE --READ_NAME_REGEX --READ_ONE_BARCODE_TAG --READ_TWO_BARCODE_TAG --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--INPUT;-I" "--OUTPUT;-O" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--help;-h" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--INPUT --OUTPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --BARCODE_TAG --help --MAX_DIFF_RATE --MAX_GROUP_RATIO --MAX_OPTICAL_DUPLICATE_SET_SIZE --MAX_READ_LENGTH --MIN_GROUP_COUNT --MIN_IDENTICAL_BASES --MIN_MEAN_QUALITY --OPTICAL_DUPLICATE_PIXEL_DISTANCE --READ_NAME_REGEX --READ_ONE_BARCODE_TAG --READ_TWO_BARCODE_TAG --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("List[File]" "File" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "List[File]" "String" "boolean" "double" "int" "long" "int" "int" "int" "int" "int" "String" "String" "String" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "LiftoverVcf" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--CHAIN --INPUT --OUTPUT --REFERENCE_SEQUENCE --REJECT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --ALLOW_MISSING_FIELDS_IN_HEADER --arguments_file --help --LIFTOVER_MIN_MATCH --LOG_FAILED_INTERVALS --RECOVER_SWAPPED_REF_ALT --TAGS_TO_DROP --TAGS_TO_REVERSE --version --WARN_ON_MISSING_CONTIG --WRITE_ORIGINAL_ALLELES --WRITE_ORIGINAL_POSITION --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--CHAIN;-C" "--INPUT;-I" "--OUTPUT;-O" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--help;-h" "--LOG_FAILED_INTERVALS;-LFI" "--WARN_ON_MISSING_CONTIG;-WMC" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--CHAIN --INPUT --OUTPUT --REFERENCE_SEQUENCE --REJECT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --ALLOW_MISSING_FIELDS_IN_HEADER --arguments_file --help --LIFTOVER_MIN_MATCH --LOG_FAILED_INTERVALS --RECOVER_SWAPPED_REF_ALT --TAGS_TO_DROP --TAGS_TO_REVERSE --version --WARN_ON_MISSING_CONTIG --WRITE_ORIGINAL_ALLELES --WRITE_ORIGINAL_POSITION --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "File" "File" "File" "File" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "boolean" "List[File]" "boolean" "double" "boolean" "boolean" "Collection[String]" "Collection[String]" "boolean" "boolean" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "MergeVcfs" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--INPUT --OUTPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --SEQUENCE_DICTIONARY --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--INPUT;-I" "--OUTPUT;-O" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--help;-h" "--SEQUENCE_DICTIONARY;-D" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--INPUT --OUTPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --SEQUENCE_DICTIONARY --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("List[File]" "File" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "List[File]" "boolean" "File" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "NonChimericOriginalAlignmentReadFilter" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=() MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=() MAX_OCCURRENCES=() ALL_LEGAL_ARGUMENTS=() ALL_ARGUMENT_VALUE_TYPES=() # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "LeftAlignAndTrimVariants" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--output --reference --variant --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --dont-trim-alleles --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --keep-original-ac --max-indel-length --max-leading-bases --sites-only-vcf-output --split-multi-allelics --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--output;-O" "--reference;-R" "--variant;-V" "--add-output-sam-program-record;-add-output-sam-program-record" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-bam-md5;-OBM" "--create-output-variant-index;-OVI" "--create-output-variant-md5;-OVM" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--input;-I" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--lenient;-LE" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--seconds-between-progress-updates;-seconds-between-progress-updates" "--sequence-dictionary;-sequence-dictionary" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--cloud-index-prefetch-buffer;-CIPB" "--cloud-prefetch-buffer;-CPB" "--disable-bam-index-caching;-DBIC" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--dont-trim-alleles;-no-trim" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--output --reference --variant --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --dont-trim-alleles --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --keep-original-ac --max-indel-length --max-leading-bases --sites-only-vcf-output --split-multi-allelics --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "String" "String" "boolean" "boolean" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "List[String]" "int" "int" "IntervalSetRule" "boolean" "Boolean" "List[String]" "List[String]" "ValidationStringency" "double" "String" "String" "boolean" "boolean" "LogLevel" "List[File]" "int" "int" "boolean" "boolean" "boolean" "int" "String" "boolean" "IntervalMergingRule" "List[String]" "boolean" "int" "int" "boolean" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "ASEReadCounter" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--input --variant --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --count-overlap-reads-handling --disable-bam-index-caching --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --maxDepthPerSample --min-base-quality --min-depth-of-non-filtered-base --min-mapping-quality --output --output-format --reference --sites-only-vcf-output --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--input;-I" "--variant;-V" "--add-output-sam-program-record;-add-output-sam-program-record" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-bam-md5;-OBM" "--create-output-variant-index;-OVI" "--create-output-variant-md5;-OVM" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--lenient;-LE" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--seconds-between-progress-updates;-seconds-between-progress-updates" "--sequence-dictionary;-sequence-dictionary" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--cloud-index-prefetch-buffer;-CIPB" "--cloud-prefetch-buffer;-CPB" "--count-overlap-reads-handling;-overlap" "--disable-bam-index-caching;-DBIC" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--maxDepthPerSample;-maxDepthPerSample" "--min-base-quality;-mbq" "--min-depth-of-non-filtered-base;-min-depth" "--min-mapping-quality;-mmq" "--output;-O" "--reference;-R" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--input --variant --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --count-overlap-reads-handling --disable-bam-index-caching --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --maxDepthPerSample --min-base-quality --min-depth-of-non-filtered-base --min-mapping-quality --output --output-format --reference --sites-only-vcf-output --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("List[String]" "List[FeatureInput[VariantContext]]" "boolean" "boolean" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "int" "int" "IntervalSetRule" "boolean" "Boolean" "List[String]" "List[String]" "ValidationStringency" "double" "String" "String" "boolean" "boolean" "LogLevel" "List[File]" "int" "int" "CountPileupType" "boolean" "boolean" "int" "String" "boolean" "IntervalMergingRule" "List[String]" "int" "byte" "int" "int" "File" "OUTPUT_FORMAT" "String" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "ValidAlignmentEndReadFilter" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=() MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=() MAX_OCCURRENCES=() ALL_LEGAL_ARGUMENTS=() ALL_ARGUMENT_VALUE_TYPES=() # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "FindBadGenomicKmersSpark" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--output --reference --add-output-vcf-command-line --create-output-bam-index --create-output-bam-splitting-index --create-output-variant-index --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --read-filter --read-index --read-validation-stringency --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --bam-partition-size --conf --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --high-copy-fasta --interval-merging-rule --intervals --kmer-max-dust-score --k-size --num-reducers --output-shard-tmp-dir --program-name --sharded-output --spark-master --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=("--output-shard-tmp-dir;sharded-output" "--sharded-output;output-shard-tmp-dir" ) SYNONYMOUS_ARGS=("--output;-O" "--reference;-R" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-variant-index;-OVI" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--input;-I" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--conf;-conf" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--output --reference --add-output-vcf-command-line --create-output-bam-index --create-output-bam-splitting-index --create-output-variant-index --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --read-filter --read-index --read-validation-stringency --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --bam-partition-size --conf --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --high-copy-fasta --interval-merging-rule --intervals --kmer-max-dust-score --k-size --num-reducers --output-shard-tmp-dir --program-name --sharded-output --spark-master --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("String" "String" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "List[String]" "int" "int" "IntervalSetRule" "Boolean" "List[String]" "List[String]" "ValidationStringency" "String" "boolean" "boolean" "LogLevel" "List[File]" "long" "List[String]" "boolean" "int" "String" "boolean" "String" "IntervalMergingRule" "List[String]" "int" "int" "int" "String" "String" "boolean" "String" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "CNNVariantWriteTensors" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--output-tensor-dir --reference --truth-bed --truth-vcf --variant --gatk-config-file --QUIET --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --bam-file --downsample-indels --downsample-snps --gcs-max-retries --gcs-project-for-requester-pays --help --max-tensors --tensor-type --version --annotation-set --channels-last --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--output-tensor-dir;-output-tensor-dir" "--reference;-R" "--truth-bed;-truth-bed" "--truth-vcf;-truth-vcf" "--variant;-V" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--bam-file;-bam-file" "--downsample-indels;-downsample-indels" "--downsample-snps;-downsample-snps" "--gcs-max-retries;-gcs-retries" "--help;-h" "--max-tensors;-max-tensors" "--tensor-type;-tensor-type" "--annotation-set;-annotation-set" "--channels-last;-channels-last" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--output-tensor-dir --reference --truth-bed --truth-vcf --variant --gatk-config-file --QUIET --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --bam-file --downsample-indels --downsample-snps --gcs-max-retries --gcs-project-for-requester-pays --help --max-tensors --tensor-type --version --annotation-set --channels-last --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("String" "String" "String" "String" "String" "String" "Boolean" "String" "boolean" "boolean" "LogLevel" "List[File]" "String" "float" "float" "int" "String" "boolean" "int" "TensorType" "boolean" "String" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "SortVcf" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--INPUT --OUTPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --SEQUENCE_DICTIONARY --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--INPUT;-I" "--OUTPUT;-O" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--help;-h" "--SEQUENCE_DICTIONARY;-SD" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--INPUT --OUTPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --SEQUENCE_DICTIONARY --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("List[File]" "File" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "List[File]" "boolean" "File" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "ReferenceBases" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=() MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=() MAX_OCCURRENCES=() ALL_LEGAL_ARGUMENTS=() ALL_ARGUMENT_VALUE_TYPES=() # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "ClusterCrosscheckMetrics" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--INPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --LOD_THRESHOLD --OUTPUT --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--INPUT;-I" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--help;-h" "--LOD_THRESHOLD;-LOD" "--OUTPUT;-O" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--INPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --LOD_THRESHOLD --OUTPUT --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "List[File]" "boolean" "double" "File" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "AnnotateVcfWithBamDepth" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--output --variant --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --reference --sites-only-vcf-output --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--output;-O" "--variant;-V" "--add-output-sam-program-record;-add-output-sam-program-record" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-bam-md5;-OBM" "--create-output-variant-index;-OVI" "--create-output-variant-md5;-OVM" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--input;-I" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--lenient;-LE" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--seconds-between-progress-updates;-seconds-between-progress-updates" "--sequence-dictionary;-sequence-dictionary" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--cloud-index-prefetch-buffer;-CIPB" "--cloud-prefetch-buffer;-CPB" "--disable-bam-index-caching;-DBIC" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--reference;-R" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--output --variant --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --reference --sites-only-vcf-output --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("String" "String" "boolean" "boolean" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "List[String]" "int" "int" "IntervalSetRule" "boolean" "Boolean" "List[String]" "List[String]" "ValidationStringency" "double" "String" "String" "boolean" "boolean" "LogLevel" "List[File]" "int" "int" "boolean" "boolean" "int" "String" "boolean" "IntervalMergingRule" "List[String]" "String" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "AS_BaseQualityRankSumTest" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=() MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=() MAX_OCCURRENCES=() ALL_LEGAL_ARGUMENTS=() ALL_ARGUMENT_VALUE_TYPES=() # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "CreateReadCountPanelOfNormals" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--input --output --gatk-config-file --QUIET --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --annotated-intervals --arguments_file --conf --do-impute-zeros --extreme-outlier-truncation-percentile --extreme-sample-median-percentile --gcs-max-retries --gcs-project-for-requester-pays --help --maximum-zeros-in-interval-percentage --maximum-zeros-in-sample-percentage --minimum-interval-median-percentile --number-of-eigensamples --program-name --spark-master --version --maximum-chunk-size --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--input;-I" "--output;-O" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--conf;-conf" "--gcs-max-retries;-gcs-retries" "--help;-h" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--input --output --gatk-config-file --QUIET --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --annotated-intervals --arguments_file --conf --do-impute-zeros --extreme-outlier-truncation-percentile --extreme-sample-median-percentile --gcs-max-retries --gcs-project-for-requester-pays --help --maximum-zeros-in-interval-percentage --maximum-zeros-in-sample-percentage --minimum-interval-median-percentile --number-of-eigensamples --program-name --spark-master --version --maximum-chunk-size --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("List[File]" "File" "String" "Boolean" "String" "boolean" "boolean" "LogLevel" "File" "List[File]" "List[String]" "boolean" "double" "double" "int" "String" "boolean" "double" "double" "double" "int" "String" "String" "boolean" "int" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "AS_InbreedingCoeff" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=() MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=() MAX_OCCURRENCES=() ALL_LEGAL_ARGUMENTS=() ALL_ARGUMENT_VALUE_TYPES=() # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "CollectInsertSizeMetricsSpark" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--histogram-plot-file --input --output --add-output-vcf-command-line --create-output-bam-index --create-output-bam-splitting-index --create-output-variant-index --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --read-filter --read-index --read-validation-stringency --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --bam-partition-size --conf --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --histogram-plot-deviations-tolerance --interval-merging-rule --intervals --metric-accumulation-level --min-category-reads-percentage --num-reducers --output-shard-tmp-dir --produce-plot --program-name --reference --sharded-output --spark-master --version --width --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=("--output-shard-tmp-dir;sharded-output" "--sharded-output;output-shard-tmp-dir" ) SYNONYMOUS_ARGS=("--histogram-plot-file;-H" "--input;-I" "--output;-O" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-variant-index;-OVI" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--conf;-conf" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--gcs-max-retries;-gcs-retries" "--help;-h" "--histogram-plot-deviations-tolerance;-TOL" "--interval-merging-rule;-imr" "--intervals;-L" "--metric-accumulation-level;-LEVEL" "--min-category-reads-percentage;-M" "--reference;-R" "--width;-W" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--histogram-plot-file --input --output --add-output-vcf-command-line --create-output-bam-index --create-output-bam-splitting-index --create-output-variant-index --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --read-filter --read-index --read-validation-stringency --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --bam-partition-size --conf --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --histogram-plot-deviations-tolerance --interval-merging-rule --intervals --metric-accumulation-level --min-category-reads-percentage --num-reducers --output-shard-tmp-dir --produce-plot --program-name --reference --sharded-output --spark-master --version --width --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("String" "List[String]" "String" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "int" "int" "IntervalSetRule" "Boolean" "List[String]" "List[String]" "ValidationStringency" "String" "boolean" "boolean" "LogLevel" "List[File]" "long" "List[String]" "boolean" "int" "String" "boolean" "double" "IntervalMergingRule" "List[String]" "Set[MetricAccumulationLevel]" "float" "int" "String" "boolean" "String" "String" "boolean" "String" "boolean" "Integer" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "MappingQuality" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=() MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=() MAX_OCCURRENCES=() ALL_LEGAL_ARGUMENTS=() ALL_ARGUMENT_VALUE_TYPES=() # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "ReadLengthReadFilter" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--max-read-length --min-read-length ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=(0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--max-read-length --min-read-length ) ALL_ARGUMENT_VALUE_TYPES=("Integer" "int" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "CollectMultipleMetricsSpark" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--output --add-output-vcf-command-line --create-output-bam-index --create-output-bam-splitting-index --create-output-variant-index --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --read-filter --read-index --read-validation-stringency --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --assume-sorted --bam-partition-size --collectors --conf --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --metric-accumulation-level --num-reducers --output-shard-tmp-dir --program-name --reference --sharded-output --spark-master --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=("--output-shard-tmp-dir;sharded-output" "--sharded-output;output-shard-tmp-dir" ) SYNONYMOUS_ARGS=("--output;-O" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-variant-index;-OVI" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--input;-I" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--assume-sorted;-AS" "--conf;-conf" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--metric-accumulation-level;-LEVEL" "--reference;-R" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--output --add-output-vcf-command-line --create-output-bam-index --create-output-bam-splitting-index --create-output-variant-index --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --read-filter --read-index --read-validation-stringency --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --assume-sorted --bam-partition-size --collectors --conf --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --metric-accumulation-level --num-reducers --output-shard-tmp-dir --program-name --reference --sharded-output --spark-master --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("String" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "List[String]" "int" "int" "IntervalSetRule" "Boolean" "List[String]" "List[String]" "ValidationStringency" "String" "boolean" "boolean" "LogLevel" "List[File]" "boolean" "long" "List[SparkCollectors]" "List[String]" "boolean" "int" "String" "boolean" "IntervalMergingRule" "List[String]" "Set[MetricAccumulationLevel]" "int" "String" "String" "String" "boolean" "String" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "MergeSamFiles" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--INPUT --OUTPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --ASSUME_SORTED --COMMENT --help --INTERVALS --MERGE_SEQUENCE_DICTIONARIES --SORT_ORDER --USE_THREADING --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--INPUT;-I" "--OUTPUT;-O" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--ASSUME_SORTED;-AS" "--COMMENT;-CO" "--help;-h" "--INTERVALS;-RGN" "--MERGE_SEQUENCE_DICTIONARIES;-MSD" "--SORT_ORDER;-SO" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--INPUT --OUTPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --ASSUME_SORTED --COMMENT --help --INTERVALS --MERGE_SEQUENCE_DICTIONARIES --SORT_ORDER --USE_THREADING --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("List[File]" "File" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "List[File]" "boolean" "List[String]" "boolean" "File" "boolean" "SortOrder" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "CountBasesInReference" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--reference --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --sites-only-vcf-output --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--reference;-R" "--add-output-sam-program-record;-add-output-sam-program-record" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-bam-md5;-OBM" "--create-output-variant-index;-OVI" "--create-output-variant-md5;-OVM" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--input;-I" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--lenient;-LE" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--seconds-between-progress-updates;-seconds-between-progress-updates" "--sequence-dictionary;-sequence-dictionary" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--cloud-index-prefetch-buffer;-CIPB" "--cloud-prefetch-buffer;-CPB" "--disable-bam-index-caching;-DBIC" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--reference --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --sites-only-vcf-output --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("String" "boolean" "boolean" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "List[String]" "int" "int" "IntervalSetRule" "boolean" "Boolean" "List[String]" "List[String]" "ValidationStringency" "double" "String" "String" "boolean" "boolean" "LogLevel" "List[File]" "int" "int" "boolean" "boolean" "int" "String" "boolean" "IntervalMergingRule" "List[String]" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "CountFalsePositives" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--output --variant --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --reference --sites-only-vcf-output --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--output;-O" "--variant;-V" "--add-output-sam-program-record;-add-output-sam-program-record" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-bam-md5;-OBM" "--create-output-variant-index;-OVI" "--create-output-variant-md5;-OVM" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--input;-I" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--lenient;-LE" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--seconds-between-progress-updates;-seconds-between-progress-updates" "--sequence-dictionary;-sequence-dictionary" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--cloud-index-prefetch-buffer;-CIPB" "--cloud-prefetch-buffer;-CPB" "--disable-bam-index-caching;-DBIC" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--reference;-R" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--output --variant --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --reference --sites-only-vcf-output --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "String" "boolean" "boolean" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "List[String]" "int" "int" "IntervalSetRule" "boolean" "Boolean" "List[String]" "List[String]" "ValidationStringency" "double" "String" "String" "boolean" "boolean" "LogLevel" "List[File]" "int" "int" "boolean" "boolean" "int" "String" "boolean" "IntervalMergingRule" "List[String]" "String" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "PrintVariantsSpark" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--output --variant --add-output-vcf-command-line --create-output-bam-index --create-output-bam-splitting-index --create-output-variant-index --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --read-filter --read-index --read-validation-stringency --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --bam-partition-size --conf --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --num-reducers --output-shard-tmp-dir --program-name --reference --sharded-output --shuffle --spark-master --variantShardSize --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=("--output-shard-tmp-dir;sharded-output" "--sharded-output;output-shard-tmp-dir" ) SYNONYMOUS_ARGS=("--output;-O" "--variant;-V" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-variant-index;-OVI" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--input;-I" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--conf;-conf" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--reference;-R" "--shuffle;-shuffle" "--variantShardSize;-variantShardSize" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--output --variant --add-output-vcf-command-line --create-output-bam-index --create-output-bam-splitting-index --create-output-variant-index --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --read-filter --read-index --read-validation-stringency --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --bam-partition-size --conf --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --num-reducers --output-shard-tmp-dir --program-name --reference --sharded-output --shuffle --spark-master --variantShardSize --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("String" "String" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "List[String]" "int" "int" "IntervalSetRule" "Boolean" "List[String]" "List[String]" "ValidationStringency" "String" "boolean" "boolean" "LogLevel" "List[File]" "long" "List[String]" "boolean" "int" "String" "boolean" "IntervalMergingRule" "List[String]" "int" "String" "String" "String" "boolean" "boolean" "String" "int" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "MarkDuplicatesSpark" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--input --output --add-output-vcf-command-line --create-output-bam-index --create-output-bam-splitting-index --create-output-variant-index --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --read-filter --read-index --read-validation-stringency --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --bam-partition-size --conf --disable-sequence-dictionary-validation --do-not-mark-unmapped-mates --duplicate-scoring-strategy --duplicate-tagging-policy --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --metrics-file --num-reducers --optical-duplicate-pixel-distance --output-shard-tmp-dir --program-name --read-name-regex --reference --remove-all-duplicates --remove-sequencing-duplicates --sharded-output --spark-master --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=("--duplicate-tagging-policy;remove-all-duplicates,remove-sequencing-duplicates" "--output-shard-tmp-dir;sharded-output" "--remove-all-duplicates;duplicate-tagging-policy,remove-sequencing-duplicates" "--remove-sequencing-duplicates;duplicate-tagging-policy,remove-all-duplicates" "--sharded-output;output-shard-tmp-dir" ) SYNONYMOUS_ARGS=("--input;-I" "--output;-O" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-variant-index;-OVI" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--conf;-conf" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--duplicate-scoring-strategy;-DS" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--metrics-file;-M" "--reference;-R" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--input --output --add-output-vcf-command-line --create-output-bam-index --create-output-bam-splitting-index --create-output-variant-index --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --read-filter --read-index --read-validation-stringency --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --bam-partition-size --conf --disable-sequence-dictionary-validation --do-not-mark-unmapped-mates --duplicate-scoring-strategy --duplicate-tagging-policy --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --metrics-file --num-reducers --optical-duplicate-pixel-distance --output-shard-tmp-dir --program-name --read-name-regex --reference --remove-all-duplicates --remove-sequencing-duplicates --sharded-output --spark-master --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("List[String]" "String" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "int" "int" "IntervalSetRule" "Boolean" "List[String]" "List[String]" "ValidationStringency" "String" "boolean" "boolean" "LogLevel" "List[File]" "long" "List[String]" "boolean" "boolean" "MarkDuplicatesScoringStrategy" "DuplicateTaggingPolicy" "int" "String" "boolean" "IntervalMergingRule" "List[String]" "String" "int" "int" "String" "String" "String" "String" "boolean" "boolean" "boolean" "String" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "AccumulateVariantCallingMetrics" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--INPUT --OUTPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--INPUT;-I" "--OUTPUT;-O" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--help;-h" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--INPUT --OUTPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("List[File]" "File" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "List[File]" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "FilterVcf" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--INPUT --OUTPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --JAVASCRIPT_FILE --MAX_FS --MIN_AB --MIN_DP --MIN_GQ --MIN_QD --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--INPUT;-I" "--OUTPUT;-O" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--help;-h" "--JAVASCRIPT_FILE;-JS" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--INPUT --OUTPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --JAVASCRIPT_FILE --MAX_FS --MIN_AB --MIN_DP --MIN_GQ --MIN_QD --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "File" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "List[File]" "boolean" "File" "double" "double" "int" "int" "double" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "FisherStrand" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=() MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=() MAX_OCCURRENCES=() ALL_LEGAL_ARGUMENTS=() ALL_ARGUMENT_VALUE_TYPES=() # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "ChromosomeCounts" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=() MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=() MAX_OCCURRENCES=() ALL_LEGAL_ARGUMENTS=() ALL_ARGUMENT_VALUE_TYPES=() # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "QualityScoreDistributionSpark" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--add-output-vcf-command-line --create-output-bam-index --create-output-bam-splitting-index --create-output-variant-index --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --read-filter --read-index --read-validation-stringency --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --alignedReadsOnly --arguments_file --bam-partition-size --chart --conf --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --includeNoCalls --interval-merging-rule --intervals --num-reducers --output --output-shard-tmp-dir --pfReadsOnly --program-name --reference --sharded-output --spark-master --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=("--output-shard-tmp-dir;sharded-output" "--sharded-output;output-shard-tmp-dir" ) SYNONYMOUS_ARGS=("--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-variant-index;-OVI" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--input;-I" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--alignedReadsOnly;-A" "--chart;-C" "--conf;-conf" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--gcs-max-retries;-gcs-retries" "--help;-h" "--includeNoCalls;-NC" "--interval-merging-rule;-imr" "--intervals;-L" "--output;-O" "--pfReadsOnly;-F" "--reference;-R" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--add-output-vcf-command-line --create-output-bam-index --create-output-bam-splitting-index --create-output-variant-index --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --read-filter --read-index --read-validation-stringency --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --alignedReadsOnly --arguments_file --bam-partition-size --chart --conf --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --includeNoCalls --interval-merging-rule --intervals --num-reducers --output --output-shard-tmp-dir --pfReadsOnly --program-name --reference --sharded-output --spark-master --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "List[String]" "int" "int" "IntervalSetRule" "Boolean" "List[String]" "List[String]" "ValidationStringency" "String" "boolean" "boolean" "LogLevel" "boolean" "List[File]" "long" "File" "List[String]" "boolean" "int" "String" "boolean" "boolean" "IntervalMergingRule" "List[String]" "int" "String" "String" "boolean" "String" "String" "boolean" "String" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "GatherVcfs" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--INPUT --OUTPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--INPUT;-I" "--OUTPUT;-O" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--help;-h" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--INPUT --OUTPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("List[File]" "File" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "List[File]" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "MatchingBasesAndQualsReadFilter" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=() MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=() MAX_OCCURRENCES=() ALL_LEGAL_ARGUMENTS=() ALL_ARGUMENT_VALUE_TYPES=() # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "PathSeqBwaSpark" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--microbe-bwa-image --microbe-fasta --add-output-vcf-command-line --create-output-bam-index --create-output-bam-splitting-index --create-output-variant-index --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --read-filter --read-index --read-validation-stringency --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --bam-partition-size --bwa-score-threshold --conf --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --max-alternate-hits --microbe-min-seed-length --num-reducers --output-shard-tmp-dir --paired-input --paired-output --program-name --reference --sharded-output --spark-master --unpaired-input --unpaired-output --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=("--output-shard-tmp-dir;sharded-output" "--sharded-output;output-shard-tmp-dir" ) SYNONYMOUS_ARGS=("--microbe-bwa-image;-MI" "--microbe-fasta;-MF" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-variant-index;-OVI" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--input;-I" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--bwa-score-threshold;-bwa-score-threshold" "--conf;-conf" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--max-alternate-hits;-max-alternate-hits" "--microbe-min-seed-length;-microbe-min-seed-length" "--paired-input;-PI" "--paired-output;-PO" "--reference;-R" "--unpaired-input;-UI" "--unpaired-output;-UO" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--microbe-bwa-image --microbe-fasta --add-output-vcf-command-line --create-output-bam-index --create-output-bam-splitting-index --create-output-variant-index --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --read-filter --read-index --read-validation-stringency --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --bam-partition-size --bwa-score-threshold --conf --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --max-alternate-hits --microbe-min-seed-length --num-reducers --output-shard-tmp-dir --paired-input --paired-output --program-name --reference --sharded-output --spark-master --unpaired-input --unpaired-output --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("String" "String" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "List[String]" "int" "int" "IntervalSetRule" "Boolean" "List[String]" "List[String]" "ValidationStringency" "String" "boolean" "boolean" "LogLevel" "List[File]" "long" "int" "List[String]" "boolean" "int" "String" "boolean" "IntervalMergingRule" "List[String]" "int" "int" "int" "String" "String" "String" "String" "String" "boolean" "String" "String" "String" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "RenameSampleInVcf" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--INPUT --NEW_SAMPLE_NAME --OUTPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --OLD_SAMPLE_NAME --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--INPUT;-I" "--OUTPUT;-O" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--help;-h" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--INPUT --NEW_SAMPLE_NAME --OUTPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --OLD_SAMPLE_NAME --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "String" "File" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "List[File]" "boolean" "String" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "CountVariants" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--variant --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --reference --sites-only-vcf-output --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--variant;-V" "--add-output-sam-program-record;-add-output-sam-program-record" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-bam-md5;-OBM" "--create-output-variant-index;-OVI" "--create-output-variant-md5;-OVM" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--input;-I" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--lenient;-LE" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--seconds-between-progress-updates;-seconds-between-progress-updates" "--sequence-dictionary;-sequence-dictionary" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--cloud-index-prefetch-buffer;-CIPB" "--cloud-prefetch-buffer;-CPB" "--disable-bam-index-caching;-DBIC" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--reference;-R" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--variant --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --reference --sites-only-vcf-output --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("String" "boolean" "boolean" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "List[String]" "int" "int" "IntervalSetRule" "boolean" "Boolean" "List[String]" "List[String]" "ValidationStringency" "double" "String" "String" "boolean" "boolean" "LogLevel" "List[File]" "int" "int" "boolean" "boolean" "int" "String" "boolean" "IntervalMergingRule" "List[String]" "String" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "DownsampleSam" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--INPUT --OUTPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --ACCURACY --arguments_file --help --METRICS_FILE --PROBABILITY --RANDOM_SEED --REFERENCE_SEQUENCE --STRATEGY --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--INPUT;-I" "--OUTPUT;-O" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--ACCURACY;-A" "--help;-h" "--METRICS_FILE;-M" "--PROBABILITY;-P" "--RANDOM_SEED;-R" "--STRATEGY;-S" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--INPUT --OUTPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --ACCURACY --arguments_file --help --METRICS_FILE --PROBABILITY --RANDOM_SEED --REFERENCE_SEQUENCE --STRATEGY --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "File" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "double" "List[File]" "boolean" "File" "double" "Integer" "File" "Strategy" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "CollectHiSeqXPfFailMetrics" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--BASECALLS_DIR --LANE --OUTPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --N_CYCLES --NUM_PROCESSORS --PROB_EXPLICIT_READS --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--BASECALLS_DIR;-B" "--LANE;-L" "--OUTPUT;-O" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--help;-h" "--NUM_PROCESSORS;-NP" "--PROB_EXPLICIT_READS;-P" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--BASECALLS_DIR --LANE --OUTPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --N_CYCLES --NUM_PROCESSORS --PROB_EXPLICIT_READS --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "Integer" "File" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "List[File]" "boolean" "int" "int" "double" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "RMSMappingQuality" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=() MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=() MAX_OCCURRENCES=() ALL_LEGAL_ARGUMENTS=() ALL_ARGUMENT_VALUE_TYPES=() # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "MappingQualityReadFilter" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--maximum-mapping-quality --minimum-mapping-quality ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=(0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--maximum-mapping-quality --minimum-mapping-quality ) ALL_ARGUMENT_VALUE_TYPES=("Integer" "int" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "MappingQualityZero" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=() MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=() MAX_OCCURRENCES=() ALL_LEGAL_ARGUMENTS=() ALL_ARGUMENT_VALUE_TYPES=() # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "IntervalListToBed" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--INPUT --OUTPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --SCORE --SORT --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--INPUT;-I" "--OUTPUT;-O" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--help;-h" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--INPUT --OUTPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --SCORE --SORT --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "File" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "List[File]" "boolean" "int" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "CollectJumpingLibraryMetrics" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--INPUT --OUTPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --CHIMERA_KB_MIN --help --MINIMUM_MAPPING_QUALITY --TAIL_LIMIT --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--INPUT;-I" "--OUTPUT;-O" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--help;-h" "--MINIMUM_MAPPING_QUALITY;-MQ" "--TAIL_LIMIT;-T" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--INPUT --OUTPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --CHIMERA_KB_MIN --help --MINIMUM_MAPPING_QUALITY --TAIL_LIMIT --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("List[File]" "File" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "List[File]" "int" "boolean" "Integer" "int" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "CNNVariantTrain" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--input-tensor-dir --gatk-config-file --QUIET --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --annotation-shortcut --annotation-units --arguments_file --conv-batch-normalize --conv-dropout --conv-height --conv-layers --conv-width --epochs --fc-batch-normalize --fc-dropout --fc-layers --gcs-max-retries --gcs-project-for-requester-pays --help --image-dir --model-name --output-dir --padding --spatial-dropout --tensor-type --training-steps --validation-steps --version --annotation-set --channels-last --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--input-tensor-dir;-input-tensor-dir" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--annotation-shortcut;-annotation-shortcut" "--annotation-units;-annotation-units" "--conv-batch-normalize;-conv-batch-normalize" "--conv-dropout;-conv-dropout" "--conv-height;-conv-height" "--conv-layers;-conv-layers" "--conv-width;-conv-width" "--epochs;-epochs" "--fc-batch-normalize;-fc-batch-normalize" "--fc-dropout;-fc-dropout" "--fc-layers;-fc-layers" "--gcs-max-retries;-gcs-retries" "--help;-h" "--image-dir;-image-dir" "--model-name;-model-name" "--output-dir;-output-dir" "--padding;-padding" "--spatial-dropout;-spatial-dropout" "--tensor-type;-tensor-type" "--training-steps;-training-steps" "--validation-steps;-validation-steps" "--annotation-set;-annotation-set" "--channels-last;-channels-last" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--input-tensor-dir --gatk-config-file --QUIET --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --annotation-shortcut --annotation-units --arguments_file --conv-batch-normalize --conv-dropout --conv-height --conv-layers --conv-width --epochs --fc-batch-normalize --fc-dropout --fc-layers --gcs-max-retries --gcs-project-for-requester-pays --help --image-dir --model-name --output-dir --padding --spatial-dropout --tensor-type --training-steps --validation-steps --version --annotation-set --channels-last --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("String" "String" "Boolean" "String" "boolean" "boolean" "LogLevel" "boolean" "int" "List[File]" "boolean" "float" "int" "List[Integer]" "int" "int" "boolean" "float" "List[Integer]" "int" "String" "boolean" "String" "String" "String" "String" "boolean" "TensorType" "int" "int" "boolean" "String" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "ExtractSequences" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--INTERVAL_LIST --OUTPUT --REFERENCE_SEQUENCE --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --LINE_LENGTH --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--OUTPUT;-O" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--help;-h" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--INTERVAL_LIST --OUTPUT --REFERENCE_SEQUENCE --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --LINE_LENGTH --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "File" "File" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "List[File]" "boolean" "int" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "ReadLengthEqualsCigarLengthReadFilter" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=() MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=() MAX_OCCURRENCES=() ALL_LEGAL_ARGUMENTS=() ALL_ARGUMENT_VALUE_TYPES=() # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "FirstOfPairReadFilter" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=() MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=() MAX_OCCURRENCES=() ALL_LEGAL_ARGUMENTS=() ALL_ARGUMENT_VALUE_TYPES=() # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "CollectReadCounts" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--input --intervals --output --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --format --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --reference --sites-only-vcf-output --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--input;-I" "--intervals;-L" "--output;-O" "--add-output-sam-program-record;-add-output-sam-program-record" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-bam-md5;-OBM" "--create-output-variant-index;-OVI" "--create-output-variant-md5;-OVM" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--lenient;-LE" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--seconds-between-progress-updates;-seconds-between-progress-updates" "--sequence-dictionary;-sequence-dictionary" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--cloud-index-prefetch-buffer;-CIPB" "--cloud-prefetch-buffer;-CPB" "--disable-bam-index-caching;-DBIC" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--reference;-R" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--input --intervals --output --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --format --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --reference --sites-only-vcf-output --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("List[String]" "List[String]" "File" "boolean" "boolean" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "int" "int" "IntervalSetRule" "boolean" "Boolean" "List[String]" "List[String]" "ValidationStringency" "double" "String" "String" "boolean" "boolean" "LogLevel" "List[File]" "int" "int" "boolean" "boolean" "Format" "int" "String" "boolean" "IntervalMergingRule" "String" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "ReplaceSamHeader" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--HEADER --INPUT --OUTPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--INPUT;-I" "--OUTPUT;-O" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--help;-h" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--HEADER --INPUT --OUTPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "File" "File" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "List[File]" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "Mutect2" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--input --output --reference --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --activity-profile-out --af-of-alleles-not-in-resource --alleles --annotate-with-num-discovered-alleles --annotation --annotation-group --annotations-to-exclude --arguments_file --assembly-region-out --base-quality-score-threshold --cloud-index-prefetch-buffer --cloud-prefetch-buffer --contamination-fraction-to-filter --correct-overlapping-quality --count-reads --disable-bam-index-caching --disable-sequence-dictionary-validation --downsampling-stride --founder-id --gcs-max-retries --gcs-project-for-requester-pays --genotype-germline-sites --genotype-pon-sites --genotyping-mode --germline-resource --graph-output --help --heterozygosity --heterozygosity-stdev --ignore-itr-artifacts --indel-heterozygosity --initial-pcr-qual --initial-tumor-lod --interval-merging-rule --intervals --max-population-af --max-reads-per-alignment-start --min-base-quality-score --mitochondria-mode --native-pair-hmm-threads --native-pair-hmm-use-double-precision --normal-lod --normal-sample --num-reference-samples-if-no-call --orientation-bias-artifact-priors --output-mode --panel-of-normals --pedigree --population-callset --sample-ploidy --sites-only-vcf-output --standard-min-confidence-threshold-for-calling --tumor-lod-to-emit --use-old-qual-calculator --version --active-probability-threshold --adaptive-pruning-initial-error-rate --allow-non-unique-kmers-in-ref --all-site-pls --assembly-region-padding --bam-output --bam-writer-type --contamination-fraction-per-sample-file --debug --disable-adaptive-pruning --disable-tool-default-annotations --do-not-run-physical-phasing --dont-increase-kmer-sizes-for-cycles --dont-trim-active-regions --dont-use-soft-clipped-bases --emit-ref-confidence --enable-all-annotations --genotype-filtered-alleles --gvcf-lod-band --input-prior --kmer-size --max-alternate-alleles --max-assembly-region-size --max-genotype-count --max-mnp-distance --max-num-haplotypes-in-population --max-prob-propagation-distance --max-suspicious-reads-per-alignment-start --max-unpruned-variants --median-autosomal-coverage --min-assembly-region-size --min-dangling-branch-length --minimum-allele-fraction --min-pruning --num-pruning-samples --pair-hmm-gap-continuation-penalty --pair-hmm-implementation --pcr-indel-model --phred-scaled-global-read-mismapping-rate --pruning-lod-threshold --showHidden --smith-waterman --use-filtered-reads-for-annotations --tumor-sample --use-new-qual-calculator ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--input;-I" "--output;-O" "--reference;-R" "--add-output-sam-program-record;-add-output-sam-program-record" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-bam-md5;-OBM" "--create-output-variant-index;-OVI" "--create-output-variant-md5;-OVM" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--lenient;-LE" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--seconds-between-progress-updates;-seconds-between-progress-updates" "--sequence-dictionary;-sequence-dictionary" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--af-of-alleles-not-in-resource;-default-af" "--annotation;-A" "--annotation-group;-G" "--annotations-to-exclude;-AX" "--cloud-index-prefetch-buffer;-CIPB" "--cloud-prefetch-buffer;-CPB" "--contamination-fraction-to-filter;-contamination" "--disable-bam-index-caching;-DBIC" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--downsampling-stride;-stride" "--founder-id;-founder-id" "--gcs-max-retries;-gcs-retries" "--graph-output;-graph" "--help;-h" "--initial-tumor-lod;-init-lod" "--interval-merging-rule;-imr" "--intervals;-L" "--max-population-af;-max-af" "--min-base-quality-score;-mbq" "--normal-sample;-normal" "--panel-of-normals;-pon" "--pedigree;-ped" "--population-callset;-population" "--sample-ploidy;-ploidy" "--standard-min-confidence-threshold-for-calling;-stand-call-conf" "--tumor-lod-to-emit;-emit-lod" "--use-old-qual-calculator;-old-qual" "--bam-output;-bamout" "--contamination-fraction-per-sample-file;-contamination-file" "--debug;-debug" "--disable-tool-default-annotations;-disable-tool-default-annotations" "--emit-ref-confidence;-ERC" "--gvcf-lod-band;-LODB" "--max-mnp-distance;-mnp-dist" "--minimum-allele-fraction;-min-AF" "--pair-hmm-implementation;-pairHMM" "--showHidden;-showHidden" "--tumor-sample;-tumor" "--use-new-qual-calculator;-new-qual" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--input --output --reference --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --activity-profile-out --af-of-alleles-not-in-resource --alleles --annotate-with-num-discovered-alleles --annotation --annotation-group --annotations-to-exclude --arguments_file --assembly-region-out --base-quality-score-threshold --cloud-index-prefetch-buffer --cloud-prefetch-buffer --contamination-fraction-to-filter --correct-overlapping-quality --count-reads --disable-bam-index-caching --disable-sequence-dictionary-validation --downsampling-stride --founder-id --gcs-max-retries --gcs-project-for-requester-pays --genotype-germline-sites --genotype-pon-sites --genotyping-mode --germline-resource --graph-output --help --heterozygosity --heterozygosity-stdev --ignore-itr-artifacts --indel-heterozygosity --initial-pcr-qual --initial-tumor-lod --interval-merging-rule --intervals --max-population-af --max-reads-per-alignment-start --min-base-quality-score --mitochondria-mode --native-pair-hmm-threads --native-pair-hmm-use-double-precision --normal-lod --normal-sample --num-reference-samples-if-no-call --orientation-bias-artifact-priors --output-mode --panel-of-normals --pedigree --population-callset --sample-ploidy --sites-only-vcf-output --standard-min-confidence-threshold-for-calling --tumor-lod-to-emit --use-old-qual-calculator --version --active-probability-threshold --adaptive-pruning-initial-error-rate --allow-non-unique-kmers-in-ref --all-site-pls --assembly-region-padding --bam-output --bam-writer-type --contamination-fraction-per-sample-file --debug --disable-adaptive-pruning --disable-tool-default-annotations --do-not-run-physical-phasing --dont-increase-kmer-sizes-for-cycles --dont-trim-active-regions --dont-use-soft-clipped-bases --emit-ref-confidence --enable-all-annotations --genotype-filtered-alleles --gvcf-lod-band --input-prior --kmer-size --max-alternate-alleles --max-assembly-region-size --max-genotype-count --max-mnp-distance --max-num-haplotypes-in-population --max-prob-propagation-distance --max-suspicious-reads-per-alignment-start --max-unpruned-variants --median-autosomal-coverage --min-assembly-region-size --min-dangling-branch-length --minimum-allele-fraction --min-pruning --num-pruning-samples --pair-hmm-gap-continuation-penalty --pair-hmm-implementation --pcr-indel-model --phred-scaled-global-read-mismapping-rate --pruning-lod-threshold --showHidden --smith-waterman --use-filtered-reads-for-annotations --tumor-sample --use-new-qual-calculator ) ALL_ARGUMENT_VALUE_TYPES=("List[String]" "File" "String" "boolean" "boolean" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "int" "int" "IntervalSetRule" "boolean" "Boolean" "List[String]" "List[String]" "ValidationStringency" "double" "String" "String" "boolean" "boolean" "LogLevel" "String" "double" "FeatureInput[VariantContext]" "boolean" "List[String]" "List[String]" "List[String]" "List[File]" "String" "byte" "int" "int" "double" "boolean" "boolean" "boolean" "boolean" "int" "List[String]" "int" "String" "boolean" "boolean" "GenotypingOutputMode" "FeatureInput[VariantContext]" "String" "boolean" "Double" "double" "boolean" "double" "int" "double" "IntervalMergingRule" "List[String]" "double" "int" "byte" "Boolean" "int" "boolean" "double" "List[String]" "int" "List[File]" "OutputMode" "FeatureInput[VariantContext]" "File" "FeatureInput[VariantContext]" "int" "boolean" "double" "double" "boolean" "boolean" "double" "double" "boolean" "boolean" "int" "String" "WriterType" "File" "boolean" "boolean" "boolean" "boolean" "boolean" "boolean" "boolean" "ReferenceConfidenceMode" "boolean" "boolean" "List[Double]" "List[Double]" "List[Integer]" "int" "int" "int" "int" "int" "int" "int" "int" "double" "int" "int" "double" "int" "int" "int" "Implementation" "PCRErrorModel" "int" "double" "boolean" "Implementation" "boolean" "String" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "CollectQualityYieldMetricsSpark" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--input --output --add-output-vcf-command-line --create-output-bam-index --create-output-bam-splitting-index --create-output-variant-index --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --read-filter --read-index --read-validation-stringency --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --bam-partition-size --conf --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --num-reducers --output-shard-tmp-dir --program-name --reference --sharded-output --spark-master --use-original-qualities --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=("--output-shard-tmp-dir;sharded-output" "--sharded-output;output-shard-tmp-dir" ) SYNONYMOUS_ARGS=("--input;-I" "--output;-O" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-variant-index;-OVI" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--conf;-conf" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--reference;-R" "--use-original-qualities;-OQ" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--input --output --add-output-vcf-command-line --create-output-bam-index --create-output-bam-splitting-index --create-output-variant-index --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --read-filter --read-index --read-validation-stringency --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --bam-partition-size --conf --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --num-reducers --output-shard-tmp-dir --program-name --reference --sharded-output --spark-master --use-original-qualities --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("List[String]" "String" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "int" "int" "IntervalSetRule" "Boolean" "List[String]" "List[String]" "ValidationStringency" "String" "boolean" "boolean" "LogLevel" "List[File]" "long" "List[String]" "boolean" "int" "String" "boolean" "IntervalMergingRule" "List[String]" "int" "String" "String" "String" "boolean" "String" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "Concordance" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--evaluation --summary --truth --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --confidence --disable-bam-index-caching --disable-sequence-dictionary-validation --filter-analysis --filtered-true-negatives-and-false-negatives --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --reference --sites-only-vcf-output --true-positives-and-false-negatives --true-positives-and-false-positives --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--evaluation;-eval" "--summary;-S" "--truth;-truth" "--add-output-sam-program-record;-add-output-sam-program-record" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-bam-md5;-OBM" "--create-output-variant-index;-OVI" "--create-output-variant-md5;-OVM" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--input;-I" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--lenient;-LE" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--seconds-between-progress-updates;-seconds-between-progress-updates" "--sequence-dictionary;-sequence-dictionary" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--cloud-index-prefetch-buffer;-CIPB" "--cloud-prefetch-buffer;-CPB" "--confidence;-C" "--disable-bam-index-caching;-DBIC" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--filtered-true-negatives-and-false-negatives;-ftnfn" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--reference;-R" "--true-positives-and-false-negatives;-tpfn" "--true-positives-and-false-positives;-tpfp" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--evaluation --summary --truth --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --confidence --disable-bam-index-caching --disable-sequence-dictionary-validation --filter-analysis --filtered-true-negatives-and-false-negatives --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --reference --sites-only-vcf-output --true-positives-and-false-negatives --true-positives-and-false-positives --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("String" "File" "String" "boolean" "boolean" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "List[String]" "int" "int" "IntervalSetRule" "boolean" "Boolean" "List[String]" "List[String]" "ValidationStringency" "double" "String" "String" "boolean" "boolean" "LogLevel" "List[File]" "int" "int" "File" "boolean" "boolean" "File" "File" "int" "String" "boolean" "IntervalMergingRule" "List[String]" "String" "boolean" "File" "File" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "EvaluateInfoFieldConcordance" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--eval-info-key --evaluation --summary --truth --truth-info-key --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --confidence --disable-bam-index-caching --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --reference --sites-only-vcf-output --version --epsilon --showHidden --warn-big-differences ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--eval-info-key;-eval-info-key" "--evaluation;-eval" "--summary;-S" "--truth;-truth" "--truth-info-key;-truth-info-key" "--add-output-sam-program-record;-add-output-sam-program-record" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-bam-md5;-OBM" "--create-output-variant-index;-OVI" "--create-output-variant-md5;-OVM" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--input;-I" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--lenient;-LE" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--seconds-between-progress-updates;-seconds-between-progress-updates" "--sequence-dictionary;-sequence-dictionary" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--cloud-index-prefetch-buffer;-CIPB" "--cloud-prefetch-buffer;-CPB" "--confidence;-C" "--disable-bam-index-caching;-DBIC" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--reference;-R" "--epsilon;-epsilon" "--showHidden;-showHidden" "--warn-big-differences;-warn-big-differences" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--eval-info-key --evaluation --summary --truth --truth-info-key --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --confidence --disable-bam-index-caching --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --reference --sites-only-vcf-output --version --epsilon --showHidden --warn-big-differences ) ALL_ARGUMENT_VALUE_TYPES=("String" "String" "String" "String" "String" "boolean" "boolean" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "List[String]" "int" "int" "IntervalSetRule" "boolean" "Boolean" "List[String]" "List[String]" "ValidationStringency" "double" "String" "String" "boolean" "boolean" "LogLevel" "List[File]" "int" "int" "File" "boolean" "boolean" "int" "String" "boolean" "IntervalMergingRule" "List[String]" "String" "boolean" "boolean" "double" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "AS_FisherStrand" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=() MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=() MAX_OCCURRENCES=() ALL_LEGAL_ARGUMENTS=() ALL_ARGUMENT_VALUE_TYPES=() # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "ScatterIntervalsByNs" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--OUTPUT --REFERENCE --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --MAX_TO_MERGE --OUTPUT_TYPE --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--OUTPUT;-O" "--REFERENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--help;-h" "--MAX_TO_MERGE;-N" "--OUTPUT_TYPE;-OT" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--OUTPUT --REFERENCE --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --MAX_TO_MERGE --OUTPUT_TYPE --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "File" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "List[File]" "boolean" "int" "OutputType" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "AS_ReadPosRankSumTest" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=() MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=() MAX_OCCURRENCES=() ALL_LEGAL_ARGUMENTS=() ALL_ARGUMENT_VALUE_TYPES=() # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "VariantAnnotator" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--output --variant --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --annotation --annotation-group --annotations-to-exclude --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --dbsnp --disable-bam-index-caching --disable-sequence-dictionary-validation --expression --founder-id --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --pedigree --reference --resource --resource-allele-concordance --sites-only-vcf-output --version --comp --disable-tool-default-annotations --enable-all-annotations --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--output;-O" "--variant;-V" "--add-output-sam-program-record;-add-output-sam-program-record" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-bam-md5;-OBM" "--create-output-variant-index;-OVI" "--create-output-variant-md5;-OVM" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--input;-I" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--lenient;-LE" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--seconds-between-progress-updates;-seconds-between-progress-updates" "--sequence-dictionary;-sequence-dictionary" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--annotation;-A" "--annotation-group;-G" "--annotations-to-exclude;-AX" "--cloud-index-prefetch-buffer;-CIPB" "--cloud-prefetch-buffer;-CPB" "--dbsnp;-D" "--disable-bam-index-caching;-DBIC" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--expression;-E" "--founder-id;-founder-id" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--pedigree;-ped" "--reference;-R" "--resource-allele-concordance;-rac" "--disable-tool-default-annotations;-disable-tool-default-annotations" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--output --variant --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --annotation --annotation-group --annotations-to-exclude --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --dbsnp --disable-bam-index-caching --disable-sequence-dictionary-validation --expression --founder-id --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --pedigree --reference --resource --resource-allele-concordance --sites-only-vcf-output --version --comp --disable-tool-default-annotations --enable-all-annotations --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "String" "boolean" "boolean" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "List[String]" "int" "int" "IntervalSetRule" "boolean" "Boolean" "List[String]" "List[String]" "ValidationStringency" "double" "String" "String" "boolean" "boolean" "LogLevel" "List[String]" "List[String]" "List[String]" "List[File]" "int" "int" "FeatureInput[VariantContext]" "boolean" "boolean" "Set[String]" "List[String]" "int" "String" "boolean" "IntervalMergingRule" "List[String]" "File" "String" "List[FeatureInput[VariantContext]]" "Boolean" "boolean" "boolean" "List[FeatureInput[VariantContext]]" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "MergeBamAlignment" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--OUTPUT --REFERENCE_SEQUENCE --UNMAPPED_BAM --ADD_PG_TAG_TO_READS --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --ADD_MATE_CIGAR --ALIGNED_BAM --ALIGNED_READS_ONLY --ALIGNER_PROPER_PAIR_FLAGS --arguments_file --ATTRIBUTES_TO_REMOVE --ATTRIBUTES_TO_RETAIN --ATTRIBUTES_TO_REVERSE --ATTRIBUTES_TO_REVERSE_COMPLEMENT --CLIP_ADAPTERS --CLIP_OVERLAPPING_READS --EXPECTED_ORIENTATIONS --help --INCLUDE_SECONDARY_ALIGNMENTS --IS_BISULFITE_SEQUENCE --MATCHING_DICTIONARY_TAGS --MAX_INSERTIONS_OR_DELETIONS --MIN_UNCLIPPED_BASES --PRIMARY_ALIGNMENT_STRATEGY --PROGRAM_GROUP_COMMAND_LINE --PROGRAM_GROUP_NAME --PROGRAM_GROUP_VERSION --PROGRAM_RECORD_ID --READ1_ALIGNED_BAM --READ1_TRIM --READ2_ALIGNED_BAM --READ2_TRIM --SORT_ORDER --UNMAP_CONTAMINANT_READS --UNMAPPED_READ_STRATEGY --version --showHidden --JUMP_SIZE --PAIRED_RUN ) MUTUALLY_EXCLUSIVE_ARGS=("--ALIGNED_BAM;READ1_ALIGNED_BAM,READ2_ALIGNED_BAM,R1_ALIGNED,R2_ALIGNED" "--EXPECTED_ORIENTATIONS;JUMP_SIZE" "--READ1_ALIGNED_BAM;ALIGNED_BAM" "--READ2_ALIGNED_BAM;ALIGNED_BAM" "--JUMP_SIZE;EXPECTED_ORIENTATIONS,ORIENTATIONS" ) SYNONYMOUS_ARGS=("--OUTPUT;-O" "--REFERENCE_SEQUENCE;-R" "--UNMAPPED_BAM;-UNMAPPED" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--ADD_MATE_CIGAR;-MC" "--ALIGNED_BAM;-ALIGNED" "--ATTRIBUTES_TO_REVERSE;-RV" "--ATTRIBUTES_TO_REVERSE_COMPLEMENT;-RC" "--EXPECTED_ORIENTATIONS;-ORIENTATIONS" "--help;-h" "--MAX_INSERTIONS_OR_DELETIONS;-MAX_GAPS" "--PROGRAM_GROUP_COMMAND_LINE;-PG_COMMAND" "--PROGRAM_GROUP_NAME;-PG_NAME" "--PROGRAM_GROUP_VERSION;-PG_VERSION" "--PROGRAM_RECORD_ID;-PG" "--READ1_ALIGNED_BAM;-R1_ALIGNED" "--READ1_TRIM;-R1_TRIM" "--READ2_ALIGNED_BAM;-R2_ALIGNED" "--READ2_TRIM;-R2_TRIM" "--SORT_ORDER;-SO" "--UNMAP_CONTAMINANT_READS;-UNMAP_CONTAM" "--showHidden;-showHidden" "--JUMP_SIZE;-JUMP" "--PAIRED_RUN;-PE" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--OUTPUT --REFERENCE_SEQUENCE --UNMAPPED_BAM --ADD_PG_TAG_TO_READS --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --ADD_MATE_CIGAR --ALIGNED_BAM --ALIGNED_READS_ONLY --ALIGNER_PROPER_PAIR_FLAGS --arguments_file --ATTRIBUTES_TO_REMOVE --ATTRIBUTES_TO_RETAIN --ATTRIBUTES_TO_REVERSE --ATTRIBUTES_TO_REVERSE_COMPLEMENT --CLIP_ADAPTERS --CLIP_OVERLAPPING_READS --EXPECTED_ORIENTATIONS --help --INCLUDE_SECONDARY_ALIGNMENTS --IS_BISULFITE_SEQUENCE --MATCHING_DICTIONARY_TAGS --MAX_INSERTIONS_OR_DELETIONS --MIN_UNCLIPPED_BASES --PRIMARY_ALIGNMENT_STRATEGY --PROGRAM_GROUP_COMMAND_LINE --PROGRAM_GROUP_NAME --PROGRAM_GROUP_VERSION --PROGRAM_RECORD_ID --READ1_ALIGNED_BAM --READ1_TRIM --READ2_ALIGNED_BAM --READ2_TRIM --SORT_ORDER --UNMAP_CONTAMINANT_READS --UNMAPPED_READ_STRATEGY --version --showHidden --JUMP_SIZE --PAIRED_RUN ) ALL_ARGUMENT_VALUE_TYPES=("File" "File" "File" "boolean" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "Boolean" "List[File]" "boolean" "boolean" "List[File]" "List[String]" "List[String]" "Set[String]" "Set[String]" "boolean" "boolean" "List[PairOrientation]" "boolean" "boolean" "boolean" "List[String]" "int" "int" "PrimaryAlignmentStrategy" "String" "String" "String" "String" "List[File]" "int" "List[File]" "int" "SortOrder" "boolean" "UnmappingReadStrategy" "boolean" "boolean" "Integer" "Boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "SamToFastq" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--FASTQ --INPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --CLIPPING_ACTION --CLIPPING_ATTRIBUTE --CLIPPING_MIN_LENGTH --COMPRESS_OUTPUTS_PER_RG --help --INCLUDE_NON_PF_READS --INCLUDE_NON_PRIMARY_ALIGNMENTS --INTERLEAVE --OUTPUT_DIR --OUTPUT_PER_RG --QUALITY --RE_REVERSE --READ1_MAX_BASES_TO_WRITE --READ1_TRIM --READ2_MAX_BASES_TO_WRITE --READ2_TRIM --RG_TAG --SECOND_END_FASTQ --UNPAIRED_FASTQ --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=("--FASTQ;OUTPUT_PER_RG,COMPRESS_OUTPUTS_PER_RG,OUTPUT_DIR,OPRG,GZOPRG" "--COMPRESS_OUTPUTS_PER_RG;FASTQ,SECOND_END_FASTQ,UNPAIRED_FASTQ" "--OUTPUT_PER_RG;FASTQ,SECOND_END_FASTQ,UNPAIRED_FASTQ" "--SECOND_END_FASTQ;OUTPUT_PER_RG,COMPRESS_OUTPUTS_PER_RG,OPRG,GZOPRG" "--UNPAIRED_FASTQ;OUTPUT_PER_RG,COMPRESS_OUTPUTS_PER_RG,OPRG,GZOPRG" ) SYNONYMOUS_ARGS=("--FASTQ;-F" "--INPUT;-I" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--CLIPPING_ACTION;-CLIP_ACT" "--CLIPPING_ATTRIBUTE;-CLIP_ATTR" "--CLIPPING_MIN_LENGTH;-CLIP_MIN" "--COMPRESS_OUTPUTS_PER_RG;-GZOPRG" "--help;-h" "--INCLUDE_NON_PF_READS;-NON_PF" "--INTERLEAVE;-INTER" "--OUTPUT_DIR;-ODIR" "--OUTPUT_PER_RG;-OPRG" "--QUALITY;-Q" "--RE_REVERSE;-RC" "--READ1_MAX_BASES_TO_WRITE;-R1_MAX_BASES" "--READ1_TRIM;-R1_TRIM" "--READ2_MAX_BASES_TO_WRITE;-R2_MAX_BASES" "--READ2_TRIM;-R2_TRIM" "--RG_TAG;-RGT" "--SECOND_END_FASTQ;-F2" "--UNPAIRED_FASTQ;-FU" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--FASTQ --INPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --CLIPPING_ACTION --CLIPPING_ATTRIBUTE --CLIPPING_MIN_LENGTH --COMPRESS_OUTPUTS_PER_RG --help --INCLUDE_NON_PF_READS --INCLUDE_NON_PRIMARY_ALIGNMENTS --INTERLEAVE --OUTPUT_DIR --OUTPUT_PER_RG --QUALITY --RE_REVERSE --READ1_MAX_BASES_TO_WRITE --READ1_TRIM --READ2_MAX_BASES_TO_WRITE --READ2_TRIM --RG_TAG --SECOND_END_FASTQ --UNPAIRED_FASTQ --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "File" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "List[File]" "String" "String" "int" "Boolean" "boolean" "boolean" "boolean" "boolean" "File" "boolean" "Integer" "boolean" "Integer" "int" "Integer" "int" "String" "File" "File" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "AddCommentsToBam" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--COMMENT --INPUT --OUTPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--COMMENT;-C" "--INPUT;-I" "--OUTPUT;-O" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--help;-h" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--COMMENT --INPUT --OUTPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("List[String]" "File" "File" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "List[File]" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "CreateSequenceDictionary" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--REFERENCE --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --ALT_NAMES --arguments_file --GENOME_ASSEMBLY --help --NUM_SEQUENCES --OUTPUT --SPECIES --TRUNCATE_NAMES_AT_WHITESPACE --URI --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--REFERENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--ALT_NAMES;-AN" "--GENOME_ASSEMBLY;-AS" "--help;-h" "--OUTPUT;-O" "--SPECIES;-SP" "--URI;-UR" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--REFERENCE --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --ALT_NAMES --arguments_file --GENOME_ASSEMBLY --help --NUM_SEQUENCES --OUTPUT --SPECIES --TRUNCATE_NAMES_AT_WHITESPACE --URI --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "File" "List[File]" "String" "boolean" "int" "File" "String" "boolean" "String" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "WellformedReadFilter" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=() MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=() MAX_OCCURRENCES=() ALL_LEGAL_ARGUMENTS=() ALL_ARGUMENT_VALUE_TYPES=() # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "CollectIlluminaBasecallingMetrics" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--BASECALLS_DIR --LANE --READ_STRUCTURE --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --BARCODES_DIR --help --INPUT --OUTPUT --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--BASECALLS_DIR;-B" "--LANE;-L" "--READ_STRUCTURE;-RS" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--BARCODES_DIR;-BCD" "--help;-h" "--INPUT;-I" "--OUTPUT;-O" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--BASECALLS_DIR --LANE --READ_STRUCTURE --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --BARCODES_DIR --help --INPUT --OUTPUT --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "Integer" "String" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "List[File]" "File" "boolean" "File" "File" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "ReadStrandFilter" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--keep-reverse-strand-only ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=(0 ) MAX_OCCURRENCES=(2147483647 ) ALL_LEGAL_ARGUMENTS=(--keep-reverse-strand-only ) ALL_ARGUMENT_VALUE_TYPES=("Boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "SampleReadFilter" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--sample ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--sample;-sample" ) MIN_OCCURRENCES=(0 ) MAX_OCCURRENCES=(2147483647 ) ALL_LEGAL_ARGUMENTS=(--sample ) ALL_ARGUMENT_VALUE_TYPES=("Set[String]" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "MateDifferentStrandReadFilter" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=() MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=() MAX_OCCURRENCES=() ALL_LEGAL_ARGUMENTS=() ALL_ARGUMENT_VALUE_TYPES=() # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "ApplyBQSR" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--bqsr-recal-file --input --output --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --emit-original-quals --gcs-max-retries --gcs-project-for-requester-pays --global-qscore-prior --help --interval-merging-rule --intervals --preserve-qscores-less-than --quantize-quals --reference --sites-only-vcf-output --use-original-qualities --version --round-down-quantized --showHidden --static-quantized-quals ) MUTUALLY_EXCLUSIVE_ARGS=("--quantize-quals;static-quantized-quals,round-down-quantized" "--round-down-quantized;quantize-quals" "--static-quantized-quals;quantize-quals" ) SYNONYMOUS_ARGS=("--bqsr-recal-file;-bqsr" "--input;-I" "--output;-O" "--add-output-sam-program-record;-add-output-sam-program-record" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-bam-md5;-OBM" "--create-output-variant-index;-OVI" "--create-output-variant-md5;-OVM" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--lenient;-LE" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--seconds-between-progress-updates;-seconds-between-progress-updates" "--sequence-dictionary;-sequence-dictionary" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--cloud-index-prefetch-buffer;-CIPB" "--cloud-prefetch-buffer;-CPB" "--disable-bam-index-caching;-DBIC" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--reference;-R" "--use-original-qualities;-OQ" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--bqsr-recal-file --input --output --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --emit-original-quals --gcs-max-retries --gcs-project-for-requester-pays --global-qscore-prior --help --interval-merging-rule --intervals --preserve-qscores-less-than --quantize-quals --reference --sites-only-vcf-output --use-original-qualities --version --round-down-quantized --showHidden --static-quantized-quals ) ALL_ARGUMENT_VALUE_TYPES=("File" "List[String]" "String" "boolean" "boolean" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "int" "int" "IntervalSetRule" "boolean" "Boolean" "List[String]" "List[String]" "ValidationStringency" "double" "String" "String" "boolean" "boolean" "LogLevel" "List[File]" "int" "int" "boolean" "boolean" "boolean" "int" "String" "double" "boolean" "IntervalMergingRule" "List[String]" "int" "int" "String" "boolean" "Boolean" "boolean" "boolean" "boolean" "List[Integer]" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "AnnotatePairOrientation" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--input --output --variant --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --min-base-quality-cutoff --reference --sites-only-vcf-output --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--input;-I" "--output;-O" "--variant;-V" "--add-output-sam-program-record;-add-output-sam-program-record" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-bam-md5;-OBM" "--create-output-variant-index;-OVI" "--create-output-variant-md5;-OVM" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--lenient;-LE" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--seconds-between-progress-updates;-seconds-between-progress-updates" "--sequence-dictionary;-sequence-dictionary" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--cloud-index-prefetch-buffer;-CIPB" "--cloud-prefetch-buffer;-CPB" "--disable-bam-index-caching;-DBIC" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--min-base-quality-cutoff;-cutoff" "--reference;-R" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--input --output --variant --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --min-base-quality-cutoff --reference --sites-only-vcf-output --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("List[String]" "File" "String" "boolean" "boolean" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "int" "int" "IntervalSetRule" "boolean" "Boolean" "List[String]" "List[String]" "ValidationStringency" "double" "String" "String" "boolean" "boolean" "LogLevel" "List[File]" "int" "int" "boolean" "boolean" "int" "String" "boolean" "IntervalMergingRule" "List[String]" "int" "String" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "RevertBaseQualityScores" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--input --output --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --reference --sites-only-vcf-output --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--input;-I" "--output;-O" "--add-output-sam-program-record;-add-output-sam-program-record" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-bam-md5;-OBM" "--create-output-variant-index;-OVI" "--create-output-variant-md5;-OVM" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--lenient;-LE" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--seconds-between-progress-updates;-seconds-between-progress-updates" "--sequence-dictionary;-sequence-dictionary" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--cloud-index-prefetch-buffer;-CIPB" "--cloud-prefetch-buffer;-CPB" "--disable-bam-index-caching;-DBIC" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--reference;-R" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--input --output --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --reference --sites-only-vcf-output --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("List[String]" "String" "boolean" "boolean" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "int" "int" "IntervalSetRule" "boolean" "Boolean" "List[String]" "List[String]" "ValidationStringency" "double" "String" "String" "boolean" "boolean" "LogLevel" "List[File]" "int" "int" "boolean" "boolean" "int" "String" "boolean" "IntervalMergingRule" "List[String]" "String" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "ViewSam" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--INPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --ALIGNMENT_STATUS --arguments_file --HEADER_ONLY --help --INTERVAL_LIST --PF_STATUS --RECORDS_ONLY --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--INPUT;-I" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--help;-h" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--INPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --ALIGNMENT_STATUS --arguments_file --HEADER_ONLY --help --INTERVAL_LIST --PF_STATUS --RECORDS_ONLY --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("String" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "AlignmentStatus" "List[File]" "boolean" "boolean" "File" "PfStatus" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "IlluminaBasecallsToSam" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--BARCODE_PARAMS --BASECALLS_DIR --LANE --LIBRARY_PARAMS --OUTPUT --READ_STRUCTURE --RUN_BARCODE --SAMPLE_ALIAS --SEQUENCING_CENTER --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --ADAPTERS_TO_CHECK --APPLY_EAMSS_FILTER --arguments_file --BARCODE_POPULATION_STRATEGY --BARCODES_DIR --FIRST_TILE --FIVE_PRIME_ADAPTER --FORCE_GC --help --IGNORE_UNEXPECTED_BARCODES --INCLUDE_BARCODE_QUALITY --INCLUDE_BC_IN_RG_TAG --INCLUDE_NON_PF_READS --LIBRARY_NAME --MAX_READS_IN_RAM_PER_TILE --MINIMUM_QUALITY --MOLECULAR_INDEX_BASE_QUALITY_TAG --MOLECULAR_INDEX_TAG --NUM_PROCESSORS --PLATFORM --PROCESS_SINGLE_TILE --READ_GROUP_ID --RUN_START_DATE --TAG_PER_MOLECULAR_INDEX --THREE_PRIME_ADAPTER --TILE_LIMIT --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=("--BARCODE_PARAMS;OUTPUT,SAMPLE_ALIAS,LIBRARY_NAME,LIBRARY_PARAMS" "--LIBRARY_PARAMS;OUTPUT,SAMPLE_ALIAS,LIBRARY_NAME,BARCODE_PARAMS" "--OUTPUT;BARCODE_PARAMS,LIBRARY_PARAMS" "--SAMPLE_ALIAS;BARCODE_PARAMS,LIBRARY_PARAMS" "--FIRST_TILE;PROCESS_SINGLE_TILE" "--LIBRARY_NAME;BARCODE_PARAMS,LIBRARY_PARAMS" "--PROCESS_SINGLE_TILE;FIRST_TILE" ) SYNONYMOUS_ARGS=("--BASECALLS_DIR;-B" "--LANE;-L" "--OUTPUT;-O" "--READ_STRUCTURE;-RS" "--SAMPLE_ALIAS;-ALIAS" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--BARCODES_DIR;-BCD" "--help;-h" "--IGNORE_UNEXPECTED_BARCODES;-IGNORE_UNEXPECTED" "--INCLUDE_NON_PF_READS;-NONPF" "--LIBRARY_NAME;-LIB" "--READ_GROUP_ID;-RG" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--BARCODE_PARAMS --BASECALLS_DIR --LANE --LIBRARY_PARAMS --OUTPUT --READ_STRUCTURE --RUN_BARCODE --SAMPLE_ALIAS --SEQUENCING_CENTER --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --ADAPTERS_TO_CHECK --APPLY_EAMSS_FILTER --arguments_file --BARCODE_POPULATION_STRATEGY --BARCODES_DIR --FIRST_TILE --FIVE_PRIME_ADAPTER --FORCE_GC --help --IGNORE_UNEXPECTED_BARCODES --INCLUDE_BARCODE_QUALITY --INCLUDE_BC_IN_RG_TAG --INCLUDE_NON_PF_READS --LIBRARY_NAME --MAX_READS_IN_RAM_PER_TILE --MINIMUM_QUALITY --MOLECULAR_INDEX_BASE_QUALITY_TAG --MOLECULAR_INDEX_TAG --NUM_PROCESSORS --PLATFORM --PROCESS_SINGLE_TILE --READ_GROUP_ID --RUN_START_DATE --TAG_PER_MOLECULAR_INDEX --THREE_PRIME_ADAPTER --TILE_LIMIT --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "File" "Integer" "File" "File" "String" "String" "String" "String" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "List[IlluminaAdapterPair]" "boolean" "List[File]" "PopulateBarcode" "File" "Integer" "String" "Boolean" "boolean" "boolean" "boolean" "boolean" "boolean" "String" "int" "int" "String" "String" "Integer" "String" "Integer" "String" "Date" "List[String]" "String" "Integer" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "DiscoverVariantsFromContigAlignmentsSAMSpark" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--input --output --reference --add-output-vcf-command-line --create-output-bam-index --create-output-bam-splitting-index --create-output-variant-index --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --read-filter --read-index --read-validation-stringency --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --assembly-imprecise-evidence-overlap-uncertainty --bam-partition-size --cnv-calls --conf --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --imprecise-variant-evidence-threshold --interval-merging-rule --intervals --max-callable-imprecise-deletion-size --min-align-length --min-mq --num-reducers --output-shard-tmp-dir --program-name --sharded-output --spark-master --truth-interval-padding --version --debug-mode --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=("--output-shard-tmp-dir;sharded-output" "--sharded-output;output-shard-tmp-dir" ) SYNONYMOUS_ARGS=("--input;-I" "--output;-O" "--reference;-R" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-variant-index;-OVI" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--conf;-conf" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--min-mq;-mq" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--input --output --reference --add-output-vcf-command-line --create-output-bam-index --create-output-bam-splitting-index --create-output-variant-index --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --read-filter --read-index --read-validation-stringency --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --assembly-imprecise-evidence-overlap-uncertainty --bam-partition-size --cnv-calls --conf --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --imprecise-variant-evidence-threshold --interval-merging-rule --intervals --max-callable-imprecise-deletion-size --min-align-length --min-mq --num-reducers --output-shard-tmp-dir --program-name --sharded-output --spark-master --truth-interval-padding --version --debug-mode --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("List[String]" "String" "String" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "int" "int" "IntervalSetRule" "Boolean" "List[String]" "List[String]" "ValidationStringency" "String" "boolean" "boolean" "LogLevel" "List[File]" "int" "long" "String" "List[String]" "boolean" "int" "String" "boolean" "int" "IntervalMergingRule" "List[String]" "int" "Integer" "Integer" "int" "String" "String" "boolean" "String" "int" "boolean" "Boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "AS_MappingQualityRankSumTest" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=() MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=() MAX_OCCURRENCES=() ALL_LEGAL_ARGUMENTS=() ALL_ARGUMENT_VALUE_TYPES=() # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "NonNFastaSize" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--INPUT --OUTPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --INTERVALS --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--INPUT;-I" "--OUTPUT;-O" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--help;-h" "--INTERVALS;-INTERVALS" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--INPUT --OUTPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --INTERVALS --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "File" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "List[File]" "boolean" "File" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "ReblockGVCF" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--output --variant --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --annotate-with-num-discovered-alleles --annotation --annotation-group --annotations-to-exclude --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --dbsnp --disable-bam-index-caching --disable-sequence-dictionary-validation --founder-id --gcs-max-retries --gcs-project-for-requester-pays --help --heterozygosity --heterozygosity-stdev --indel-heterozygosity --interval-merging-rule --intervals --num-reference-samples-if-no-call --pedigree --population-callset --reference --sample-ploidy --sites-only-vcf-output --standard-min-confidence-threshold-for-calling --use-old-qual-calculator --version --disable-tool-default-annotations --do-qual-score-approximation --drop-low-quals --enable-all-annotations --gvcf-gq-bands --input-prior --max-alternate-alleles --max-genotype-count --rgq-threshold-to-no-call --showHidden --use-new-qual-calculator ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--output;-O" "--variant;-V" "--add-output-sam-program-record;-add-output-sam-program-record" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-bam-md5;-OBM" "--create-output-variant-index;-OVI" "--create-output-variant-md5;-OVM" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--input;-I" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--lenient;-LE" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--seconds-between-progress-updates;-seconds-between-progress-updates" "--sequence-dictionary;-sequence-dictionary" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--annotation;-A" "--annotation-group;-G" "--annotations-to-exclude;-AX" "--cloud-index-prefetch-buffer;-CIPB" "--cloud-prefetch-buffer;-CPB" "--dbsnp;-D" "--disable-bam-index-caching;-DBIC" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--founder-id;-founder-id" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--pedigree;-ped" "--population-callset;-population" "--reference;-R" "--sample-ploidy;-ploidy" "--standard-min-confidence-threshold-for-calling;-stand-call-conf" "--use-old-qual-calculator;-old-qual" "--disable-tool-default-annotations;-disable-tool-default-annotations" "--do-qual-score-approximation;-do-qual-approx" "--drop-low-quals;-drop-low-quals" "--gvcf-gq-bands;-GQB" "--rgq-threshold-to-no-call;-rgq-threshold" "--showHidden;-showHidden" "--use-new-qual-calculator;-new-qual" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--output --variant --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --annotate-with-num-discovered-alleles --annotation --annotation-group --annotations-to-exclude --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --dbsnp --disable-bam-index-caching --disable-sequence-dictionary-validation --founder-id --gcs-max-retries --gcs-project-for-requester-pays --help --heterozygosity --heterozygosity-stdev --indel-heterozygosity --interval-merging-rule --intervals --num-reference-samples-if-no-call --pedigree --population-callset --reference --sample-ploidy --sites-only-vcf-output --standard-min-confidence-threshold-for-calling --use-old-qual-calculator --version --disable-tool-default-annotations --do-qual-score-approximation --drop-low-quals --enable-all-annotations --gvcf-gq-bands --input-prior --max-alternate-alleles --max-genotype-count --rgq-threshold-to-no-call --showHidden --use-new-qual-calculator ) ALL_ARGUMENT_VALUE_TYPES=("File" "String" "boolean" "boolean" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "List[String]" "int" "int" "IntervalSetRule" "boolean" "Boolean" "List[String]" "List[String]" "ValidationStringency" "double" "String" "String" "boolean" "boolean" "LogLevel" "boolean" "List[String]" "List[String]" "List[String]" "List[File]" "int" "int" "FeatureInput[VariantContext]" "boolean" "boolean" "List[String]" "int" "String" "boolean" "Double" "double" "double" "IntervalMergingRule" "List[String]" "int" "File" "FeatureInput[VariantContext]" "String" "int" "boolean" "double" "boolean" "boolean" "boolean" "boolean" "boolean" "boolean" "List[Integer]" "List[Double]" "int" "int" "double" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "LikelihoodRankSumTest" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=() MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=() MAX_OCCURRENCES=() ALL_LEGAL_ARGUMENTS=() ALL_ARGUMENT_VALUE_TYPES=() # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "MappedReadFilter" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=() MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=() MAX_OCCURRENCES=() ALL_LEGAL_ARGUMENTS=() ALL_ARGUMENT_VALUE_TYPES=() # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "SplitNCigarReads" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--input --output --reference --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --do-not-fix-overhangs --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --max-bases-in-overhang --max-mismatches-in-overhang --process-secondary-alignments --refactor-cigar-string --sites-only-vcf-output --skip-mapping-quality-transform --version --max-reads-in-memory --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--input;-I" "--output;-O" "--reference;-R" "--add-output-sam-program-record;-add-output-sam-program-record" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-bam-md5;-OBM" "--create-output-variant-index;-OVI" "--create-output-variant-md5;-OVM" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--lenient;-LE" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--seconds-between-progress-updates;-seconds-between-progress-updates" "--sequence-dictionary;-sequence-dictionary" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--cloud-index-prefetch-buffer;-CIPB" "--cloud-prefetch-buffer;-CPB" "--disable-bam-index-caching;-DBIC" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--refactor-cigar-string;-fixNDN" "--skip-mapping-quality-transform;-skip-mq-transform" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--input --output --reference --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --do-not-fix-overhangs --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --max-bases-in-overhang --max-mismatches-in-overhang --process-secondary-alignments --refactor-cigar-string --sites-only-vcf-output --skip-mapping-quality-transform --version --max-reads-in-memory --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("List[String]" "String" "String" "boolean" "boolean" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "int" "int" "IntervalSetRule" "boolean" "Boolean" "List[String]" "List[String]" "ValidationStringency" "double" "String" "String" "boolean" "boolean" "LogLevel" "List[File]" "int" "int" "boolean" "boolean" "boolean" "int" "String" "boolean" "IntervalMergingRule" "List[String]" "int" "int" "boolean" "boolean" "boolean" "boolean" "boolean" "int" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "SvDiscoverFromLocalAssemblyContigAlignmentsSpark" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--input --output --reference --add-output-vcf-command-line --create-output-bam-index --create-output-bam-splitting-index --create-output-variant-index --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --read-filter --read-index --read-validation-stringency --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --assembly-imprecise-evidence-overlap-uncertainty --bam-partition-size --cnv-calls --conf --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --imprecise-variant-evidence-threshold --interval-merging-rule --intervals --max-callable-imprecise-deletion-size --min-align-length --min-mq --non-canonical-contig-names-file --num-reducers --output-shard-tmp-dir --program-name --sharded-output --spark-master --truth-interval-padding --version --write-sam --debug-mode --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=("--output-shard-tmp-dir;sharded-output" "--sharded-output;output-shard-tmp-dir" ) SYNONYMOUS_ARGS=("--input;-I" "--output;-O" "--reference;-R" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-variant-index;-OVI" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--conf;-conf" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--min-mq;-mq" "--non-canonical-contig-names-file;-alt-tigs" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--input --output --reference --add-output-vcf-command-line --create-output-bam-index --create-output-bam-splitting-index --create-output-variant-index --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --read-filter --read-index --read-validation-stringency --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --assembly-imprecise-evidence-overlap-uncertainty --bam-partition-size --cnv-calls --conf --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --imprecise-variant-evidence-threshold --interval-merging-rule --intervals --max-callable-imprecise-deletion-size --min-align-length --min-mq --non-canonical-contig-names-file --num-reducers --output-shard-tmp-dir --program-name --sharded-output --spark-master --truth-interval-padding --version --write-sam --debug-mode --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("List[String]" "String" "String" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "int" "int" "IntervalSetRule" "Boolean" "List[String]" "List[String]" "ValidationStringency" "String" "boolean" "boolean" "LogLevel" "List[File]" "int" "long" "String" "List[String]" "boolean" "int" "String" "boolean" "int" "IntervalMergingRule" "List[String]" "int" "Integer" "Integer" "String" "int" "String" "String" "boolean" "String" "int" "boolean" "boolean" "Boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "QualByDepth" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=() MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=() MAX_OCCURRENCES=() ALL_LEGAL_ARGUMENTS=() ALL_ARGUMENT_VALUE_TYPES=() # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "MappingQualityRankSumTest" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=() MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=() MAX_OCCURRENCES=() ALL_LEGAL_ARGUMENTS=() ALL_ARGUMENT_VALUE_TYPES=() # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "BaitDesigner" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--DESIGN_NAME --REFERENCE_SEQUENCE --TARGETS --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --BAIT_OFFSET --BAIT_SIZE --DESIGN_ON_TARGET_STRAND --DESIGN_STRATEGY --FILL_POOLS --help --LEFT_PRIMER --MERGE_NEARBY_TARGETS --MINIMUM_BAITS_PER_TARGET --OUTPUT_AGILENT_FILES --OUTPUT_DIRECTORY --PADDING --POOL_SIZE --REPEAT_TOLERANCE --RIGHT_PRIMER --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--REFERENCE_SEQUENCE;-R" "--TARGETS;-T" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--help;-h" "--OUTPUT_DIRECTORY;-O" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--DESIGN_NAME --REFERENCE_SEQUENCE --TARGETS --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --BAIT_OFFSET --BAIT_SIZE --DESIGN_ON_TARGET_STRAND --DESIGN_STRATEGY --FILL_POOLS --help --LEFT_PRIMER --MERGE_NEARBY_TARGETS --MINIMUM_BAITS_PER_TARGET --OUTPUT_AGILENT_FILES --OUTPUT_DIRECTORY --PADDING --POOL_SIZE --REPEAT_TOLERANCE --RIGHT_PRIMER --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("String" "File" "File" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "List[File]" "int" "int" "boolean" "DesignStrategy" "boolean" "boolean" "String" "boolean" "int" "boolean" "File" "int" "int" "int" "String" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "CollectIndependentReplicateMetrics" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--INPUT --OUTPUT --VCF --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --BARCODE_BQ --BARCODE_TAG --help --MATRIX_OUTPUT --MINIMUM_BARCODE_BQ --MINIMUM_BQ --MINIMUM_GQ --MINIMUM_MQ --SAMPLE --STOP_AFTER --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--INPUT;-I" "--OUTPUT;-O" "--VCF;-V" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--help;-h" "--MATRIX_OUTPUT;-MO" "--MINIMUM_BARCODE_BQ;-MBQ" "--MINIMUM_BQ;-BQ" "--MINIMUM_GQ;-GQ" "--MINIMUM_MQ;-MQ" "--SAMPLE;-ALIAS" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--INPUT --OUTPUT --VCF --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --BARCODE_BQ --BARCODE_TAG --help --MATRIX_OUTPUT --MINIMUM_BARCODE_BQ --MINIMUM_BQ --MINIMUM_GQ --MINIMUM_MQ --SAMPLE --STOP_AFTER --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "File" "File" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "List[File]" "String" "String" "boolean" "File" "Integer" "Integer" "Integer" "Integer" "String" "Integer" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "ReadPosRankSumTest" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=() MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=() MAX_OCCURRENCES=() ALL_LEGAL_ARGUMENTS=() ALL_ARGUMENT_VALUE_TYPES=() # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "ReadsPipelineSpark" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--input --known-sites --output --reference --add-output-vcf-command-line --create-output-bam-index --create-output-bam-splitting-index --create-output-variant-index --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --read-filter --read-index --read-validation-stringency --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --align --alleles --annotate-with-num-discovered-alleles --annotation --annotation-group --annotations-to-exclude --arguments_file --assemblyRegionPadding --bam-partition-size --base-quality-score-threshold --binary-tag-name --bqsr-baq-gap-open-penalty --bwa-mem-index-image --conf --contamination-fraction-to-filter --correct-overlapping-quality --dbsnp --default-base-qualities --deletions-default-quality --disable-sequence-dictionary-validation --do-not-mark-unmapped-mates --duplicate-scoring-strategy --duplicate-tagging-policy --emit-original-quals --founder-id --gcs-max-retries --gcs-project-for-requester-pays --genotyping-mode --global-qscore-prior --graph-output --help --heterozygosity --heterozygosity-stdev --indel-heterozygosity --indels-context-size --insertions-default-quality --interval-merging-rule --intervals --low-quality-tail --maxAssemblyRegionSize --maximum-cycle-value --maxReadsPerAlignmentStart --minAssemblyRegionSize --min-base-quality-score --mismatches-context-size --mismatches-default-quality --native-pair-hmm-threads --native-pair-hmm-use-double-precision --num-reducers --num-reference-samples-if-no-call --output-bam --output-mode --output-shard-tmp-dir --pedigree --population-callset --preserve-qscores-less-than --program-name --quantize-quals --quantizing-levels --readShardPadding --readShardSize --remove-all-duplicates --remove-sequencing-duplicates --sample-name --sample-ploidy --sharded-output --single-end-alignment --spark-master --standard-min-confidence-threshold-for-calling --strict --use-old-qual-calculator --use-original-qualities --version --activeProbabilityThreshold --adaptive-pruning --adaptive-pruning-initial-error-rate --allow-non-unique-kmers-in-ref --all-site-pls --bam-output --bam-writer-type --comp --consensus --contamination-fraction-per-sample-file --debug --disable-optimizations --disable-tool-default-annotations --do-not-run-physical-phasing --dont-increase-kmer-sizes-for-cycles --dont-trim-active-regions --dont-use-soft-clipped-bases --emit-ref-confidence --enable-all-annotations --genotype-filtered-alleles --gvcf-gq-bands --indel-size-to-eliminate-in-ref-model --input-prior --kmer-size --max-alternate-alleles --max-genotype-count --max-mnp-distance --max-num-haplotypes-in-population --maxProbPropagationDistance --max-unpruned-variants --min-dangling-branch-length --min-pruning --num-pruning-samples --pair-hmm-gap-continuation-penalty --pair-hmm-implementation --pcr-indel-model --phred-scaled-global-read-mismapping-rate --pruning-lod-threshold --round-down-quantized --showHidden --smith-waterman --static-quantized-quals --use-alleles-trigger --use-filtered-reads-for-annotations --recover-dangling-heads --use-new-qual-calculator ) MUTUALLY_EXCLUSIVE_ARGS=("--duplicate-tagging-policy;remove-all-duplicates,remove-sequencing-duplicates" "--output-shard-tmp-dir;sharded-output" "--quantize-quals;static-quantized-quals,round-down-quantized" "--remove-all-duplicates;duplicate-tagging-policy,remove-sequencing-duplicates" "--remove-sequencing-duplicates;duplicate-tagging-policy,remove-all-duplicates" "--sharded-output;output-shard-tmp-dir" "--round-down-quantized;quantize-quals" "--static-quantized-quals;quantize-quals" ) SYNONYMOUS_ARGS=("--input;-I" "--output;-O" "--reference;-R" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-variant-index;-OVI" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--annotation;-A" "--annotation-group;-G" "--annotations-to-exclude;-AX" "--assemblyRegionPadding;-assemblyRegionPadding" "--bwa-mem-index-image;-image" "--conf;-conf" "--contamination-fraction-to-filter;-contamination" "--dbsnp;-D" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--duplicate-scoring-strategy;-DS" "--founder-id;-founder-id" "--gcs-max-retries;-gcs-retries" "--graph-output;-graph" "--help;-h" "--indels-context-size;-ics" "--interval-merging-rule;-imr" "--intervals;-L" "--maxAssemblyRegionSize;-maxAssemblyRegionSize" "--maximum-cycle-value;-max-cycle" "--maxReadsPerAlignmentStart;-maxReadsPerAlignmentStart" "--minAssemblyRegionSize;-minAssemblyRegionSize" "--min-base-quality-score;-mbq" "--mismatches-context-size;-mcs" "--pedigree;-ped" "--population-callset;-population" "--readShardPadding;-readShardPadding" "--readShardSize;-readShardSize" "--sample-name;-ALIAS" "--sample-ploidy;-ploidy" "--single-end-alignment;-se" "--standard-min-confidence-threshold-for-calling;-stand-call-conf" "--use-old-qual-calculator;-old-qual" "--use-original-qualities;-OQ" "--activeProbabilityThreshold;-activeProbabilityThreshold" "--bam-output;-bamout" "--comp;-comp" "--contamination-fraction-per-sample-file;-contamination-file" "--debug;-debug" "--disable-tool-default-annotations;-disable-tool-default-annotations" "--emit-ref-confidence;-ERC" "--gvcf-gq-bands;-GQB" "--max-mnp-distance;-mnp-dist" "--maxProbPropagationDistance;-maxProbPropagationDistance" "--pair-hmm-implementation;-pairHMM" "--showHidden;-showHidden" "--use-new-qual-calculator;-new-qual" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--input --known-sites --output --reference --add-output-vcf-command-line --create-output-bam-index --create-output-bam-splitting-index --create-output-variant-index --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --read-filter --read-index --read-validation-stringency --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --align --alleles --annotate-with-num-discovered-alleles --annotation --annotation-group --annotations-to-exclude --arguments_file --assemblyRegionPadding --bam-partition-size --base-quality-score-threshold --binary-tag-name --bqsr-baq-gap-open-penalty --bwa-mem-index-image --conf --contamination-fraction-to-filter --correct-overlapping-quality --dbsnp --default-base-qualities --deletions-default-quality --disable-sequence-dictionary-validation --do-not-mark-unmapped-mates --duplicate-scoring-strategy --duplicate-tagging-policy --emit-original-quals --founder-id --gcs-max-retries --gcs-project-for-requester-pays --genotyping-mode --global-qscore-prior --graph-output --help --heterozygosity --heterozygosity-stdev --indel-heterozygosity --indels-context-size --insertions-default-quality --interval-merging-rule --intervals --low-quality-tail --maxAssemblyRegionSize --maximum-cycle-value --maxReadsPerAlignmentStart --minAssemblyRegionSize --min-base-quality-score --mismatches-context-size --mismatches-default-quality --native-pair-hmm-threads --native-pair-hmm-use-double-precision --num-reducers --num-reference-samples-if-no-call --output-bam --output-mode --output-shard-tmp-dir --pedigree --population-callset --preserve-qscores-less-than --program-name --quantize-quals --quantizing-levels --readShardPadding --readShardSize --remove-all-duplicates --remove-sequencing-duplicates --sample-name --sample-ploidy --sharded-output --single-end-alignment --spark-master --standard-min-confidence-threshold-for-calling --strict --use-old-qual-calculator --use-original-qualities --version --activeProbabilityThreshold --adaptive-pruning --adaptive-pruning-initial-error-rate --allow-non-unique-kmers-in-ref --all-site-pls --bam-output --bam-writer-type --comp --consensus --contamination-fraction-per-sample-file --debug --disable-optimizations --disable-tool-default-annotations --do-not-run-physical-phasing --dont-increase-kmer-sizes-for-cycles --dont-trim-active-regions --dont-use-soft-clipped-bases --emit-ref-confidence --enable-all-annotations --genotype-filtered-alleles --gvcf-gq-bands --indel-size-to-eliminate-in-ref-model --input-prior --kmer-size --max-alternate-alleles --max-genotype-count --max-mnp-distance --max-num-haplotypes-in-population --maxProbPropagationDistance --max-unpruned-variants --min-dangling-branch-length --min-pruning --num-pruning-samples --pair-hmm-gap-continuation-penalty --pair-hmm-implementation --pcr-indel-model --phred-scaled-global-read-mismapping-rate --pruning-lod-threshold --round-down-quantized --showHidden --smith-waterman --static-quantized-quals --use-alleles-trigger --use-filtered-reads-for-annotations --recover-dangling-heads --use-new-qual-calculator ) ALL_ARGUMENT_VALUE_TYPES=("List[String]" "List[String]" "String" "String" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "int" "int" "IntervalSetRule" "Boolean" "List[String]" "List[String]" "ValidationStringency" "String" "boolean" "boolean" "LogLevel" "boolean" "FeatureInput[VariantContext]" "boolean" "List[String]" "List[String]" "List[String]" "List[File]" "int" "long" "byte" "String" "double" "String" "List[String]" "double" "boolean" "FeatureInput[VariantContext]" "byte" "byte" "boolean" "boolean" "MarkDuplicatesScoringStrategy" "DuplicateTaggingPolicy" "boolean" "List[String]" "int" "String" "GenotypingOutputMode" "double" "String" "boolean" "Double" "double" "double" "int" "byte" "IntervalMergingRule" "List[String]" "byte" "int" "int" "int" "int" "byte" "int" "byte" "int" "boolean" "int" "int" "String" "OutputMode" "String" "File" "FeatureInput[VariantContext]" "int" "String" "int" "int" "int" "int" "boolean" "boolean" "String" "int" "boolean" "boolean" "String" "double" "boolean" "boolean" "Boolean" "boolean" "double" "boolean" "double" "boolean" "boolean" "String" "WriterType" "List[FeatureInput[VariantContext]]" "boolean" "File" "boolean" "boolean" "boolean" "boolean" "boolean" "boolean" "boolean" "ReferenceConfidenceMode" "boolean" "boolean" "List[Integer]" "int" "List[Double]" "List[Integer]" "int" "int" "int" "int" "int" "int" "int" "int" "int" "int" "Implementation" "PCRErrorModel" "int" "double" "boolean" "boolean" "Implementation" "List[Integer]" "boolean" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "AnnotateVcfWithExpectedAlleleFraction" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--mixing-fractions --output --variant --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --reference --sites-only-vcf-output --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--mixing-fractions;-mixing-fractions" "--output;-O" "--variant;-V" "--add-output-sam-program-record;-add-output-sam-program-record" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-bam-md5;-OBM" "--create-output-variant-index;-OVI" "--create-output-variant-md5;-OVM" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--input;-I" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--lenient;-LE" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--seconds-between-progress-updates;-seconds-between-progress-updates" "--sequence-dictionary;-sequence-dictionary" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--cloud-index-prefetch-buffer;-CIPB" "--cloud-prefetch-buffer;-CPB" "--disable-bam-index-caching;-DBIC" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--reference;-R" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--mixing-fractions --output --variant --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --reference --sites-only-vcf-output --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "File" "String" "boolean" "boolean" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "List[String]" "int" "int" "IntervalSetRule" "boolean" "Boolean" "List[String]" "List[String]" "ValidationStringency" "double" "String" "String" "boolean" "boolean" "LogLevel" "List[File]" "int" "int" "boolean" "boolean" "int" "String" "boolean" "IntervalMergingRule" "List[String]" "String" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "CpxVariantReInterpreterSpark" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--cpx-vcf --input --prefix-out-vcf --reference --add-output-vcf-command-line --create-output-bam-index --create-output-bam-splitting-index --create-output-variant-index --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --read-filter --read-index --read-validation-stringency --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --assembly-imprecise-evidence-overlap-uncertainty --bam-partition-size --cnv-calls --conf --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --imprecise-variant-evidence-threshold --interval-merging-rule --intervals --max-callable-imprecise-deletion-size --min-align-length --min-mq --non-canonical-contig-names-file --num-reducers --output-shard-tmp-dir --program-name --sharded-output --spark-master --truth-interval-padding --version --debug-mode --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=("--output-shard-tmp-dir;sharded-output" "--sharded-output;output-shard-tmp-dir" ) SYNONYMOUS_ARGS=("--input;-I" "--reference;-R" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-variant-index;-OVI" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--conf;-conf" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--min-mq;-mq" "--non-canonical-contig-names-file;-alt-tigs" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--cpx-vcf --input --prefix-out-vcf --reference --add-output-vcf-command-line --create-output-bam-index --create-output-bam-splitting-index --create-output-variant-index --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --read-filter --read-index --read-validation-stringency --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --assembly-imprecise-evidence-overlap-uncertainty --bam-partition-size --cnv-calls --conf --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --imprecise-variant-evidence-threshold --interval-merging-rule --intervals --max-callable-imprecise-deletion-size --min-align-length --min-mq --non-canonical-contig-names-file --num-reducers --output-shard-tmp-dir --program-name --sharded-output --spark-master --truth-interval-padding --version --debug-mode --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("String" "List[String]" "String" "String" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "int" "int" "IntervalSetRule" "Boolean" "List[String]" "List[String]" "ValidationStringency" "String" "boolean" "boolean" "LogLevel" "List[File]" "int" "long" "String" "List[String]" "boolean" "int" "String" "boolean" "int" "IntervalMergingRule" "List[String]" "int" "Integer" "Integer" "String" "int" "String" "String" "boolean" "String" "int" "boolean" "Boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "ExcessHet" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=() MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=() MAX_OCCURRENCES=() ALL_LEGAL_ARGUMENTS=() ALL_ARGUMENT_VALUE_TYPES=() # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "ReadGroupReadFilter" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--keep-read-group ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=(0 ) MAX_OCCURRENCES=(2147483647 ) ALL_LEGAL_ARGUMENTS=(--keep-read-group ) ALL_ARGUMENT_VALUE_TYPES=("String" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "TandemRepeat" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=() MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=() MAX_OCCURRENCES=() ALL_LEGAL_ARGUMENTS=() ALL_ARGUMENT_VALUE_TYPES=() # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "ModelSegments" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--output --output-prefix --gatk-config-file --QUIET --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --allelic-counts --arguments_file --denoised-copy-ratios --gcs-max-retries --gcs-project-for-requester-pays --genotyping-base-error-rate --genotyping-homozygous-log-ratio-threshold --help --kernel-approximation-dimension --kernel-scaling-allele-fraction --kernel-variance-allele-fraction --kernel-variance-copy-ratio --maximum-number-of-segments-per-chromosome --maximum-number-of-smoothing-iterations --minimum-total-allele-count-case --minimum-total-allele-count-normal --minor-allele-fraction-prior-alpha --normal-allelic-counts --number-of-burn-in-samples-allele-fraction --number-of-burn-in-samples-copy-ratio --number-of-changepoints-penalty-factor --number-of-samples-allele-fraction --number-of-samples-copy-ratio --number-of-smoothing-iterations-per-fit --smoothing-credible-interval-threshold-allele-fraction --smoothing-credible-interval-threshold-copy-ratio --version --window-size --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--output;-O" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--gcs-max-retries;-gcs-retries" "--help;-h" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--output --output-prefix --gatk-config-file --QUIET --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --allelic-counts --arguments_file --denoised-copy-ratios --gcs-max-retries --gcs-project-for-requester-pays --genotyping-base-error-rate --genotyping-homozygous-log-ratio-threshold --help --kernel-approximation-dimension --kernel-scaling-allele-fraction --kernel-variance-allele-fraction --kernel-variance-copy-ratio --maximum-number-of-segments-per-chromosome --maximum-number-of-smoothing-iterations --minimum-total-allele-count-case --minimum-total-allele-count-normal --minor-allele-fraction-prior-alpha --normal-allelic-counts --number-of-burn-in-samples-allele-fraction --number-of-burn-in-samples-copy-ratio --number-of-changepoints-penalty-factor --number-of-samples-allele-fraction --number-of-samples-copy-ratio --number-of-smoothing-iterations-per-fit --smoothing-credible-interval-threshold-allele-fraction --smoothing-credible-interval-threshold-copy-ratio --version --window-size --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("String" "String" "String" "Boolean" "String" "boolean" "boolean" "LogLevel" "File" "List[File]" "File" "int" "String" "double" "double" "boolean" "int" "double" "double" "double" "int" "int" "int" "int" "double" "File" "int" "int" "double" "int" "int" "int" "double" "double" "boolean" "List[Integer]" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "CallCopyRatioSegments" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--input --output --gatk-config-file --QUIET --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --calling-copy-ratio-z-score-threshold --gcs-max-retries --gcs-project-for-requester-pays --help --neutral-segment-copy-ratio-lower-bound --neutral-segment-copy-ratio-upper-bound --outlier-neutral-segment-copy-ratio-z-score-threshold --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--input;-I" "--output;-O" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--gcs-max-retries;-gcs-retries" "--help;-h" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--input --output --gatk-config-file --QUIET --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --calling-copy-ratio-z-score-threshold --gcs-max-retries --gcs-project-for-requester-pays --help --neutral-segment-copy-ratio-lower-bound --neutral-segment-copy-ratio-upper-bound --outlier-neutral-segment-copy-ratio-z-score-threshold --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "File" "String" "Boolean" "String" "boolean" "boolean" "LogLevel" "List[File]" "double" "int" "String" "boolean" "double" "double" "double" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "SetNmMdAndUqTags" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--INPUT --OUTPUT --REFERENCE_SEQUENCE --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --IS_BISULFITE_SEQUENCE --SET_ONLY_UQ --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--INPUT;-I" "--OUTPUT;-O" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--help;-h" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--INPUT --OUTPUT --REFERENCE_SEQUENCE --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --IS_BISULFITE_SEQUENCE --SET_ONLY_UQ --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "File" "File" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "List[File]" "boolean" "boolean" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "CountReadsSpark" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--input --add-output-vcf-command-line --create-output-bam-index --create-output-bam-splitting-index --create-output-variant-index --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --read-filter --read-index --read-validation-stringency --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --bam-partition-size --conf --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --num-reducers --output --output-shard-tmp-dir --program-name --reference --sharded-output --spark-master --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=("--output-shard-tmp-dir;sharded-output" "--sharded-output;output-shard-tmp-dir" ) SYNONYMOUS_ARGS=("--input;-I" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-variant-index;-OVI" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--conf;-conf" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--output;-O" "--reference;-R" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--input --add-output-vcf-command-line --create-output-bam-index --create-output-bam-splitting-index --create-output-variant-index --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --read-filter --read-index --read-validation-stringency --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --bam-partition-size --conf --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --num-reducers --output --output-shard-tmp-dir --program-name --reference --sharded-output --spark-master --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("List[String]" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "int" "int" "IntervalSetRule" "Boolean" "List[String]" "List[String]" "ValidationStringency" "String" "boolean" "boolean" "LogLevel" "List[File]" "long" "List[String]" "boolean" "int" "String" "boolean" "IntervalMergingRule" "List[String]" "int" "String" "String" "String" "String" "boolean" "String" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "CollectQualityYieldMetrics" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--INPUT --OUTPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --ASSUME_SORTED --help --INCLUDE_SECONDARY_ALIGNMENTS --INCLUDE_SUPPLEMENTAL_ALIGNMENTS --STOP_AFTER --USE_ORIGINAL_QUALITIES --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--INPUT;-I" "--OUTPUT;-O" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--ASSUME_SORTED;-AS" "--help;-h" "--USE_ORIGINAL_QUALITIES;-OQ" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--INPUT --OUTPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --ASSUME_SORTED --help --INCLUDE_SECONDARY_ALIGNMENTS --INCLUDE_SUPPLEMENTAL_ALIGNMENTS --STOP_AFTER --USE_ORIGINAL_QUALITIES --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "File" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "List[File]" "boolean" "boolean" "boolean" "boolean" "long" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "AllowAllReadsReadFilter" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=() MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=() MAX_OCCURRENCES=() ALL_LEGAL_ARGUMENTS=() ALL_ARGUMENT_VALUE_TYPES=() # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "AnnotateIntervals" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--intervals --output --reference --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --feature-query-lookahead --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --mappability-track --segmental-duplication-track --sites-only-vcf-output --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--intervals;-L" "--output;-O" "--reference;-R" "--add-output-sam-program-record;-add-output-sam-program-record" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-bam-md5;-OBM" "--create-output-variant-index;-OVI" "--create-output-variant-md5;-OVM" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--input;-I" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--lenient;-LE" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--seconds-between-progress-updates;-seconds-between-progress-updates" "--sequence-dictionary;-sequence-dictionary" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--cloud-index-prefetch-buffer;-CIPB" "--cloud-prefetch-buffer;-CPB" "--disable-bam-index-caching;-DBIC" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--intervals --output --reference --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --feature-query-lookahead --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --mappability-track --segmental-duplication-track --sites-only-vcf-output --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("List[String]" "File" "String" "boolean" "boolean" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "List[String]" "int" "int" "IntervalSetRule" "boolean" "Boolean" "List[String]" "List[String]" "ValidationStringency" "double" "String" "String" "boolean" "boolean" "LogLevel" "List[File]" "int" "int" "boolean" "boolean" "int" "int" "String" "boolean" "IntervalMergingRule" "FeatureInput[BEDFeature]" "FeatureInput[BEDFeature]" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "CollectInsertSizeMetrics" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--Histogram_FILE --INPUT --OUTPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --ASSUME_SORTED --DEVIATIONS --help --HISTOGRAM_WIDTH --INCLUDE_DUPLICATES --METRIC_ACCUMULATION_LEVEL --MINIMUM_PCT --STOP_AFTER --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--Histogram_FILE;-H" "--INPUT;-I" "--OUTPUT;-O" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--ASSUME_SORTED;-AS" "--help;-h" "--HISTOGRAM_WIDTH;-W" "--METRIC_ACCUMULATION_LEVEL;-LEVEL" "--MINIMUM_PCT;-M" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--Histogram_FILE --INPUT --OUTPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --ASSUME_SORTED --DEVIATIONS --help --HISTOGRAM_WIDTH --INCLUDE_DUPLICATES --METRIC_ACCUMULATION_LEVEL --MINIMUM_PCT --STOP_AFTER --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "File" "File" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "List[File]" "boolean" "double" "boolean" "Integer" "boolean" "Set[MetricAccumulationLevel]" "float" "long" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "CNNScoreVariants" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--output --reference --variant --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --architecture --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --filter-symbolic-and-sv --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --read-limit --sites-only-vcf-output --tensor-type --version --weights --window-size --disable-avx-check --inference-batch-size --info-annotation-keys --inter-op-threads --intra-op-threads --output-tensor-dir --showHidden --transfer-batch-size ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--output;-O" "--reference;-R" "--variant;-V" "--add-output-sam-program-record;-add-output-sam-program-record" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-bam-md5;-OBM" "--create-output-variant-index;-OVI" "--create-output-variant-md5;-OVM" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--input;-I" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--lenient;-LE" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--seconds-between-progress-updates;-seconds-between-progress-updates" "--sequence-dictionary;-sequence-dictionary" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--architecture;-architecture" "--cloud-index-prefetch-buffer;-CIPB" "--cloud-prefetch-buffer;-CPB" "--disable-bam-index-caching;-DBIC" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--filter-symbolic-and-sv;-filter-symbolic-and-sv" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--read-limit;-read-limit" "--tensor-type;-tensor-type" "--weights;-weights" "--window-size;-window-size" "--disable-avx-check;-disable-avx-check" "--inference-batch-size;-inference-batch-size" "--info-annotation-keys;-info-annotation-keys" "--inter-op-threads;-inter-op-threads" "--intra-op-threads;-intra-op-threads" "--output-tensor-dir;-output-tensor-dir" "--showHidden;-showHidden" "--transfer-batch-size;-transfer-batch-size" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--output --reference --variant --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --architecture --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --filter-symbolic-and-sv --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --read-limit --sites-only-vcf-output --tensor-type --version --weights --window-size --disable-avx-check --inference-batch-size --info-annotation-keys --inter-op-threads --intra-op-threads --output-tensor-dir --showHidden --transfer-batch-size ) ALL_ARGUMENT_VALUE_TYPES=("String" "String" "String" "boolean" "boolean" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "List[String]" "int" "int" "IntervalSetRule" "boolean" "Boolean" "List[String]" "List[String]" "ValidationStringency" "double" "String" "String" "boolean" "boolean" "LogLevel" "String" "List[File]" "int" "int" "boolean" "boolean" "boolean" "int" "String" "boolean" "IntervalMergingRule" "List[String]" "int" "boolean" "TensorType" "boolean" "String" "int" "boolean" "int" "List[String]" "int" "int" "String" "boolean" "int" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "LibraryReadFilter" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--library ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--library;-library" ) MIN_OCCURRENCES=(0 ) MAX_OCCURRENCES=(2147483647 ) ALL_LEGAL_ARGUMENTS=(--library ) ALL_ARGUMENT_VALUE_TYPES=("Set[String]" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "FifoBuffer" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --BUFFER_SIZE --DEBUG_FREQUENCY --help --IO_SIZE --NAME --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--help;-h" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --BUFFER_SIZE --DEBUG_FREQUENCY --help --IO_SIZE --NAME --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "List[File]" "int" "int" "boolean" "int" "String" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "UpdateVcfSequenceDictionary" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--INPUT --OUTPUT --SEQUENCE_DICTIONARY --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--INPUT;-I" "--OUTPUT;-O" "--SEQUENCE_DICTIONARY;-SD" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--help;-h" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--INPUT --OUTPUT --SEQUENCE_DICTIONARY --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "File" "File" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "List[File]" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "IntervalListTools" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--INPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --ACTION --arguments_file --BREAK_BANDS_AT_MULTIPLES_OF --COMMENT --help --INCLUDE_FILTERED --INVERT --OUTPUT --OUTPUT_VALUE --PADDING --SCATTER_CONTENT --SCATTER_COUNT --SECOND_INPUT --SORT --SUBDIVISION_MODE --UNIQUE --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--INPUT;-I" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--BREAK_BANDS_AT_MULTIPLES_OF;-BRK" "--help;-h" "--OUTPUT;-O" "--SECOND_INPUT;-SI" "--SUBDIVISION_MODE;-M" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--INPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --ACTION --arguments_file --BREAK_BANDS_AT_MULTIPLES_OF --COMMENT --help --INCLUDE_FILTERED --INVERT --OUTPUT --OUTPUT_VALUE --PADDING --SCATTER_CONTENT --SCATTER_COUNT --SECOND_INPUT --SORT --SUBDIVISION_MODE --UNIQUE --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("List[File]" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "Action" "List[File]" "int" "List[String]" "boolean" "boolean" "boolean" "File" "Output" "int" "Integer" "int" "List[File]" "boolean" "IntervalListScatterMode" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "PossibleDeNovo" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=() MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=() MAX_OCCURRENCES=() ALL_LEGAL_ARGUMENTS=() ALL_ARGUMENT_VALUE_TYPES=() # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "CollectWgsMetricsWithNonZeroCoverage" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--CHART_OUTPUT --INPUT --OUTPUT --REFERENCE_SEQUENCE --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --ALLELE_FRACTION --arguments_file --COUNT_UNPAIRED --COVERAGE_CAP --help --INCLUDE_BQ_HISTOGRAM --INTERVALS --LOCUS_ACCUMULATION_CAP --MINIMUM_BASE_QUALITY --MINIMUM_MAPPING_QUALITY --READ_LENGTH --SAMPLE_SIZE --STOP_AFTER --THEORETICAL_SENSITIVITY_OUTPUT --USE_FAST_ALGORITHM --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--CHART_OUTPUT;-CHART" "--INPUT;-I" "--OUTPUT;-O" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--COVERAGE_CAP;-CAP" "--help;-h" "--MINIMUM_BASE_QUALITY;-Q" "--MINIMUM_MAPPING_QUALITY;-MQ" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--CHART_OUTPUT --INPUT --OUTPUT --REFERENCE_SEQUENCE --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --ALLELE_FRACTION --arguments_file --COUNT_UNPAIRED --COVERAGE_CAP --help --INCLUDE_BQ_HISTOGRAM --INTERVALS --LOCUS_ACCUMULATION_CAP --MINIMUM_BASE_QUALITY --MINIMUM_MAPPING_QUALITY --READ_LENGTH --SAMPLE_SIZE --STOP_AFTER --THEORETICAL_SENSITIVITY_OUTPUT --USE_FAST_ALGORITHM --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "File" "File" "File" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "List[Double]" "List[File]" "boolean" "int" "boolean" "boolean" "File" "int" "int" "int" "int" "int" "long" "File" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "GermlineCNVCaller" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--contig-ploidy-calls --input --output --output-prefix --run-mode --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --active-class-padding-hybrid-mode --adamax-beta-1 --adamax-beta-2 --annotated-intervals --arguments_file --caller-external-admixing-rate --caller-internal-admixing-rate --caller-update-convergence-threshold --class-coherence-length --cnv-coherence-length --convergence-snr-averaging-window --convergence-snr-countdown-window --convergence-snr-trigger-threshold --copy-number-posterior-expectation-mode --depth-correction-tau --disable-annealing --disable-caller --disable-sampler --enable-bias-factors --gc-curve-standard-deviation --gcs-max-retries --gcs-project-for-requester-pays --help --init-ard-rel-unexplained-variance --initial-temperature --interval-merging-rule --interval-psi-scale --intervals --learning-rate --log-emission-samples-per-round --log-emission-sampling-median-rel-error --log-emission-sampling-rounds --log-mean-bias-standard-deviation --mapping-error-rate --max-advi-iter-first-epoch --max-advi-iter-subsequent-epochs --max-bias-factors --max-calling-iters --max-copy-number --max-training-epochs --min-training-epochs --model --num-gc-bins --num-thermal-advi-iters --p-active --p-alt --sample-psi-scale --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--input;-I" "--output;-O" "--exclude-intervals;-XL" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--contig-ploidy-calls --input --output --output-prefix --run-mode --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --active-class-padding-hybrid-mode --adamax-beta-1 --adamax-beta-2 --annotated-intervals --arguments_file --caller-external-admixing-rate --caller-internal-admixing-rate --caller-update-convergence-threshold --class-coherence-length --cnv-coherence-length --convergence-snr-averaging-window --convergence-snr-countdown-window --convergence-snr-trigger-threshold --copy-number-posterior-expectation-mode --depth-correction-tau --disable-annealing --disable-caller --disable-sampler --enable-bias-factors --gc-curve-standard-deviation --gcs-max-retries --gcs-project-for-requester-pays --help --init-ard-rel-unexplained-variance --initial-temperature --interval-merging-rule --interval-psi-scale --intervals --learning-rate --log-emission-samples-per-round --log-emission-sampling-median-rel-error --log-emission-sampling-rounds --log-mean-bias-standard-deviation --mapping-error-rate --max-advi-iter-first-epoch --max-advi-iter-subsequent-epochs --max-bias-factors --max-calling-iters --max-copy-number --max-training-epochs --min-training-epochs --model --num-gc-bins --num-thermal-advi-iters --p-active --p-alt --sample-psi-scale --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("String" "List[File]" "String" "String" "RunMode" "List[String]" "String" "int" "int" "IntervalSetRule" "Boolean" "String" "boolean" "boolean" "LogLevel" "int" "double" "double" "File" "List[File]" "double" "double" "double" "double" "double" "int" "int" "double" "CopyNumberPosteriorExpectationMode" "double" "boolean" "boolean" "boolean" "boolean" "double" "int" "String" "boolean" "double" "double" "IntervalMergingRule" "double" "List[String]" "double" "int" "double" "int" "double" "double" "int" "int" "int" "int" "int" "int" "int" "String" "int" "int" "double" "double" "double" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "AS_StrandOddsRatio" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=() MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=() MAX_OCCURRENCES=() ALL_LEGAL_ARGUMENTS=() ALL_ARGUMENT_VALUE_TYPES=() # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "CollectVariantCallingMetrics" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--DBSNP --INPUT --OUTPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --GVCF_INPUT --help --SEQUENCE_DICTIONARY --TARGET_INTERVALS --THREAD_COUNT --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--INPUT;-I" "--OUTPUT;-O" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--help;-h" "--SEQUENCE_DICTIONARY;-SD" "--TARGET_INTERVALS;-TI" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--DBSNP --INPUT --OUTPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --GVCF_INPUT --help --SEQUENCE_DICTIONARY --TARGET_INTERVALS --THREAD_COUNT --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "File" "File" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "List[File]" "boolean" "boolean" "File" "File" "int" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "CountBasesSpark" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--input --add-output-vcf-command-line --create-output-bam-index --create-output-bam-splitting-index --create-output-variant-index --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --read-filter --read-index --read-validation-stringency --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --bam-partition-size --conf --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --num-reducers --output --output-shard-tmp-dir --program-name --reference --sharded-output --spark-master --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=("--output-shard-tmp-dir;sharded-output" "--sharded-output;output-shard-tmp-dir" ) SYNONYMOUS_ARGS=("--input;-I" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-variant-index;-OVI" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--conf;-conf" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--output;-O" "--reference;-R" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--input --add-output-vcf-command-line --create-output-bam-index --create-output-bam-splitting-index --create-output-variant-index --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --read-filter --read-index --read-validation-stringency --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --bam-partition-size --conf --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --num-reducers --output --output-shard-tmp-dir --program-name --reference --sharded-output --spark-master --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("List[String]" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "int" "int" "IntervalSetRule" "Boolean" "List[String]" "List[String]" "ValidationStringency" "String" "boolean" "boolean" "LogLevel" "List[File]" "long" "List[String]" "boolean" "int" "String" "boolean" "IntervalMergingRule" "List[String]" "int" "String" "String" "String" "String" "boolean" "String" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "ConvertHeaderlessHadoopBamShardToBam" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--bam-shard --bam-with-header --output --gatk-config-file --QUIET --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --gcs-max-retries --gcs-project-for-requester-pays --help --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--output;-O" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--gcs-max-retries;-gcs-retries" "--help;-h" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--bam-shard --bam-with-header --output --gatk-config-file --QUIET --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --gcs-max-retries --gcs-project-for-requester-pays --help --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "File" "File" "String" "Boolean" "String" "boolean" "boolean" "LogLevel" "List[File]" "int" "String" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "FastqToSam" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--FASTQ --OUTPUT --SAMPLE_NAME --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --ALLOW_AND_IGNORE_EMPTY_LINES --arguments_file --COMMENT --DESCRIPTION --FASTQ2 --help --LIBRARY_NAME --MAX_Q --MIN_Q --PLATFORM --PLATFORM_MODEL --PLATFORM_UNIT --PREDICTED_INSERT_SIZE --PROGRAM_GROUP --QUALITY_FORMAT --READ_GROUP_NAME --RUN_DATE --SEQUENCING_CENTER --SORT_ORDER --USE_SEQUENTIAL_FASTQS --version --showHidden --STRIP_UNPAIRED_MATE_NUMBER ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--FASTQ;-F1" "--OUTPUT;-O" "--SAMPLE_NAME;-SM" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--COMMENT;-CO" "--DESCRIPTION;-DS" "--FASTQ2;-F2" "--help;-h" "--LIBRARY_NAME;-LB" "--PLATFORM;-PL" "--PLATFORM_MODEL;-PM" "--PLATFORM_UNIT;-PU" "--PREDICTED_INSERT_SIZE;-PI" "--PROGRAM_GROUP;-PG" "--QUALITY_FORMAT;-V" "--READ_GROUP_NAME;-RG" "--RUN_DATE;-DT" "--SEQUENCING_CENTER;-CN" "--SORT_ORDER;-SO" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--FASTQ --OUTPUT --SAMPLE_NAME --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --ALLOW_AND_IGNORE_EMPTY_LINES --arguments_file --COMMENT --DESCRIPTION --FASTQ2 --help --LIBRARY_NAME --MAX_Q --MIN_Q --PLATFORM --PLATFORM_MODEL --PLATFORM_UNIT --PREDICTED_INSERT_SIZE --PROGRAM_GROUP --QUALITY_FORMAT --READ_GROUP_NAME --RUN_DATE --SEQUENCING_CENTER --SORT_ORDER --USE_SEQUENTIAL_FASTQS --version --showHidden --STRIP_UNPAIRED_MATE_NUMBER ) ALL_ARGUMENT_VALUE_TYPES=("File" "File" "String" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "Boolean" "List[File]" "List[String]" "String" "File" "boolean" "String" "int" "int" "String" "String" "String" "Integer" "String" "FastqQualityFormat" "String" "Iso8601Date" "String" "SortOrder" "boolean" "boolean" "boolean" "Boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "MarkIlluminaAdapters" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--INPUT --METRICS --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --ADAPTER_TRUNCATION_LENGTH --ADAPTERS --arguments_file --FIVE_PRIME_ADAPTER --help --MAX_ERROR_RATE_PE --MAX_ERROR_RATE_SE --MIN_MATCH_BASES_PE --MIN_MATCH_BASES_SE --NUM_ADAPTERS_TO_KEEP --OUTPUT --PAIRED_RUN --PRUNE_ADAPTER_LIST_AFTER_THIS_MANY_ADAPTERS_SEEN --THREE_PRIME_ADAPTER --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--INPUT;-I" "--METRICS;-M" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--help;-h" "--OUTPUT;-O" "--PAIRED_RUN;-PE" "--PRUNE_ADAPTER_LIST_AFTER_THIS_MANY_ADAPTERS_SEEN;-APT" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--INPUT --METRICS --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --ADAPTER_TRUNCATION_LENGTH --ADAPTERS --arguments_file --FIVE_PRIME_ADAPTER --help --MAX_ERROR_RATE_PE --MAX_ERROR_RATE_SE --MIN_MATCH_BASES_PE --MIN_MATCH_BASES_SE --NUM_ADAPTERS_TO_KEEP --OUTPUT --PAIRED_RUN --PRUNE_ADAPTER_LIST_AFTER_THIS_MANY_ADAPTERS_SEEN --THREE_PRIME_ADAPTER --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "File" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "int" "List[IlluminaAdapterPair]" "List[File]" "String" "boolean" "double" "double" "int" "int" "int" "File" "Boolean" "int" "String" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "CollectIlluminaLaneMetrics" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--OUTPUT_DIRECTORY --OUTPUT_PREFIX --RUN_DIRECTORY --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --FILE_EXTENSION --help --IS_NOVASEQ --READ_STRUCTURE --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--OUTPUT_PREFIX;-O" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--FILE_EXTENSION;-EXT" "--help;-h" "--READ_STRUCTURE;-RS" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--OUTPUT_DIRECTORY --OUTPUT_PREFIX --RUN_DIRECTORY --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --FILE_EXTENSION --help --IS_NOVASEQ --READ_STRUCTURE --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "String" "File" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "List[File]" "String" "boolean" "boolean" "ReadStructure" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "GenotypeGVCFs" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--output --reference --variant --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --annotate-with-num-discovered-alleles --annotation --annotation-group --annotations-to-exclude --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --dbsnp --disable-bam-index-caching --disable-sequence-dictionary-validation --founder-id --gcs-max-retries --gcs-project-for-requester-pays --help --heterozygosity --heterozygosity-stdev --include-non-variant-sites --indel-heterozygosity --interval-merging-rule --intervals --num-reference-samples-if-no-call --pedigree --population-callset --sample-ploidy --sites-only-vcf-output --standard-min-confidence-threshold-for-calling --use-old-qual-calculator --version --disable-tool-default-annotations --enable-all-annotations --input-prior --max-alternate-alleles --max-genotype-count --only-output-calls-starting-in-intervals --showHidden --use-new-qual-calculator ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--output;-O" "--reference;-R" "--variant;-V" "--add-output-sam-program-record;-add-output-sam-program-record" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-bam-md5;-OBM" "--create-output-variant-index;-OVI" "--create-output-variant-md5;-OVM" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--input;-I" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--lenient;-LE" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--seconds-between-progress-updates;-seconds-between-progress-updates" "--sequence-dictionary;-sequence-dictionary" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--annotation;-A" "--annotation-group;-G" "--annotations-to-exclude;-AX" "--cloud-index-prefetch-buffer;-CIPB" "--cloud-prefetch-buffer;-CPB" "--dbsnp;-D" "--disable-bam-index-caching;-DBIC" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--founder-id;-founder-id" "--gcs-max-retries;-gcs-retries" "--help;-h" "--include-non-variant-sites;-all-sites" "--interval-merging-rule;-imr" "--intervals;-L" "--pedigree;-ped" "--population-callset;-population" "--sample-ploidy;-ploidy" "--standard-min-confidence-threshold-for-calling;-stand-call-conf" "--use-old-qual-calculator;-old-qual" "--disable-tool-default-annotations;-disable-tool-default-annotations" "--showHidden;-showHidden" "--use-new-qual-calculator;-new-qual" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--output --reference --variant --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --annotate-with-num-discovered-alleles --annotation --annotation-group --annotations-to-exclude --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --dbsnp --disable-bam-index-caching --disable-sequence-dictionary-validation --founder-id --gcs-max-retries --gcs-project-for-requester-pays --help --heterozygosity --heterozygosity-stdev --include-non-variant-sites --indel-heterozygosity --interval-merging-rule --intervals --num-reference-samples-if-no-call --pedigree --population-callset --sample-ploidy --sites-only-vcf-output --standard-min-confidence-threshold-for-calling --use-old-qual-calculator --version --disable-tool-default-annotations --enable-all-annotations --input-prior --max-alternate-alleles --max-genotype-count --only-output-calls-starting-in-intervals --showHidden --use-new-qual-calculator ) ALL_ARGUMENT_VALUE_TYPES=("File" "String" "String" "boolean" "boolean" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "List[String]" "int" "int" "IntervalSetRule" "boolean" "Boolean" "List[String]" "List[String]" "ValidationStringency" "double" "String" "String" "boolean" "boolean" "LogLevel" "boolean" "List[String]" "List[String]" "List[String]" "List[File]" "int" "int" "FeatureInput[VariantContext]" "boolean" "boolean" "List[String]" "int" "String" "boolean" "Double" "double" "boolean" "double" "IntervalMergingRule" "List[String]" "int" "File" "FeatureInput[VariantContext]" "int" "boolean" "double" "boolean" "boolean" "boolean" "boolean" "List[Double]" "int" "int" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "HaplotypeCallerSpark" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--input --output --reference --add-output-vcf-command-line --create-output-bam-index --create-output-bam-splitting-index --create-output-variant-index --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --read-filter --read-index --read-validation-stringency --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --alleles --annotate-with-num-discovered-alleles --annotation --annotation-group --annotations-to-exclude --arguments_file --assemblyRegionPadding --bam-partition-size --base-quality-score-threshold --conf --contamination-fraction-to-filter --correct-overlapping-quality --dbsnp --disable-sequence-dictionary-validation --founder-id --gcs-max-retries --gcs-project-for-requester-pays --genotyping-mode --graph-output --help --heterozygosity --heterozygosity-stdev --indel-heterozygosity --interval-merging-rule --intervals --maxAssemblyRegionSize --maxReadsPerAlignmentStart --minAssemblyRegionSize --min-base-quality-score --native-pair-hmm-threads --native-pair-hmm-use-double-precision --num-reducers --num-reference-samples-if-no-call --output-mode --output-shard-tmp-dir --pedigree --population-callset --program-name --readShardPadding --readShardSize --sample-name --sample-ploidy --sharded-output --shuffle --spark-master --standard-min-confidence-threshold-for-calling --strict --use-old-qual-calculator --version --activeProbabilityThreshold --adaptive-pruning --adaptive-pruning-initial-error-rate --allow-non-unique-kmers-in-ref --all-site-pls --bam-output --bam-writer-type --comp --consensus --contamination-fraction-per-sample-file --debug --disable-optimizations --disable-tool-default-annotations --do-not-run-physical-phasing --dont-increase-kmer-sizes-for-cycles --dont-trim-active-regions --dont-use-soft-clipped-bases --emit-ref-confidence --enable-all-annotations --genotype-filtered-alleles --gvcf-gq-bands --indel-size-to-eliminate-in-ref-model --input-prior --kmer-size --max-alternate-alleles --max-genotype-count --max-mnp-distance --max-num-haplotypes-in-population --maxProbPropagationDistance --max-unpruned-variants --min-dangling-branch-length --min-pruning --num-pruning-samples --pair-hmm-gap-continuation-penalty --pair-hmm-implementation --pcr-indel-model --phred-scaled-global-read-mismapping-rate --pruning-lod-threshold --showHidden --smith-waterman --use-alleles-trigger --use-filtered-reads-for-annotations --recover-dangling-heads --use-new-qual-calculator ) MUTUALLY_EXCLUSIVE_ARGS=("--output-shard-tmp-dir;sharded-output" "--sharded-output;output-shard-tmp-dir" ) SYNONYMOUS_ARGS=("--input;-I" "--output;-O" "--reference;-R" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-variant-index;-OVI" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--annotation;-A" "--annotation-group;-G" "--annotations-to-exclude;-AX" "--assemblyRegionPadding;-assemblyRegionPadding" "--conf;-conf" "--contamination-fraction-to-filter;-contamination" "--dbsnp;-D" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--founder-id;-founder-id" "--gcs-max-retries;-gcs-retries" "--graph-output;-graph" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--maxAssemblyRegionSize;-maxAssemblyRegionSize" "--maxReadsPerAlignmentStart;-maxReadsPerAlignmentStart" "--minAssemblyRegionSize;-minAssemblyRegionSize" "--min-base-quality-score;-mbq" "--pedigree;-ped" "--population-callset;-population" "--readShardPadding;-readShardPadding" "--readShardSize;-readShardSize" "--sample-name;-ALIAS" "--sample-ploidy;-ploidy" "--shuffle;-shuffle" "--standard-min-confidence-threshold-for-calling;-stand-call-conf" "--use-old-qual-calculator;-old-qual" "--activeProbabilityThreshold;-activeProbabilityThreshold" "--bam-output;-bamout" "--comp;-comp" "--contamination-fraction-per-sample-file;-contamination-file" "--debug;-debug" "--disable-tool-default-annotations;-disable-tool-default-annotations" "--emit-ref-confidence;-ERC" "--gvcf-gq-bands;-GQB" "--max-mnp-distance;-mnp-dist" "--maxProbPropagationDistance;-maxProbPropagationDistance" "--pair-hmm-implementation;-pairHMM" "--showHidden;-showHidden" "--use-new-qual-calculator;-new-qual" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--input --output --reference --add-output-vcf-command-line --create-output-bam-index --create-output-bam-splitting-index --create-output-variant-index --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --read-filter --read-index --read-validation-stringency --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --alleles --annotate-with-num-discovered-alleles --annotation --annotation-group --annotations-to-exclude --arguments_file --assemblyRegionPadding --bam-partition-size --base-quality-score-threshold --conf --contamination-fraction-to-filter --correct-overlapping-quality --dbsnp --disable-sequence-dictionary-validation --founder-id --gcs-max-retries --gcs-project-for-requester-pays --genotyping-mode --graph-output --help --heterozygosity --heterozygosity-stdev --indel-heterozygosity --interval-merging-rule --intervals --maxAssemblyRegionSize --maxReadsPerAlignmentStart --minAssemblyRegionSize --min-base-quality-score --native-pair-hmm-threads --native-pair-hmm-use-double-precision --num-reducers --num-reference-samples-if-no-call --output-mode --output-shard-tmp-dir --pedigree --population-callset --program-name --readShardPadding --readShardSize --sample-name --sample-ploidy --sharded-output --shuffle --spark-master --standard-min-confidence-threshold-for-calling --strict --use-old-qual-calculator --version --activeProbabilityThreshold --adaptive-pruning --adaptive-pruning-initial-error-rate --allow-non-unique-kmers-in-ref --all-site-pls --bam-output --bam-writer-type --comp --consensus --contamination-fraction-per-sample-file --debug --disable-optimizations --disable-tool-default-annotations --do-not-run-physical-phasing --dont-increase-kmer-sizes-for-cycles --dont-trim-active-regions --dont-use-soft-clipped-bases --emit-ref-confidence --enable-all-annotations --genotype-filtered-alleles --gvcf-gq-bands --indel-size-to-eliminate-in-ref-model --input-prior --kmer-size --max-alternate-alleles --max-genotype-count --max-mnp-distance --max-num-haplotypes-in-population --maxProbPropagationDistance --max-unpruned-variants --min-dangling-branch-length --min-pruning --num-pruning-samples --pair-hmm-gap-continuation-penalty --pair-hmm-implementation --pcr-indel-model --phred-scaled-global-read-mismapping-rate --pruning-lod-threshold --showHidden --smith-waterman --use-alleles-trigger --use-filtered-reads-for-annotations --recover-dangling-heads --use-new-qual-calculator ) ALL_ARGUMENT_VALUE_TYPES=("List[String]" "String" "String" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "int" "int" "IntervalSetRule" "Boolean" "List[String]" "List[String]" "ValidationStringency" "String" "boolean" "boolean" "LogLevel" "FeatureInput[VariantContext]" "boolean" "List[String]" "List[String]" "List[String]" "List[File]" "int" "long" "byte" "List[String]" "double" "boolean" "FeatureInput[VariantContext]" "boolean" "List[String]" "int" "String" "GenotypingOutputMode" "String" "boolean" "Double" "double" "double" "IntervalMergingRule" "List[String]" "int" "int" "int" "byte" "int" "boolean" "int" "int" "OutputMode" "String" "File" "FeatureInput[VariantContext]" "String" "int" "int" "String" "int" "boolean" "boolean" "String" "double" "boolean" "boolean" "boolean" "double" "boolean" "double" "boolean" "boolean" "String" "WriterType" "List[FeatureInput[VariantContext]]" "boolean" "File" "boolean" "boolean" "boolean" "boolean" "boolean" "boolean" "boolean" "ReferenceConfidenceMode" "boolean" "boolean" "List[Integer]" "int" "List[Double]" "List[Integer]" "int" "int" "int" "int" "int" "int" "int" "int" "int" "int" "Implementation" "PCRErrorModel" "int" "double" "boolean" "Implementation" "boolean" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "SimpleMarkDuplicatesWithMateCigar" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--INPUT --METRICS_FILE --OUTPUT --ADD_PG_TAG_TO_READS --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --ASSUME_SORT_ORDER --BARCODE_TAG --CLEAR_DT --COMMENT --DUPLEX_UMI --DUPLICATE_SCORING_STRATEGY --help --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP --MAX_OPTICAL_DUPLICATE_SET_SIZE --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP --MOLECULAR_IDENTIFIER_TAG --OPTICAL_DUPLICATE_PIXEL_DISTANCE --PROGRAM_GROUP_COMMAND_LINE --PROGRAM_GROUP_NAME --PROGRAM_GROUP_VERSION --PROGRAM_RECORD_ID --READ_NAME_REGEX --READ_ONE_BARCODE_TAG --READ_TWO_BARCODE_TAG --REMOVE_DUPLICATES --REMOVE_SEQUENCING_DUPLICATES --SORTING_COLLECTION_SIZE_RATIO --TAG_DUPLICATE_SET_MEMBERS --TAGGING_POLICY --version --showHidden --ASSUME_SORTED ) MUTUALLY_EXCLUSIVE_ARGS=("--ASSUME_SORT_ORDER;ASSUME_SORTED" "--ASSUME_SORTED;ASSUME_SORT_ORDER,ASO" ) SYNONYMOUS_ARGS=("--INPUT;-I" "--METRICS_FILE;-M" "--OUTPUT;-O" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--ASSUME_SORT_ORDER;-ASO" "--COMMENT;-CO" "--DUPLICATE_SCORING_STRATEGY;-DS" "--help;-h" "--MAX_FILE_HANDLES_FOR_READ_ENDS_MAP;-MAX_FILE_HANDLES" "--MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP;-MAX_SEQS" "--PROGRAM_GROUP_COMMAND_LINE;-PG_COMMAND" "--PROGRAM_GROUP_NAME;-PG_NAME" "--PROGRAM_GROUP_VERSION;-PG_VERSION" "--PROGRAM_RECORD_ID;-PG" "--showHidden;-showHidden" "--ASSUME_SORTED;-AS" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--INPUT --METRICS_FILE --OUTPUT --ADD_PG_TAG_TO_READS --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --ASSUME_SORT_ORDER --BARCODE_TAG --CLEAR_DT --COMMENT --DUPLEX_UMI --DUPLICATE_SCORING_STRATEGY --help --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP --MAX_OPTICAL_DUPLICATE_SET_SIZE --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP --MOLECULAR_IDENTIFIER_TAG --OPTICAL_DUPLICATE_PIXEL_DISTANCE --PROGRAM_GROUP_COMMAND_LINE --PROGRAM_GROUP_NAME --PROGRAM_GROUP_VERSION --PROGRAM_RECORD_ID --READ_NAME_REGEX --READ_ONE_BARCODE_TAG --READ_TWO_BARCODE_TAG --REMOVE_DUPLICATES --REMOVE_SEQUENCING_DUPLICATES --SORTING_COLLECTION_SIZE_RATIO --TAG_DUPLICATE_SET_MEMBERS --TAGGING_POLICY --version --showHidden --ASSUME_SORTED ) ALL_ARGUMENT_VALUE_TYPES=("List[String]" "File" "File" "boolean" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "List[File]" "SortOrder" "String" "boolean" "List[String]" "boolean" "ScoringStrategy" "boolean" "int" "long" "int" "String" "int" "String" "String" "String" "String" "String" "String" "String" "boolean" "boolean" "double" "boolean" "DuplicateTaggingPolicy" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "UnmarkDuplicates" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--input --output --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --reference --sites-only-vcf-output --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--input;-I" "--output;-O" "--add-output-sam-program-record;-add-output-sam-program-record" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-bam-md5;-OBM" "--create-output-variant-index;-OVI" "--create-output-variant-md5;-OVM" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--lenient;-LE" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--seconds-between-progress-updates;-seconds-between-progress-updates" "--sequence-dictionary;-sequence-dictionary" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--cloud-index-prefetch-buffer;-CIPB" "--cloud-prefetch-buffer;-CPB" "--disable-bam-index-caching;-DBIC" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--reference;-R" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--input --output --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --reference --sites-only-vcf-output --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("List[String]" "String" "boolean" "boolean" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "int" "int" "IntervalSetRule" "boolean" "Boolean" "List[String]" "List[String]" "ValidationStringency" "double" "String" "String" "boolean" "boolean" "LogLevel" "List[File]" "int" "int" "boolean" "boolean" "int" "String" "boolean" "IntervalMergingRule" "List[String]" "String" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "CountVariantsSpark" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--variant --add-output-vcf-command-line --create-output-bam-index --create-output-bam-splitting-index --create-output-variant-index --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --read-index --read-validation-stringency --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --bam-partition-size --conf --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --num-reducers --output --output-shard-tmp-dir --program-name --reference --sharded-output --spark-master --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=("--output-shard-tmp-dir;sharded-output" "--sharded-output;output-shard-tmp-dir" ) SYNONYMOUS_ARGS=("--variant;-V" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-variant-index;-OVI" "--exclude-intervals;-XL" "--input;-I" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--read-index;-read-index" "--read-validation-stringency;-VS" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--conf;-conf" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--output;-O" "--reference;-R" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--variant --add-output-vcf-command-line --create-output-bam-index --create-output-bam-splitting-index --create-output-variant-index --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --read-index --read-validation-stringency --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --bam-partition-size --conf --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --num-reducers --output --output-shard-tmp-dir --program-name --reference --sharded-output --spark-master --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("String" "boolean" "boolean" "boolean" "boolean" "List[String]" "String" "List[String]" "int" "int" "IntervalSetRule" "Boolean" "List[String]" "ValidationStringency" "String" "boolean" "boolean" "LogLevel" "List[File]" "long" "List[String]" "boolean" "int" "String" "boolean" "IntervalMergingRule" "List[String]" "int" "String" "String" "String" "String" "boolean" "String" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "DepthPerSampleHC" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=() MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=() MAX_OCCURRENCES=() ALL_LEGAL_ARGUMENTS=() ALL_ARGUMENT_VALUE_TYPES=() # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "MappingQualityNotZeroReadFilter" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=() MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=() MAX_OCCURRENCES=() ALL_LEGAL_ARGUMENTS=() ALL_ARGUMENT_VALUE_TYPES=() # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "FindMendelianViolations" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--INPUT --OUTPUT --TRIOS --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --FEMALE_CHROMS --help --MALE_CHROMS --MIN_DP --MIN_GQ --MIN_HET_FRACTION --PSEUDO_AUTOSOMAL_REGIONS --SKIP_CHROMS --TAB_MODE --THREAD_COUNT --VCF_DIR --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--INPUT;-I" "--OUTPUT;-O" "--TRIOS;-PED" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--help;-h" "--MIN_DP;-DP" "--MIN_GQ;-GQ" "--MIN_HET_FRACTION;-MINHET" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--INPUT --OUTPUT --TRIOS --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --FEMALE_CHROMS --help --MALE_CHROMS --MIN_DP --MIN_GQ --MIN_HET_FRACTION --PSEUDO_AUTOSOMAL_REGIONS --SKIP_CHROMS --TAB_MODE --THREAD_COUNT --VCF_DIR --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "File" "File" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "List[File]" "Set[String]" "boolean" "Set[String]" "int" "int" "double" "Set[String]" "Set[String]" "boolean" "int" "File" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "SamFormatConverter" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--INPUT --OUTPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--INPUT;-I" "--OUTPUT;-O" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--help;-h" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--INPUT --OUTPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "File" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "List[File]" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "SplitSamByLibrary" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--INPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --OUTPUT --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--INPUT;-I" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--help;-h" "--OUTPUT;-O" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--INPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --OUTPUT --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "List[File]" "boolean" "File" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "CompareMetrics" ]] ; then # Set up the completion information for this tool: NUM_POSITIONAL_ARGUMENTS=2 POSITIONAL_ARGUMENT_TYPE=("List[File]") DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--help;-h" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "List[File]" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "CollectSequencingArtifactMetrics" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--INPUT --OUTPUT --REFERENCE_SEQUENCE --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --ASSUME_SORTED --CONTEXT_SIZE --CONTEXTS_TO_PRINT --DB_SNP --FILE_EXTENSION --help --INCLUDE_DUPLICATES --INCLUDE_NON_PF_READS --INCLUDE_UNPAIRED --INTERVALS --MAXIMUM_INSERT_SIZE --MINIMUM_INSERT_SIZE --MINIMUM_MAPPING_QUALITY --MINIMUM_QUALITY_SCORE --STOP_AFTER --TANDEM_READS --USE_OQ --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--INPUT;-I" "--OUTPUT;-O" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--ASSUME_SORTED;-AS" "--FILE_EXTENSION;-EXT" "--help;-h" "--INCLUDE_DUPLICATES;-DUPES" "--INCLUDE_NON_PF_READS;-NON_PF" "--INCLUDE_UNPAIRED;-UNPAIRED" "--MAXIMUM_INSERT_SIZE;-MAX_INS" "--MINIMUM_INSERT_SIZE;-MIN_INS" "--MINIMUM_MAPPING_QUALITY;-MQ" "--MINIMUM_QUALITY_SCORE;-Q" "--TANDEM_READS;-TANDEM" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--INPUT --OUTPUT --REFERENCE_SEQUENCE --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --ASSUME_SORTED --CONTEXT_SIZE --CONTEXTS_TO_PRINT --DB_SNP --FILE_EXTENSION --help --INCLUDE_DUPLICATES --INCLUDE_NON_PF_READS --INCLUDE_UNPAIRED --INTERVALS --MAXIMUM_INSERT_SIZE --MINIMUM_INSERT_SIZE --MINIMUM_MAPPING_QUALITY --MINIMUM_QUALITY_SCORE --STOP_AFTER --TANDEM_READS --USE_OQ --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "File" "File" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "List[File]" "boolean" "int" "Set[String]" "File" "String" "boolean" "boolean" "boolean" "boolean" "File" "int" "int" "int" "int" "long" "boolean" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "MarkDuplicates" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--INPUT --METRICS_FILE --OUTPUT --ADD_PG_TAG_TO_READS --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --ASSUME_SORT_ORDER --BARCODE_TAG --CLEAR_DT --COMMENT --DUPLEX_UMI --DUPLICATE_SCORING_STRATEGY --help --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP --MAX_OPTICAL_DUPLICATE_SET_SIZE --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP --MOLECULAR_IDENTIFIER_TAG --OPTICAL_DUPLICATE_PIXEL_DISTANCE --PROGRAM_GROUP_COMMAND_LINE --PROGRAM_GROUP_NAME --PROGRAM_GROUP_VERSION --PROGRAM_RECORD_ID --READ_NAME_REGEX --READ_ONE_BARCODE_TAG --READ_TWO_BARCODE_TAG --REMOVE_DUPLICATES --REMOVE_SEQUENCING_DUPLICATES --SORTING_COLLECTION_SIZE_RATIO --TAG_DUPLICATE_SET_MEMBERS --TAGGING_POLICY --version --showHidden --ASSUME_SORTED ) MUTUALLY_EXCLUSIVE_ARGS=("--ASSUME_SORT_ORDER;ASSUME_SORTED" "--ASSUME_SORTED;ASSUME_SORT_ORDER,ASO" ) SYNONYMOUS_ARGS=("--INPUT;-I" "--METRICS_FILE;-M" "--OUTPUT;-O" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--ASSUME_SORT_ORDER;-ASO" "--COMMENT;-CO" "--DUPLICATE_SCORING_STRATEGY;-DS" "--help;-h" "--MAX_FILE_HANDLES_FOR_READ_ENDS_MAP;-MAX_FILE_HANDLES" "--MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP;-MAX_SEQS" "--PROGRAM_GROUP_COMMAND_LINE;-PG_COMMAND" "--PROGRAM_GROUP_NAME;-PG_NAME" "--PROGRAM_GROUP_VERSION;-PG_VERSION" "--PROGRAM_RECORD_ID;-PG" "--showHidden;-showHidden" "--ASSUME_SORTED;-AS" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--INPUT --METRICS_FILE --OUTPUT --ADD_PG_TAG_TO_READS --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --ASSUME_SORT_ORDER --BARCODE_TAG --CLEAR_DT --COMMENT --DUPLEX_UMI --DUPLICATE_SCORING_STRATEGY --help --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP --MAX_OPTICAL_DUPLICATE_SET_SIZE --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP --MOLECULAR_IDENTIFIER_TAG --OPTICAL_DUPLICATE_PIXEL_DISTANCE --PROGRAM_GROUP_COMMAND_LINE --PROGRAM_GROUP_NAME --PROGRAM_GROUP_VERSION --PROGRAM_RECORD_ID --READ_NAME_REGEX --READ_ONE_BARCODE_TAG --READ_TWO_BARCODE_TAG --REMOVE_DUPLICATES --REMOVE_SEQUENCING_DUPLICATES --SORTING_COLLECTION_SIZE_RATIO --TAG_DUPLICATE_SET_MEMBERS --TAGGING_POLICY --version --showHidden --ASSUME_SORTED ) ALL_ARGUMENT_VALUE_TYPES=("List[String]" "File" "File" "boolean" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "List[File]" "SortOrder" "String" "boolean" "List[String]" "boolean" "ScoringStrategy" "boolean" "int" "long" "int" "String" "int" "String" "String" "String" "String" "String" "String" "String" "boolean" "boolean" "double" "boolean" "DuplicateTaggingPolicy" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "SampleList" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=() MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=() MAX_OCCURRENCES=() ALL_LEGAL_ARGUMENTS=() ALL_ARGUMENT_VALUE_TYPES=() # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "CollectMultipleMetrics" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--INPUT --OUTPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --ASSUME_SORTED --DB_SNP --FILE_EXTENSION --help --IGNORE_SEQUENCE --INCLUDE_UNPAIRED --INTERVALS --METRIC_ACCUMULATION_LEVEL --PROGRAM --REF_FLAT --STOP_AFTER --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--INPUT;-I" "--OUTPUT;-O" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--ASSUME_SORTED;-AS" "--FILE_EXTENSION;-EXT" "--help;-h" "--INCLUDE_UNPAIRED;-UNPAIRED" "--METRIC_ACCUMULATION_LEVEL;-LEVEL" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--INPUT --OUTPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --ASSUME_SORTED --DB_SNP --FILE_EXTENSION --help --IGNORE_SEQUENCE --INCLUDE_UNPAIRED --INTERVALS --METRIC_ACCUMULATION_LEVEL --PROGRAM --REF_FLAT --STOP_AFTER --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "String" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "List[File]" "boolean" "File" "String" "boolean" "Set[String]" "boolean" "File" "Set[MetricAccumulationLevel]" "Set[Program]" "File" "int" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "ExtractSVEvidenceSpark" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--aligner-index-image --input --kmers-to-ignore --output --add-output-vcf-command-line --create-output-bam-index --create-output-bam-splitting-index --create-output-variant-index --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --read-filter --read-index --read-validation-stringency --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --adapter-sequence --allowed-short-fragment-overhang --arguments_file --assembled-contigs-output-order --assembly-to-mapped-size-ratio-guess --bam-partition-size --breakpoint-evidence-dir --breakpoint-intervals --cleaner-max-copy-number --cleaner-max-intervals --cleaner-min-kmer-count --conf --cross-contigs-to-ignore --disable-sequence-dictionary-validation --exclusion-interval-padding --exclusion-intervals --external-evidence --external-evidence-uncertainty --external-evidence-weight --fastq-dir --gcs-max-retries --gcs-project-for-requester-pays --help --high-coverage-intervals --high-depth-coverage-factor --high-depth-coverage-peak-factor --include-mapping-location --interval-merging-rule --interval-only-assembly --intervals --kmer-intervals --kmer-max-dust-score --k-size --max-fastq-size --max-tracked-fragment-length --min-coherent-evidence-coverage-ratio --min-evidence-coverage-ratio --min-evidence-mapq --min-evidence-match-length --min-kmers-per-interval --num-reducers --output-shard-tmp-dir --program-name --qname-intervals-for-assembly --qname-intervals-mapped --read-metadata --reference --run-without-gaps-annotation --run-without-umap-s100-annotation --sharded-output --spark-master --sv-evidence-filter-model-file --sv-evidence-filter-threshold-probability --sv-evidence-filter-type --sv-genome-gaps-file --sv-genome-umap-s100-file --target-link-file --unfiltered-breakpoint-evidence-dir --version --write-gfas --expand-assembly-graph --pop-variant-bubbles --remove-shadowed-contigs --showHidden --z-dropoff ) MUTUALLY_EXCLUSIVE_ARGS=("--output-shard-tmp-dir;sharded-output" "--sharded-output;output-shard-tmp-dir" ) SYNONYMOUS_ARGS=("--input;-I" "--output;-O" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-variant-index;-OVI" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--assembled-contigs-output-order;-sort" "--conf;-conf" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--reference;-R" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--aligner-index-image --input --kmers-to-ignore --output --add-output-vcf-command-line --create-output-bam-index --create-output-bam-splitting-index --create-output-variant-index --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --read-filter --read-index --read-validation-stringency --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --adapter-sequence --allowed-short-fragment-overhang --arguments_file --assembled-contigs-output-order --assembly-to-mapped-size-ratio-guess --bam-partition-size --breakpoint-evidence-dir --breakpoint-intervals --cleaner-max-copy-number --cleaner-max-intervals --cleaner-min-kmer-count --conf --cross-contigs-to-ignore --disable-sequence-dictionary-validation --exclusion-interval-padding --exclusion-intervals --external-evidence --external-evidence-uncertainty --external-evidence-weight --fastq-dir --gcs-max-retries --gcs-project-for-requester-pays --help --high-coverage-intervals --high-depth-coverage-factor --high-depth-coverage-peak-factor --include-mapping-location --interval-merging-rule --interval-only-assembly --intervals --kmer-intervals --kmer-max-dust-score --k-size --max-fastq-size --max-tracked-fragment-length --min-coherent-evidence-coverage-ratio --min-evidence-coverage-ratio --min-evidence-mapq --min-evidence-match-length --min-kmers-per-interval --num-reducers --output-shard-tmp-dir --program-name --qname-intervals-for-assembly --qname-intervals-mapped --read-metadata --reference --run-without-gaps-annotation --run-without-umap-s100-annotation --sharded-output --spark-master --sv-evidence-filter-model-file --sv-evidence-filter-threshold-probability --sv-evidence-filter-type --sv-genome-gaps-file --sv-genome-umap-s100-file --target-link-file --unfiltered-breakpoint-evidence-dir --version --write-gfas --expand-assembly-graph --pop-variant-bubbles --remove-shadowed-contigs --showHidden --z-dropoff ) ALL_ARGUMENT_VALUE_TYPES=("String" "List[String]" "String" "String" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "int" "int" "IntervalSetRule" "Boolean" "List[String]" "List[String]" "ValidationStringency" "String" "boolean" "boolean" "LogLevel" "String" "int" "List[File]" "SortOrder" "int" "long" "String" "String" "int" "int" "int" "List[String]" "String" "boolean" "int" "String" "String" "int" "int" "String" "int" "String" "boolean" "String" "int" "int" "boolean" "IntervalMergingRule" "boolean" "List[String]" "String" "int" "int" "int" "int" "double" "double" "int" "int" "int" "int" "String" "String" "String" "String" "String" "String" "boolean" "boolean" "boolean" "String" "String" "double" "SvEvidenceFilterType" "String" "String" "String" "String" "boolean" "boolean" "boolean" "boolean" "boolean" "boolean" "int" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "NotDuplicateReadFilter" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=() MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=() MAX_OCCURRENCES=() ALL_LEGAL_ARGUMENTS=() ALL_ARGUMENT_VALUE_TYPES=() # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "IlluminaBasecallsToFastq" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--BASECALLS_DIR --LANE --MULTIPLEX_PARAMS --OUTPUT_PREFIX --READ_STRUCTURE --RUN_BARCODE --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --APPLY_EAMSS_FILTER --arguments_file --BARCODES_DIR --COMPRESS_OUTPUTS --FIRST_TILE --FLOWCELL_BARCODE --FORCE_GC --help --IGNORE_UNEXPECTED_BARCODES --INCLUDE_NON_PF_READS --MACHINE_NAME --MAX_READS_IN_RAM_PER_TILE --MINIMUM_QUALITY --NUM_PROCESSORS --READ_NAME_FORMAT --TILE_LIMIT --version --showHidden --ADAPTERS_TO_CHECK ) MUTUALLY_EXCLUSIVE_ARGS=("--MULTIPLEX_PARAMS;OUTPUT_PREFIX" "--OUTPUT_PREFIX;MULTIPLEX_PARAMS" ) SYNONYMOUS_ARGS=("--BASECALLS_DIR;-B" "--LANE;-L" "--OUTPUT_PREFIX;-O" "--READ_STRUCTURE;-RS" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--BARCODES_DIR;-BCD" "--COMPRESS_OUTPUTS;-GZIP" "--help;-h" "--IGNORE_UNEXPECTED_BARCODES;-INGORE_UNEXPECTED" "--INCLUDE_NON_PF_READS;-NONPF" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--BASECALLS_DIR --LANE --MULTIPLEX_PARAMS --OUTPUT_PREFIX --READ_STRUCTURE --RUN_BARCODE --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --APPLY_EAMSS_FILTER --arguments_file --BARCODES_DIR --COMPRESS_OUTPUTS --FIRST_TILE --FLOWCELL_BARCODE --FORCE_GC --help --IGNORE_UNEXPECTED_BARCODES --INCLUDE_NON_PF_READS --MACHINE_NAME --MAX_READS_IN_RAM_PER_TILE --MINIMUM_QUALITY --NUM_PROCESSORS --READ_NAME_FORMAT --TILE_LIMIT --version --showHidden --ADAPTERS_TO_CHECK ) ALL_ARGUMENT_VALUE_TYPES=("File" "Integer" "File" "File" "String" "String" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "boolean" "List[File]" "File" "boolean" "Integer" "String" "Boolean" "boolean" "boolean" "boolean" "String" "int" "int" "Integer" "ReadNameFormat" "Integer" "boolean" "boolean" "List[IlluminaAdapterPair]" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "ReadPosition" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=() MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=() MAX_OCCURRENCES=() ALL_LEGAL_ARGUMENTS=() ALL_ARGUMENT_VALUE_TYPES=() # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "IndexFeatureFile" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--feature-file --gatk-config-file --QUIET --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --gcs-max-retries --gcs-project-for-requester-pays --help --output --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--feature-file;-F" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--gcs-max-retries;-gcs-retries" "--help;-h" "--output;-O" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--feature-file --gatk-config-file --QUIET --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --gcs-max-retries --gcs-project-for-requester-pays --help --output --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "String" "Boolean" "String" "boolean" "boolean" "LogLevel" "List[File]" "int" "String" "boolean" "File" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "AS_QualByDepth" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=() MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=() MAX_OCCURRENCES=() ALL_LEGAL_ARGUMENTS=() ALL_ARGUMENT_VALUE_TYPES=() # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "FixVcfHeader" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--INPUT --OUTPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --CHECK_FIRST_N_RECORDS --ENFORCE_SAME_SAMPLES --HEADER --help --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--INPUT;-I" "--OUTPUT;-O" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--CHECK_FIRST_N_RECORDS;-N" "--HEADER;-H" "--help;-h" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--INPUT --OUTPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --CHECK_FIRST_N_RECORDS --ENFORCE_SAME_SAMPLES --HEADER --help --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "File" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "List[File]" "int" "boolean" "File" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "PostprocessGermlineCNVCalls" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--calls-shard-path --contig-ploidy-calls --model-shard-path --output-genotyped-intervals --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --allosomal-contig --arguments_file --autosomal-ref-copy-number --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --output-genotyped-segments --reference --sample-index --sites-only-vcf-output --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--add-output-sam-program-record;-add-output-sam-program-record" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-bam-md5;-OBM" "--create-output-variant-index;-OVI" "--create-output-variant-md5;-OVM" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--input;-I" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--lenient;-LE" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--seconds-between-progress-updates;-seconds-between-progress-updates" "--sequence-dictionary;-sequence-dictionary" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--cloud-index-prefetch-buffer;-CIPB" "--cloud-prefetch-buffer;-CPB" "--disable-bam-index-caching;-DBIC" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--reference;-R" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--calls-shard-path --contig-ploidy-calls --model-shard-path --output-genotyped-intervals --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --allosomal-contig --arguments_file --autosomal-ref-copy-number --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --output-genotyped-segments --reference --sample-index --sites-only-vcf-output --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("List[File]" "File" "List[File]" "File" "boolean" "boolean" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "List[String]" "int" "int" "IntervalSetRule" "boolean" "Boolean" "List[String]" "List[String]" "ValidationStringency" "double" "String" "String" "boolean" "boolean" "LogLevel" "List[String]" "List[File]" "int" "int" "int" "boolean" "boolean" "int" "String" "boolean" "IntervalMergingRule" "List[String]" "File" "String" "int" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "StrandArtifact" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=() MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=() MAX_OCCURRENCES=() ALL_LEGAL_ARGUMENTS=() ALL_ARGUMENT_VALUE_TYPES=() # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "Coverage" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=() MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=() MAX_OCCURRENCES=() ALL_LEGAL_ARGUMENTS=() ALL_ARGUMENT_VALUE_TYPES=() # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "ReadNameReadFilter" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--read-name ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=(0 ) MAX_OCCURRENCES=(2147483647 ) ALL_LEGAL_ARGUMENTS=(--read-name ) ALL_ARGUMENT_VALUE_TYPES=("String" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "PathSeqFilterSpark" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--input --add-output-vcf-command-line --create-output-bam-index --create-output-bam-splitting-index --create-output-variant-index --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --read-filter --read-index --read-validation-stringency --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --bam-partition-size --conf --disable-sequence-dictionary-validation --dust-mask-quality --dust-t --dust-window --filter-bwa-image --filter-bwa-seed-length --filter-duplicates --filter-metrics --gcs-max-retries --gcs-project-for-requester-pays --help --host-kmer-thresh --host-min-identity --interval-merging-rule --intervals --is-host-aligned --kmer-file --max-adapter-mismatches --max-masked-bases --min-adapter-length --min-base-quality --min-clipped-read-length --num-reducers --output-shard-tmp-dir --paired-output --program-name --quality-threshold --reference --sharded-output --skip-quality-filters --spark-master --unpaired-output --version --filter-reads-per-partition --showHidden --skip-pre-bwa-repartition ) MUTUALLY_EXCLUSIVE_ARGS=("--output-shard-tmp-dir;sharded-output" "--sharded-output;output-shard-tmp-dir" ) SYNONYMOUS_ARGS=("--input;-I" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-variant-index;-OVI" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--conf;-conf" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--dust-mask-quality;-dust-mask-quality" "--dust-t;-dust-t" "--dust-window;-dust-window" "--filter-bwa-image;-FI" "--filter-bwa-seed-length;-filter-bwa-seed-length" "--filter-duplicates;-filter-duplicates" "--filter-metrics;-FM" "--gcs-max-retries;-gcs-retries" "--help;-h" "--host-kmer-thresh;-host-kmer-thresh" "--host-min-identity;-host-min-identity" "--interval-merging-rule;-imr" "--intervals;-L" "--is-host-aligned;-is-host-aligned" "--kmer-file;-K" "--max-adapter-mismatches;-max-adapter-mismatches" "--max-masked-bases;-max-masked-bases" "--min-adapter-length;-min-adapter-length" "--min-base-quality;-min-base-quality" "--min-clipped-read-length;-min-clipped-read-length" "--paired-output;-PO" "--quality-threshold;-quality-threshold" "--reference;-R" "--skip-quality-filters;-skip-quality-filters" "--unpaired-output;-UO" "--filter-reads-per-partition;-filter-reads-per-partition" "--showHidden;-showHidden" "--skip-pre-bwa-repartition;-skip-pre-bwa-repartition" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--input --add-output-vcf-command-line --create-output-bam-index --create-output-bam-splitting-index --create-output-variant-index --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --read-filter --read-index --read-validation-stringency --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --bam-partition-size --conf --disable-sequence-dictionary-validation --dust-mask-quality --dust-t --dust-window --filter-bwa-image --filter-bwa-seed-length --filter-duplicates --filter-metrics --gcs-max-retries --gcs-project-for-requester-pays --help --host-kmer-thresh --host-min-identity --interval-merging-rule --intervals --is-host-aligned --kmer-file --max-adapter-mismatches --max-masked-bases --min-adapter-length --min-base-quality --min-clipped-read-length --num-reducers --output-shard-tmp-dir --paired-output --program-name --quality-threshold --reference --sharded-output --skip-quality-filters --spark-master --unpaired-output --version --filter-reads-per-partition --showHidden --skip-pre-bwa-repartition ) ALL_ARGUMENT_VALUE_TYPES=("List[String]" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "int" "int" "IntervalSetRule" "Boolean" "List[String]" "List[String]" "ValidationStringency" "String" "boolean" "boolean" "LogLevel" "List[File]" "long" "List[String]" "boolean" "int" "double" "int" "String" "int" "boolean" "String" "int" "String" "boolean" "int" "int" "IntervalMergingRule" "List[String]" "boolean" "String" "int" "int" "int" "int" "int" "int" "String" "String" "String" "int" "String" "boolean" "boolean" "String" "String" "boolean" "int" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "BwaSpark" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--input --output --reference --add-output-vcf-command-line --create-output-bam-index --create-output-bam-splitting-index --create-output-variant-index --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --read-filter --read-index --read-validation-stringency --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --bam-partition-size --bwa-mem-index-image --conf --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --num-reducers --output-shard-tmp-dir --program-name --sharded-output --single-end-alignment --spark-master --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=("--output-shard-tmp-dir;sharded-output" "--sharded-output;output-shard-tmp-dir" ) SYNONYMOUS_ARGS=("--input;-I" "--output;-O" "--reference;-R" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-variant-index;-OVI" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--bwa-mem-index-image;-image" "--conf;-conf" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--single-end-alignment;-se" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--input --output --reference --add-output-vcf-command-line --create-output-bam-index --create-output-bam-splitting-index --create-output-variant-index --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --read-filter --read-index --read-validation-stringency --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --bam-partition-size --bwa-mem-index-image --conf --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --num-reducers --output-shard-tmp-dir --program-name --sharded-output --single-end-alignment --spark-master --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("List[String]" "String" "String" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "int" "int" "IntervalSetRule" "Boolean" "List[String]" "List[String]" "ValidationStringency" "String" "boolean" "boolean" "LogLevel" "List[File]" "long" "String" "List[String]" "int" "String" "boolean" "IntervalMergingRule" "List[String]" "int" "String" "String" "boolean" "boolean" "String" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "FilterSamReads" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--FILTER --INPUT --OUTPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --INTERVAL_LIST --JAVASCRIPT_FILE --READ_LIST_FILE --SORT_ORDER --TAG --TAG_VALUE --version --WRITE_READS_FILES --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--INPUT;-I" "--OUTPUT;-O" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--help;-h" "--INTERVAL_LIST;-IL" "--JAVASCRIPT_FILE;-JS" "--READ_LIST_FILE;-RLF" "--SORT_ORDER;-SO" "--TAG;-T" "--TAG_VALUE;-TV" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--FILTER --INPUT --OUTPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --INTERVAL_LIST --JAVASCRIPT_FILE --READ_LIST_FILE --SORT_ORDER --TAG --TAG_VALUE --version --WRITE_READS_FILES --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("Filter" "File" "File" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "List[File]" "boolean" "File" "File" "File" "SortOrder" "String" "List[String]" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "RevertSamSpark" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--input --output --output-map --add-output-vcf-command-line --create-output-bam-index --create-output-bam-splitting-index --create-output-variant-index --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --read-filter --read-index --read-validation-stringency --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --attributes-to-clear --bam-partition-size --conf --disable-sequence-dictionary-validation --dont-restore-original-qualities --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --keep-alignment-information --keep-first-duplicate --library-name --num-reducers --output-by-readgroup --output-by-readgroup-file-format --output-shard-tmp-dir --program-name --reference --remove-default-attributes-to-clear --remove-duplicate-information --sample-alias --sanitize --sharded-output --sort-order --spark-master --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=("--output;output-map" "--output-map;output" "--output-shard-tmp-dir;sharded-output" "--sharded-output;output-shard-tmp-dir" ) SYNONYMOUS_ARGS=("--input;-I" "--output;-O" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-variant-index;-OVI" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--conf;-conf" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--reference;-R" "--sample-alias;-ALIAS" "--sort-order;-SO" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--input --output --output-map --add-output-vcf-command-line --create-output-bam-index --create-output-bam-splitting-index --create-output-variant-index --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --read-filter --read-index --read-validation-stringency --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --attributes-to-clear --bam-partition-size --conf --disable-sequence-dictionary-validation --dont-restore-original-qualities --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --keep-alignment-information --keep-first-duplicate --library-name --num-reducers --output-by-readgroup --output-by-readgroup-file-format --output-shard-tmp-dir --program-name --reference --remove-default-attributes-to-clear --remove-duplicate-information --sample-alias --sanitize --sharded-output --sort-order --spark-master --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("List[String]" "String" "String" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "int" "int" "IntervalSetRule" "Boolean" "List[String]" "List[String]" "ValidationStringency" "String" "boolean" "boolean" "LogLevel" "List[File]" "Set[String]" "long" "List[String]" "boolean" "boolean" "int" "String" "boolean" "IntervalMergingRule" "List[String]" "boolean" "boolean" "String" "int" "boolean" "FileType" "String" "String" "String" "boolean" "boolean" "String" "boolean" "boolean" "SortOrder" "String" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "PositionBasedDownsampleSam" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--FRACTION --INPUT --OUTPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS --arguments_file --help --READ_NAME_REGEX --REMOVE_DUPLICATE_INFORMATION --STOP_AFTER --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--FRACTION;-F" "--INPUT;-I" "--OUTPUT;-O" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--help;-h" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--FRACTION --INPUT --OUTPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS --arguments_file --help --READ_NAME_REGEX --REMOVE_DUPLICATE_INFORMATION --STOP_AFTER --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("Double" "File" "File" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "boolean" "List[File]" "boolean" "String" "boolean" "Long" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "SeqIsStoredReadFilter" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=() MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=() MAX_OCCURRENCES=() ALL_LEGAL_ARGUMENTS=() ALL_ARGUMENT_VALUE_TYPES=() # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "CollectAlignmentSummaryMetrics" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--INPUT --OUTPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --ADAPTER_SEQUENCE --arguments_file --ASSUME_SORTED --EXPECTED_PAIR_ORIENTATIONS --help --IS_BISULFITE_SEQUENCED --MAX_INSERT_SIZE --METRIC_ACCUMULATION_LEVEL --REFERENCE_SEQUENCE --STOP_AFTER --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--INPUT;-I" "--OUTPUT;-O" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--ASSUME_SORTED;-AS" "--help;-h" "--IS_BISULFITE_SEQUENCED;-BS" "--METRIC_ACCUMULATION_LEVEL;-LEVEL" "--REFERENCE_SEQUENCE;-R" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--INPUT --OUTPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --ADAPTER_SEQUENCE --arguments_file --ASSUME_SORTED --EXPECTED_PAIR_ORIENTATIONS --help --IS_BISULFITE_SEQUENCED --MAX_INSERT_SIZE --METRIC_ACCUMULATION_LEVEL --REFERENCE_SEQUENCE --STOP_AFTER --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "File" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "List[String]" "List[File]" "boolean" "Set[PairOrientation]" "boolean" "boolean" "int" "Set[MetricAccumulationLevel]" "File" "long" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "CollectWgsMetrics" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--INPUT --OUTPUT --REFERENCE_SEQUENCE --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --ALLELE_FRACTION --arguments_file --COUNT_UNPAIRED --COVERAGE_CAP --help --INCLUDE_BQ_HISTOGRAM --INTERVALS --LOCUS_ACCUMULATION_CAP --MINIMUM_BASE_QUALITY --MINIMUM_MAPPING_QUALITY --READ_LENGTH --SAMPLE_SIZE --STOP_AFTER --THEORETICAL_SENSITIVITY_OUTPUT --USE_FAST_ALGORITHM --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--INPUT;-I" "--OUTPUT;-O" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--COVERAGE_CAP;-CAP" "--help;-h" "--MINIMUM_BASE_QUALITY;-Q" "--MINIMUM_MAPPING_QUALITY;-MQ" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--INPUT --OUTPUT --REFERENCE_SEQUENCE --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --ALLELE_FRACTION --arguments_file --COUNT_UNPAIRED --COVERAGE_CAP --help --INCLUDE_BQ_HISTOGRAM --INTERVALS --LOCUS_ACCUMULATION_CAP --MINIMUM_BASE_QUALITY --MINIMUM_MAPPING_QUALITY --READ_LENGTH --SAMPLE_SIZE --STOP_AFTER --THEORETICAL_SENSITIVITY_OUTPUT --USE_FAST_ALGORITHM --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "File" "File" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "List[Double]" "List[File]" "boolean" "int" "boolean" "boolean" "File" "int" "int" "int" "int" "int" "long" "File" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "BamToBfq" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--ANALYSIS_DIR --FLOWCELL_BARCODE --INPUT --OUTPUT_FILE_PREFIX --PAIRED_RUN --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --BASES_TO_WRITE --CLIP_ADAPTERS --help --INCLUDE_NON_PF_READS --LANE --READ_CHUNK_SIZE --READ_NAME_PREFIX --READS_TO_ALIGN --RUN_BARCODE --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=("--FLOWCELL_BARCODE;OUTPUT_FILE_PREFIX" "--OUTPUT_FILE_PREFIX;FLOWCELL_BARCODE,LANE" "--LANE;OUTPUT_FILE_PREFIX" "--RUN_BARCODE;READ_NAME_PREFIX" ) SYNONYMOUS_ARGS=("--FLOWCELL_BARCODE;-F" "--INPUT;-I" "--PAIRED_RUN;-PE" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--help;-h" "--INCLUDE_NON_PF_READS;-NONPF" "--LANE;-L" "--READ_CHUNK_SIZE;-CHUNK" "--READS_TO_ALIGN;-NUM" "--RUN_BARCODE;-RB" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--ANALYSIS_DIR --FLOWCELL_BARCODE --INPUT --OUTPUT_FILE_PREFIX --PAIRED_RUN --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --BASES_TO_WRITE --CLIP_ADAPTERS --help --INCLUDE_NON_PF_READS --LANE --READ_CHUNK_SIZE --READ_NAME_PREFIX --READS_TO_ALIGN --RUN_BARCODE --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "String" "File" "String" "Boolean" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "List[File]" "Integer" "boolean" "boolean" "Boolean" "Integer" "Integer" "String" "Integer" "String" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "CheckIlluminaDirectory" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--BASECALLS_DIR --LANES --READ_STRUCTURE --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --DATA_TYPES --FAKE_FILES --help --TILE_NUMBERS --version --showHidden --LINK_LOCS ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--BASECALLS_DIR;-B" "--LANES;-L" "--READ_STRUCTURE;-RS" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--DATA_TYPES;-DT" "--FAKE_FILES;-F" "--help;-h" "--TILE_NUMBERS;-T" "--showHidden;-showHidden" "--LINK_LOCS;-X" ) MIN_OCCURRENCES=(0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--BASECALLS_DIR --LANES --READ_STRUCTURE --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --DATA_TYPES --FAKE_FILES --help --TILE_NUMBERS --version --showHidden --LINK_LOCS ) ALL_ARGUMENT_VALUE_TYPES=("File" "List[Integer]" "String" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "List[File]" "Set[IlluminaDataType]" "Boolean" "boolean" "List[Integer]" "boolean" "boolean" "Boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "NotSecondaryAlignmentReadFilter" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=() MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=() MAX_OCCURRENCES=() ALL_LEGAL_ARGUMENTS=() ALL_ARGUMENT_VALUE_TYPES=() # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "CigarContainsNoNOperator" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=() MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=() MAX_OCCURRENCES=() ALL_LEGAL_ARGUMENTS=() ALL_ARGUMENT_VALUE_TYPES=() # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "CheckFingerprint" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--DETAIL_OUTPUT --GENOTYPES --HAPLOTYPE_MAP --INPUT --OUTPUT --SUMMARY_OUTPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --EXPECTED_SAMPLE_ALIAS --GENOTYPE_LOD_THRESHOLD --help --IGNORE_READ_GROUPS --OBSERVED_SAMPLE_ALIAS --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=("--DETAIL_OUTPUT;OUTPUT" "--OUTPUT;SUMMARY_OUTPUT,DETAIL_OUTPUT,S,D" "--SUMMARY_OUTPUT;OUTPUT" ) SYNONYMOUS_ARGS=("--DETAIL_OUTPUT;-D" "--GENOTYPES;-G" "--HAPLOTYPE_MAP;-H" "--INPUT;-I" "--OUTPUT;-O" "--SUMMARY_OUTPUT;-S" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--EXPECTED_SAMPLE_ALIAS;-SAMPLE_ALIAS" "--GENOTYPE_LOD_THRESHOLD;-LOD" "--help;-h" "--IGNORE_READ_GROUPS;-IGNORE_RG" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--DETAIL_OUTPUT --GENOTYPES --HAPLOTYPE_MAP --INPUT --OUTPUT --SUMMARY_OUTPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --EXPECTED_SAMPLE_ALIAS --GENOTYPE_LOD_THRESHOLD --help --IGNORE_READ_GROUPS --OBSERVED_SAMPLE_ALIAS --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "String" "File" "String" "String" "File" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "List[File]" "String" "double" "boolean" "boolean" "String" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "AddOrReplaceReadGroups" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--INPUT --OUTPUT --RGLB --RGPL --RGPU --RGSM --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --RGCN --RGDS --RGDT --RGFO --RGID --RGKS --RGPG --RGPI --RGPM --SORT_ORDER --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--INPUT;-I" "--OUTPUT;-O" "--RGLB;-LB" "--RGPL;-PL" "--RGPU;-PU" "--RGSM;-SM" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--help;-h" "--RGCN;-CN" "--RGDS;-DS" "--RGDT;-DT" "--RGFO;-FO" "--RGID;-ID" "--RGKS;-KS" "--RGPG;-PG" "--RGPI;-PI" "--RGPM;-PM" "--SORT_ORDER;-SO" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--INPUT --OUTPUT --RGLB --RGPL --RGPU --RGSM --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --RGCN --RGDS --RGDT --RGFO --RGID --RGKS --RGPG --RGPI --RGPM --SORT_ORDER --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("String" "File" "String" "String" "String" "String" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "List[File]" "boolean" "String" "String" "Iso8601Date" "String" "String" "String" "String" "Integer" "String" "SortOrder" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "VcfToIntervalList" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--INPUT --OUTPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --INCLUDE_FILTERED --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--INPUT;-I" "--OUTPUT;-O" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--help;-h" "--INCLUDE_FILTERED;-IF" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--INPUT --OUTPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --INCLUDE_FILTERED --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "File" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "List[File]" "boolean" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "CalculateMixingFractions" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--output --variant --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --reference --sites-only-vcf-output --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--output;-O" "--variant;-V" "--add-output-sam-program-record;-add-output-sam-program-record" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-bam-md5;-OBM" "--create-output-variant-index;-OVI" "--create-output-variant-md5;-OVM" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--input;-I" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--lenient;-LE" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--seconds-between-progress-updates;-seconds-between-progress-updates" "--sequence-dictionary;-sequence-dictionary" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--cloud-index-prefetch-buffer;-CIPB" "--cloud-prefetch-buffer;-CPB" "--disable-bam-index-caching;-DBIC" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--reference;-R" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--output --variant --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --reference --sites-only-vcf-output --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "String" "boolean" "boolean" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "List[String]" "int" "int" "IntervalSetRule" "boolean" "Boolean" "List[String]" "List[String]" "ValidationStringency" "double" "String" "String" "boolean" "boolean" "LogLevel" "List[File]" "int" "int" "boolean" "boolean" "int" "String" "boolean" "IntervalMergingRule" "List[String]" "String" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "Pileup" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--input --output --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --maxDepthPerSample --metadata --output-insert-length --reference --show-verbose --sites-only-vcf-output --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--input;-I" "--output;-O" "--add-output-sam-program-record;-add-output-sam-program-record" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-bam-md5;-OBM" "--create-output-variant-index;-OVI" "--create-output-variant-md5;-OVM" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--lenient;-LE" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--seconds-between-progress-updates;-seconds-between-progress-updates" "--sequence-dictionary;-sequence-dictionary" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--cloud-index-prefetch-buffer;-CIPB" "--cloud-prefetch-buffer;-CPB" "--disable-bam-index-caching;-DBIC" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--maxDepthPerSample;-maxDepthPerSample" "--metadata;-metadata" "--output-insert-length;-output-insert-length" "--reference;-R" "--show-verbose;-verbose" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--input --output --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --maxDepthPerSample --metadata --output-insert-length --reference --show-verbose --sites-only-vcf-output --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("List[String]" "File" "boolean" "boolean" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "int" "int" "IntervalSetRule" "boolean" "Boolean" "List[String]" "List[String]" "ValidationStringency" "double" "String" "String" "boolean" "boolean" "LogLevel" "List[File]" "int" "int" "boolean" "boolean" "int" "String" "boolean" "IntervalMergingRule" "List[String]" "int" "List[FeatureInput[Feature]]" "boolean" "String" "boolean" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "SplitReads" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--input --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --output --reference --sites-only-vcf-output --split-library-name --split-read-group --split-sample --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--input;-I" "--add-output-sam-program-record;-add-output-sam-program-record" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-bam-md5;-OBM" "--create-output-variant-index;-OVI" "--create-output-variant-md5;-OVM" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--lenient;-LE" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--seconds-between-progress-updates;-seconds-between-progress-updates" "--sequence-dictionary;-sequence-dictionary" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--cloud-index-prefetch-buffer;-CIPB" "--cloud-prefetch-buffer;-CPB" "--disable-bam-index-caching;-DBIC" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--output;-O" "--reference;-R" "--split-library-name;-LB" "--split-read-group;-RG" "--split-sample;-SM" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--input --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --output --reference --sites-only-vcf-output --split-library-name --split-read-group --split-sample --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("List[String]" "boolean" "boolean" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "int" "int" "IntervalSetRule" "boolean" "Boolean" "List[String]" "List[String]" "ValidationStringency" "double" "String" "String" "boolean" "boolean" "LogLevel" "List[File]" "int" "int" "boolean" "boolean" "int" "String" "boolean" "IntervalMergingRule" "List[String]" "File" "String" "boolean" "boolean" "boolean" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "ApplyVQSR" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--output --recal-file --variant --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --exclude-filtered --gcs-max-retries --gcs-project-for-requester-pays --help --ignore-all-filters --ignore-filter --interval-merging-rule --intervals --mode --reference --sites-only-vcf-output --tranches-file --truth-sensitivity-filter-level --use-allele-specific-annotations --version --lod-score-cutoff --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--output;-O" "--variant;-V" "--add-output-sam-program-record;-add-output-sam-program-record" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-bam-md5;-OBM" "--create-output-variant-index;-OVI" "--create-output-variant-md5;-OVM" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--input;-I" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--lenient;-LE" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--seconds-between-progress-updates;-seconds-between-progress-updates" "--sequence-dictionary;-sequence-dictionary" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--cloud-index-prefetch-buffer;-CIPB" "--cloud-prefetch-buffer;-CPB" "--disable-bam-index-caching;-DBIC" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--mode;-mode" "--reference;-R" "--truth-sensitivity-filter-level;-ts-filter-level" "--use-allele-specific-annotations;-AS" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--output --recal-file --variant --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --exclude-filtered --gcs-max-retries --gcs-project-for-requester-pays --help --ignore-all-filters --ignore-filter --interval-merging-rule --intervals --mode --reference --sites-only-vcf-output --tranches-file --truth-sensitivity-filter-level --use-allele-specific-annotations --version --lod-score-cutoff --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("String" "FeatureInput[VariantContext]" "List[String]" "boolean" "boolean" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "List[String]" "int" "int" "IntervalSetRule" "boolean" "Boolean" "List[String]" "List[String]" "ValidationStringency" "double" "String" "String" "boolean" "boolean" "LogLevel" "List[File]" "int" "int" "boolean" "boolean" "boolean" "int" "String" "boolean" "boolean" "List[String]" "IntervalMergingRule" "List[String]" "Mode" "String" "boolean" "File" "Double" "boolean" "boolean" "Double" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "PlotDenoisedCopyRatios" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--denoised-copy-ratios --output --output-prefix --sequence-dictionary --standardized-copy-ratios --gatk-config-file --QUIET --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --gcs-max-retries --gcs-project-for-requester-pays --help --minimum-contig-length --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--output;-O" "--sequence-dictionary;-sequence-dictionary" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--gcs-max-retries;-gcs-retries" "--help;-h" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--denoised-copy-ratios --output --output-prefix --sequence-dictionary --standardized-copy-ratios --gatk-config-file --QUIET --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --gcs-max-retries --gcs-project-for-requester-pays --help --minimum-contig-length --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "String" "String" "File" "File" "String" "Boolean" "String" "boolean" "boolean" "LogLevel" "List[File]" "int" "String" "boolean" "int" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "ReorderSam" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--INPUT --OUTPUT --REFERENCE --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --ALLOW_CONTIG_LENGTH_DISCORDANCE --ALLOW_INCOMPLETE_DICT_CONCORDANCE --arguments_file --help --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--INPUT;-I" "--OUTPUT;-O" "--REFERENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--ALLOW_CONTIG_LENGTH_DISCORDANCE;-U" "--ALLOW_INCOMPLETE_DICT_CONCORDANCE;-S" "--help;-h" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--INPUT --OUTPUT --REFERENCE --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --ALLOW_CONTIG_LENGTH_DISCORDANCE --ALLOW_INCOMPLETE_DICT_CONCORDANCE --arguments_file --help --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "File" "File" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "boolean" "boolean" "List[File]" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "PathSeqScoreSpark" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--scores-output --taxonomy-file --add-output-vcf-command-line --create-output-bam-index --create-output-bam-splitting-index --create-output-variant-index --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --read-filter --read-index --read-validation-stringency --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --bam-partition-size --conf --disable-sequence-dictionary-validation --divide-by-genome-length --gcs-max-retries --gcs-project-for-requester-pays --help --identity-margin --interval-merging-rule --intervals --min-score-identity --not-normalized-by-kingdom --num-reducers --output --output-shard-tmp-dir --paired-input --program-name --reference --score-metrics --score-warnings --sharded-output --spark-master --unpaired-input --version --score-reads-per-partition-estimate --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=("--output-shard-tmp-dir;sharded-output" "--sharded-output;output-shard-tmp-dir" ) SYNONYMOUS_ARGS=("--scores-output;-SO" "--taxonomy-file;-T" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-variant-index;-OVI" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--input;-I" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--conf;-conf" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--divide-by-genome-length;-divide-by-genome-length" "--gcs-max-retries;-gcs-retries" "--help;-h" "--identity-margin;-identity-margin" "--interval-merging-rule;-imr" "--intervals;-L" "--min-score-identity;-min-score-identity" "--not-normalized-by-kingdom;-not-normalized-by-kingdom" "--output;-O" "--paired-input;-PI" "--reference;-R" "--score-metrics;-SM" "--score-warnings;-SW" "--unpaired-input;-UI" "--score-reads-per-partition-estimate;-score-reads-per-partition-estimate" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--scores-output --taxonomy-file --add-output-vcf-command-line --create-output-bam-index --create-output-bam-splitting-index --create-output-variant-index --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --read-filter --read-index --read-validation-stringency --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --bam-partition-size --conf --disable-sequence-dictionary-validation --divide-by-genome-length --gcs-max-retries --gcs-project-for-requester-pays --help --identity-margin --interval-merging-rule --intervals --min-score-identity --not-normalized-by-kingdom --num-reducers --output --output-shard-tmp-dir --paired-input --program-name --reference --score-metrics --score-warnings --sharded-output --spark-master --unpaired-input --version --score-reads-per-partition-estimate --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("String" "String" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "List[String]" "int" "int" "IntervalSetRule" "Boolean" "List[String]" "List[String]" "ValidationStringency" "String" "boolean" "boolean" "LogLevel" "List[File]" "long" "List[String]" "boolean" "boolean" "int" "String" "boolean" "double" "IntervalMergingRule" "List[String]" "double" "boolean" "int" "String" "String" "String" "String" "String" "String" "String" "boolean" "String" "String" "boolean" "int" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "ProperlyPairedReadFilter" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=() MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=() MAX_OCCURRENCES=() ALL_LEGAL_ARGUMENTS=() ALL_ARGUMENT_VALUE_TYPES=() # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "ConvertSequencingArtifactToOxoG" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--INPUT_BASE --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --OUTPUT_BASE --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--INPUT_BASE;-I" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--help;-h" "--OUTPUT_BASE;-O" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--INPUT_BASE --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --OUTPUT_BASE --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "List[File]" "boolean" "File" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "FixMateInformation" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--INPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --ADD_MATE_CIGAR --arguments_file --ASSUME_SORTED --help --IGNORE_MISSING_MATES --OUTPUT --SORT_ORDER --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--INPUT;-I" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--ADD_MATE_CIGAR;-MC" "--ASSUME_SORTED;-AS" "--help;-h" "--OUTPUT;-O" "--SORT_ORDER;-SO" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--INPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --ADD_MATE_CIGAR --arguments_file --ASSUME_SORTED --help --IGNORE_MISSING_MATES --OUTPUT --SORT_ORDER --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("List[File]" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "Boolean" "List[File]" "boolean" "boolean" "Boolean" "File" "SortOrder" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "DenoiseReadCounts" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--denoised-copy-ratios --input --standardized-copy-ratios --gatk-config-file --QUIET --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --annotated-intervals --arguments_file --count-panel-of-normals --gcs-max-retries --gcs-project-for-requester-pays --help --number-of-eigensamples --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--input;-I" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--gcs-max-retries;-gcs-retries" "--help;-h" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--denoised-copy-ratios --input --standardized-copy-ratios --gatk-config-file --QUIET --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --annotated-intervals --arguments_file --count-panel-of-normals --gcs-max-retries --gcs-project-for-requester-pays --help --number-of-eigensamples --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "File" "File" "String" "Boolean" "String" "boolean" "boolean" "LogLevel" "File" "List[File]" "File" "int" "String" "boolean" "Integer" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "GenomicsDBImport" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--genomicsdb-workspace-path --intervals --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --batch-size --cloud-index-prefetch-buffer --cloud-prefetch-buffer --consolidate --disable-bam-index-caching --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --genomicsdb-segment-size --genomicsdb-vcf-buffer-size --help --interval-merging-rule --merge-input-intervals --overwrite-existing-genomicsdb-workspace --reference --sites-only-vcf-output --validate-sample-name-map --variant --version --max-num-intervals-to-import-in-parallel --reader-threads --sample-name-map --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=("--variant;sample-name-map" "--sample-name-map;variant" ) SYNONYMOUS_ARGS=("--intervals;-L" "--add-output-sam-program-record;-add-output-sam-program-record" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-bam-md5;-OBM" "--create-output-variant-index;-OVI" "--create-output-variant-md5;-OVM" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--input;-I" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--lenient;-LE" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--seconds-between-progress-updates;-seconds-between-progress-updates" "--sequence-dictionary;-sequence-dictionary" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--cloud-index-prefetch-buffer;-CIPB" "--cloud-prefetch-buffer;-CPB" "--consolidate;-consolidate" "--disable-bam-index-caching;-DBIC" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--gcs-max-retries;-gcs-retries" "--genomicsdb-vcf-buffer-size;-genomicsdb-vcf-buffer-size" "--help;-h" "--interval-merging-rule;-imr" "--merge-input-intervals;-merge-input-intervals" "--reference;-R" "--validate-sample-name-map;-validate-sample-name-map" "--variant;-V" "--max-num-intervals-to-import-in-parallel;-max-num-intervals-to-import-in-parallel" "--reader-threads;-reader-threads" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--genomicsdb-workspace-path --intervals --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --batch-size --cloud-index-prefetch-buffer --cloud-prefetch-buffer --consolidate --disable-bam-index-caching --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --genomicsdb-segment-size --genomicsdb-vcf-buffer-size --help --interval-merging-rule --merge-input-intervals --overwrite-existing-genomicsdb-workspace --reference --sites-only-vcf-output --validate-sample-name-map --variant --version --max-num-intervals-to-import-in-parallel --reader-threads --sample-name-map --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("String" "List[String]" "boolean" "boolean" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "List[String]" "int" "int" "IntervalSetRule" "boolean" "Boolean" "List[String]" "List[String]" "ValidationStringency" "double" "String" "String" "boolean" "boolean" "LogLevel" "List[File]" "int" "int" "int" "Boolean" "boolean" "boolean" "int" "String" "long" "long" "boolean" "IntervalMergingRule" "boolean" "Boolean" "String" "boolean" "Boolean" "List[String]" "boolean" "int" "int" "String" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "FuncotatorDataSourceDownloader" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--gatk-config-file --QUIET --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --extract-after-download --gcs-max-retries --gcs-project-for-requester-pays --germline --help --output --overwrite-output-file --somatic --validate-integrity --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=("--germline;somatic,testing-override-path-for-datasources-sha256,testing-override-path-for-datasources" "--somatic;germline,testing-override-path-for-datasources-sha256,testing-override-path-for-datasources" ) SYNONYMOUS_ARGS=("--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--extract-after-download;-extract-after-download" "--gcs-max-retries;-gcs-retries" "--germline;-germline" "--help;-h" "--output;-O" "--overwrite-output-file;-overwrite-output-file" "--somatic;-somatic" "--validate-integrity;-validate-integrity" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--gatk-config-file --QUIET --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --extract-after-download --gcs-max-retries --gcs-project-for-requester-pays --germline --help --output --overwrite-output-file --somatic --validate-integrity --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("String" "Boolean" "String" "boolean" "boolean" "LogLevel" "List[File]" "boolean" "int" "String" "boolean" "boolean" "File" "boolean" "boolean" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "CheckPileup" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--input --pileup --reference --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --continue-after-error --disable-bam-index-caching --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --ignore-overlaps --interval-merging-rule --intervals --maxDepthPerSample --output --sites-only-vcf-output --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--input;-I" "--reference;-R" "--add-output-sam-program-record;-add-output-sam-program-record" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-bam-md5;-OBM" "--create-output-variant-index;-OVI" "--create-output-variant-md5;-OVM" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--lenient;-LE" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--seconds-between-progress-updates;-seconds-between-progress-updates" "--sequence-dictionary;-sequence-dictionary" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--cloud-index-prefetch-buffer;-CIPB" "--cloud-prefetch-buffer;-CPB" "--disable-bam-index-caching;-DBIC" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--maxDepthPerSample;-maxDepthPerSample" "--output;-O" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--input --pileup --reference --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --continue-after-error --disable-bam-index-caching --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --ignore-overlaps --interval-merging-rule --intervals --maxDepthPerSample --output --sites-only-vcf-output --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("List[String]" "FeatureInput[SAMPileupFeature]" "String" "boolean" "boolean" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "int" "int" "IntervalSetRule" "boolean" "Boolean" "List[String]" "List[String]" "ValidationStringency" "double" "String" "String" "boolean" "boolean" "LogLevel" "List[File]" "int" "int" "boolean" "boolean" "boolean" "int" "String" "boolean" "boolean" "IntervalMergingRule" "List[String]" "int" "File" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "UmiAwareMarkDuplicatesWithMateCigar" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--INPUT --METRICS_FILE --OUTPUT --UMI_METRICS_FILE --ADD_PG_TAG_TO_READS --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --ALLOW_MISSING_UMIS --arguments_file --ASSUME_SORT_ORDER --BARCODE_TAG --CLEAR_DT --COMMENT --DUPLEX_UMI --DUPLICATE_SCORING_STRATEGY --help --MAX_EDIT_DISTANCE_TO_JOIN --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP --MAX_OPTICAL_DUPLICATE_SET_SIZE --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP --MOLECULAR_IDENTIFIER_TAG --OPTICAL_DUPLICATE_PIXEL_DISTANCE --PROGRAM_GROUP_COMMAND_LINE --PROGRAM_GROUP_NAME --PROGRAM_GROUP_VERSION --PROGRAM_RECORD_ID --READ_NAME_REGEX --READ_ONE_BARCODE_TAG --READ_TWO_BARCODE_TAG --REMOVE_DUPLICATES --REMOVE_SEQUENCING_DUPLICATES --SORTING_COLLECTION_SIZE_RATIO --TAG_DUPLICATE_SET_MEMBERS --TAGGING_POLICY --UMI_TAG_NAME --version --showHidden --ASSUME_SORTED ) MUTUALLY_EXCLUSIVE_ARGS=("--ASSUME_SORT_ORDER;ASSUME_SORTED" "--ASSUME_SORTED;ASSUME_SORT_ORDER,ASO" ) SYNONYMOUS_ARGS=("--INPUT;-I" "--METRICS_FILE;-M" "--OUTPUT;-O" "--UMI_METRICS_FILE;-UMI_METRICS" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--ASSUME_SORT_ORDER;-ASO" "--COMMENT;-CO" "--DUPLICATE_SCORING_STRATEGY;-DS" "--help;-h" "--MAX_EDIT_DISTANCE_TO_JOIN;-MAX_EDIT_DISTANCE_TO_JOIN" "--MAX_FILE_HANDLES_FOR_READ_ENDS_MAP;-MAX_FILE_HANDLES" "--MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP;-MAX_SEQS" "--PROGRAM_GROUP_COMMAND_LINE;-PG_COMMAND" "--PROGRAM_GROUP_NAME;-PG_NAME" "--PROGRAM_GROUP_VERSION;-PG_VERSION" "--PROGRAM_RECORD_ID;-PG" "--UMI_TAG_NAME;-UMI_TAG_NAME" "--showHidden;-showHidden" "--ASSUME_SORTED;-AS" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--INPUT --METRICS_FILE --OUTPUT --UMI_METRICS_FILE --ADD_PG_TAG_TO_READS --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --ALLOW_MISSING_UMIS --arguments_file --ASSUME_SORT_ORDER --BARCODE_TAG --CLEAR_DT --COMMENT --DUPLEX_UMI --DUPLICATE_SCORING_STRATEGY --help --MAX_EDIT_DISTANCE_TO_JOIN --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP --MAX_OPTICAL_DUPLICATE_SET_SIZE --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP --MOLECULAR_IDENTIFIER_TAG --OPTICAL_DUPLICATE_PIXEL_DISTANCE --PROGRAM_GROUP_COMMAND_LINE --PROGRAM_GROUP_NAME --PROGRAM_GROUP_VERSION --PROGRAM_RECORD_ID --READ_NAME_REGEX --READ_ONE_BARCODE_TAG --READ_TWO_BARCODE_TAG --REMOVE_DUPLICATES --REMOVE_SEQUENCING_DUPLICATES --SORTING_COLLECTION_SIZE_RATIO --TAG_DUPLICATE_SET_MEMBERS --TAGGING_POLICY --UMI_TAG_NAME --version --showHidden --ASSUME_SORTED ) ALL_ARGUMENT_VALUE_TYPES=("List[String]" "File" "File" "File" "boolean" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "boolean" "List[File]" "SortOrder" "String" "boolean" "List[String]" "boolean" "ScoringStrategy" "boolean" "int" "int" "long" "int" "String" "int" "String" "String" "String" "String" "String" "String" "String" "boolean" "boolean" "double" "boolean" "DuplicateTaggingPolicy" "String" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "ClipReads" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--input --output --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --clip-representation --clip-sequence --clip-sequences-file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --cycles-to-trim --disable-bam-index-caching --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --output-statistics --q-trimming-threshold --read --reference --sites-only-vcf-output --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--input;-I" "--output;-O" "--add-output-sam-program-record;-add-output-sam-program-record" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-bam-md5;-OBM" "--create-output-variant-index;-OVI" "--create-output-variant-md5;-OVM" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--lenient;-LE" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--seconds-between-progress-updates;-seconds-between-progress-updates" "--sequence-dictionary;-sequence-dictionary" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--clip-representation;-CR" "--clip-sequence;-X" "--clip-sequences-file;-XF" "--cloud-index-prefetch-buffer;-CIPB" "--cloud-prefetch-buffer;-CPB" "--cycles-to-trim;-CT" "--disable-bam-index-caching;-DBIC" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--output-statistics;-os" "--q-trimming-threshold;-QT" "--read;-read" "--reference;-R" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--input --output --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --clip-representation --clip-sequence --clip-sequences-file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --cycles-to-trim --disable-bam-index-caching --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --output-statistics --q-trimming-threshold --read --reference --sites-only-vcf-output --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("List[String]" "String" "boolean" "boolean" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "int" "int" "IntervalSetRule" "boolean" "Boolean" "List[String]" "List[String]" "ValidationStringency" "double" "String" "String" "boolean" "boolean" "LogLevel" "List[File]" "ClippingRepresentation" "List[String]" "String" "int" "int" "String" "boolean" "boolean" "int" "String" "boolean" "IntervalMergingRule" "List[String]" "File" "int" "String" "String" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "ReadGroupBlackListReadFilter" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--read-group-black-list ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=(0 ) MAX_OCCURRENCES=(2147483647 ) ALL_LEGAL_ARGUMENTS=(--read-group-black-list ) ALL_ARGUMENT_VALUE_TYPES=("List[String]" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "GetPileupSummaries" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--input --intervals --output --variant --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --maxDepthPerSample --maximum-population-allele-frequency --minimum-population-allele-frequency --min-mapping-quality --reference --sites-only-vcf-output --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--input;-I" "--intervals;-L" "--output;-O" "--variant;-V" "--add-output-sam-program-record;-add-output-sam-program-record" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-bam-md5;-OBM" "--create-output-variant-index;-OVI" "--create-output-variant-md5;-OVM" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--lenient;-LE" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--seconds-between-progress-updates;-seconds-between-progress-updates" "--sequence-dictionary;-sequence-dictionary" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--cloud-index-prefetch-buffer;-CIPB" "--cloud-prefetch-buffer;-CPB" "--disable-bam-index-caching;-DBIC" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--maxDepthPerSample;-maxDepthPerSample" "--maximum-population-allele-frequency;-max-af" "--minimum-population-allele-frequency;-min-af" "--min-mapping-quality;-mmq" "--reference;-R" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--input --intervals --output --variant --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --maxDepthPerSample --maximum-population-allele-frequency --minimum-population-allele-frequency --min-mapping-quality --reference --sites-only-vcf-output --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("List[String]" "List[String]" "File" "FeatureInput[VariantContext]" "boolean" "boolean" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "int" "int" "IntervalSetRule" "boolean" "Boolean" "List[String]" "List[String]" "ValidationStringency" "double" "String" "String" "boolean" "boolean" "LogLevel" "List[File]" "int" "int" "boolean" "boolean" "int" "String" "boolean" "IntervalMergingRule" "int" "double" "double" "int" "String" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "BuildBamIndex" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--INPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --OUTPUT --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--INPUT;-I" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--help;-h" "--OUTPUT;-O" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--INPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --OUTPUT --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("String" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "List[File]" "boolean" "File" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "AlignmentAgreesWithHeaderReadFilter" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=() MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=() MAX_OCCURRENCES=() ALL_LEGAL_ARGUMENTS=() ALL_ARGUMENT_VALUE_TYPES=() # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "NotSupplementaryAlignmentReadFilter" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=() MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=() MAX_OCCURRENCES=() ALL_LEGAL_ARGUMENTS=() ALL_ARGUMENT_VALUE_TYPES=() # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "ExtractOriginalAlignmentRecordsByNameSpark" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--input --output --read-name-file --add-output-vcf-command-line --create-output-bam-index --create-output-bam-splitting-index --create-output-variant-index --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --read-filter --read-index --read-validation-stringency --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --bam-partition-size --conf --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --invert-match --num-reducers --output-shard-tmp-dir --program-name --reference --sharded-output --spark-master --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=("--output-shard-tmp-dir;sharded-output" "--sharded-output;output-shard-tmp-dir" ) SYNONYMOUS_ARGS=("--input;-I" "--output;-O" "--read-name-file;-f" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-variant-index;-OVI" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--conf;-conf" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--invert-match;-v" "--reference;-R" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--input --output --read-name-file --add-output-vcf-command-line --create-output-bam-index --create-output-bam-splitting-index --create-output-variant-index --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --read-filter --read-index --read-validation-stringency --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --bam-partition-size --conf --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --invert-match --num-reducers --output-shard-tmp-dir --program-name --reference --sharded-output --spark-master --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("List[String]" "String" "String" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "int" "int" "IntervalSetRule" "Boolean" "List[String]" "List[String]" "ValidationStringency" "String" "boolean" "boolean" "LogLevel" "List[File]" "long" "List[String]" "boolean" "int" "String" "boolean" "IntervalMergingRule" "List[String]" "Boolean" "int" "String" "String" "String" "boolean" "String" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "AS_RMSMappingQuality" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=() MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=() MAX_OCCURRENCES=() ALL_LEGAL_ARGUMENTS=() ALL_ARGUMENT_VALUE_TYPES=() # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "BQSRPipelineSpark" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--input --known-sites --output --reference --add-output-vcf-command-line --create-output-bam-index --create-output-bam-splitting-index --create-output-variant-index --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --read-filter --read-index --read-validation-stringency --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --bam-partition-size --binary-tag-name --bqsr-baq-gap-open-penalty --conf --default-base-qualities --deletions-default-quality --disable-sequence-dictionary-validation --emit-original-quals --gcs-max-retries --gcs-project-for-requester-pays --global-qscore-prior --help --indels-context-size --insertions-default-quality --interval-merging-rule --intervals --low-quality-tail --maximum-cycle-value --mismatches-context-size --mismatches-default-quality --num-reducers --output-shard-tmp-dir --preserve-qscores-less-than --program-name --quantize-quals --quantizing-levels --sharded-output --spark-master --use-original-qualities --version --round-down-quantized --showHidden --static-quantized-quals ) MUTUALLY_EXCLUSIVE_ARGS=("--output-shard-tmp-dir;sharded-output" "--quantize-quals;static-quantized-quals,round-down-quantized" "--sharded-output;output-shard-tmp-dir" "--round-down-quantized;quantize-quals" "--static-quantized-quals;quantize-quals" ) SYNONYMOUS_ARGS=("--input;-I" "--output;-O" "--reference;-R" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-variant-index;-OVI" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--conf;-conf" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--gcs-max-retries;-gcs-retries" "--help;-h" "--indels-context-size;-ics" "--interval-merging-rule;-imr" "--intervals;-L" "--maximum-cycle-value;-max-cycle" "--mismatches-context-size;-mcs" "--use-original-qualities;-OQ" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--input --known-sites --output --reference --add-output-vcf-command-line --create-output-bam-index --create-output-bam-splitting-index --create-output-variant-index --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --read-filter --read-index --read-validation-stringency --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --bam-partition-size --binary-tag-name --bqsr-baq-gap-open-penalty --conf --default-base-qualities --deletions-default-quality --disable-sequence-dictionary-validation --emit-original-quals --gcs-max-retries --gcs-project-for-requester-pays --global-qscore-prior --help --indels-context-size --insertions-default-quality --interval-merging-rule --intervals --low-quality-tail --maximum-cycle-value --mismatches-context-size --mismatches-default-quality --num-reducers --output-shard-tmp-dir --preserve-qscores-less-than --program-name --quantize-quals --quantizing-levels --sharded-output --spark-master --use-original-qualities --version --round-down-quantized --showHidden --static-quantized-quals ) ALL_ARGUMENT_VALUE_TYPES=("List[String]" "List[String]" "String" "String" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "int" "int" "IntervalSetRule" "Boolean" "List[String]" "List[String]" "ValidationStringency" "String" "boolean" "boolean" "LogLevel" "List[File]" "long" "String" "double" "List[String]" "byte" "byte" "boolean" "boolean" "int" "String" "double" "boolean" "int" "byte" "IntervalMergingRule" "List[String]" "byte" "int" "int" "byte" "int" "String" "int" "String" "int" "int" "boolean" "String" "Boolean" "boolean" "boolean" "boolean" "List[Integer]" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "FilterFuncotations" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--output --ref-version --variant --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --reference --sites-only-vcf-output --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--output;-O" "--variant;-V" "--add-output-sam-program-record;-add-output-sam-program-record" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-bam-md5;-OBM" "--create-output-variant-index;-OVI" "--create-output-variant-md5;-OVM" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--input;-I" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--lenient;-LE" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--seconds-between-progress-updates;-seconds-between-progress-updates" "--sequence-dictionary;-sequence-dictionary" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--cloud-index-prefetch-buffer;-CIPB" "--cloud-prefetch-buffer;-CPB" "--disable-bam-index-caching;-DBIC" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--reference;-R" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--output --ref-version --variant --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --reference --sites-only-vcf-output --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "Reference" "String" "boolean" "boolean" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "List[String]" "int" "int" "IntervalSetRule" "boolean" "Boolean" "List[String]" "List[String]" "ValidationStringency" "double" "String" "String" "boolean" "boolean" "LogLevel" "List[File]" "int" "int" "boolean" "boolean" "int" "String" "boolean" "IntervalMergingRule" "List[String]" "String" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "UpdateVCFSequenceDictionary" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--output --variant --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --reference --replace --sites-only-vcf-output --source-dictionary --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--output;-O" "--variant;-V" "--add-output-sam-program-record;-add-output-sam-program-record" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-bam-md5;-OBM" "--create-output-variant-index;-OVI" "--create-output-variant-md5;-OVM" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--input;-I" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--lenient;-LE" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--seconds-between-progress-updates;-seconds-between-progress-updates" "--sequence-dictionary;-sequence-dictionary" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--cloud-index-prefetch-buffer;-CIPB" "--cloud-prefetch-buffer;-CPB" "--disable-bam-index-caching;-DBIC" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--reference;-R" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--output --variant --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --reference --replace --sites-only-vcf-output --source-dictionary --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("String" "String" "boolean" "boolean" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "List[String]" "int" "int" "IntervalSetRule" "boolean" "Boolean" "List[String]" "List[String]" "ValidationStringency" "double" "String" "String" "boolean" "boolean" "LogLevel" "List[File]" "int" "int" "boolean" "boolean" "int" "String" "boolean" "IntervalMergingRule" "List[String]" "String" "boolean" "boolean" "String" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "BaseRecalibratorSpark" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--input --known-sites --output --reference --add-output-vcf-command-line --create-output-bam-index --create-output-bam-splitting-index --create-output-variant-index --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --read-filter --read-index --read-validation-stringency --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --bam-partition-size --binary-tag-name --bqsr-baq-gap-open-penalty --conf --default-base-qualities --deletions-default-quality --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --indels-context-size --insertions-default-quality --interval-merging-rule --intervals --low-quality-tail --maximum-cycle-value --mismatches-context-size --mismatches-default-quality --num-reducers --output-shard-tmp-dir --preserve-qscores-less-than --program-name --quantizing-levels --sharded-output --spark-master --use-original-qualities --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=("--output-shard-tmp-dir;sharded-output" "--sharded-output;output-shard-tmp-dir" ) SYNONYMOUS_ARGS=("--input;-I" "--output;-O" "--reference;-R" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-variant-index;-OVI" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--conf;-conf" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--gcs-max-retries;-gcs-retries" "--help;-h" "--indels-context-size;-ics" "--interval-merging-rule;-imr" "--intervals;-L" "--maximum-cycle-value;-max-cycle" "--mismatches-context-size;-mcs" "--use-original-qualities;-OQ" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--input --known-sites --output --reference --add-output-vcf-command-line --create-output-bam-index --create-output-bam-splitting-index --create-output-variant-index --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --read-filter --read-index --read-validation-stringency --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --bam-partition-size --binary-tag-name --bqsr-baq-gap-open-penalty --conf --default-base-qualities --deletions-default-quality --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --indels-context-size --insertions-default-quality --interval-merging-rule --intervals --low-quality-tail --maximum-cycle-value --mismatches-context-size --mismatches-default-quality --num-reducers --output-shard-tmp-dir --preserve-qscores-less-than --program-name --quantizing-levels --sharded-output --spark-master --use-original-qualities --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("List[String]" "List[String]" "String" "String" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "int" "int" "IntervalSetRule" "Boolean" "List[String]" "List[String]" "ValidationStringency" "String" "boolean" "boolean" "LogLevel" "List[File]" "long" "String" "double" "List[String]" "byte" "byte" "boolean" "int" "String" "boolean" "int" "byte" "IntervalMergingRule" "List[String]" "byte" "int" "int" "byte" "int" "String" "int" "String" "int" "boolean" "String" "Boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "CollectRawWgsMetrics" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--INPUT --OUTPUT --REFERENCE_SEQUENCE --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --ALLELE_FRACTION --arguments_file --COUNT_UNPAIRED --COVERAGE_CAP --help --INCLUDE_BQ_HISTOGRAM --INTERVALS --LOCUS_ACCUMULATION_CAP --MINIMUM_BASE_QUALITY --MINIMUM_MAPPING_QUALITY --READ_LENGTH --SAMPLE_SIZE --STOP_AFTER --THEORETICAL_SENSITIVITY_OUTPUT --USE_FAST_ALGORITHM --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--INPUT;-I" "--OUTPUT;-O" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--COVERAGE_CAP;-CAP" "--help;-h" "--MINIMUM_BASE_QUALITY;-Q" "--MINIMUM_MAPPING_QUALITY;-MQ" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--INPUT --OUTPUT --REFERENCE_SEQUENCE --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --ALLELE_FRACTION --arguments_file --COUNT_UNPAIRED --COVERAGE_CAP --help --INCLUDE_BQ_HISTOGRAM --INTERVALS --LOCUS_ACCUMULATION_CAP --MINIMUM_BASE_QUALITY --MINIMUM_MAPPING_QUALITY --READ_LENGTH --SAMPLE_SIZE --STOP_AFTER --THEORETICAL_SENSITIVITY_OUTPUT --USE_FAST_ALGORITHM --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "File" "File" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "List[Double]" "List[File]" "boolean" "int" "boolean" "boolean" "File" "int" "int" "int" "int" "int" "long" "File" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "DepthPerAlleleBySample" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=() MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=() MAX_OCCURRENCES=() ALL_LEGAL_ARGUMENTS=() ALL_ARGUMENT_VALUE_TYPES=() # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "SelectVariants" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--output --variant --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --concordance --disable-bam-index-caching --disable-sequence-dictionary-validation --discordance --drop-genotype-annotation --drop-info-annotation --exclude-filtered --exclude-ids --exclude-non-variants --exclude-sample-expressions --exclude-sample-name --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --invert-mendelian-violation --invertSelect --keep-ids --keep-original-ac --keep-original-dp --max-filtered-genotypes --max-fraction-filtered-genotypes --max-indel-size --max-nocall-fraction --max-nocall-number --mendelian-violation --mendelian-violation-qual-threshold --min-filtered-genotypes --min-fraction-filtered-genotypes --min-indel-size --pedigree --preserve-alleles --reference --remove-fraction-genotypes --remove-unused-alternates --restrict-alleles-to --sample-expressions --sample-name --selectExpressions --select-random-fraction --select-type-to-exclude --select-type-to-include --set-filtered-gt-to-nocall --sites-only-vcf-output --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--output;-O" "--variant;-V" "--add-output-sam-program-record;-add-output-sam-program-record" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-bam-md5;-OBM" "--create-output-variant-index;-OVI" "--create-output-variant-md5;-OVM" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--input;-I" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--lenient;-LE" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--seconds-between-progress-updates;-seconds-between-progress-updates" "--sequence-dictionary;-sequence-dictionary" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--cloud-index-prefetch-buffer;-CIPB" "--cloud-prefetch-buffer;-CPB" "--concordance;-conc" "--disable-bam-index-caching;-DBIC" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--discordance;-disc" "--drop-genotype-annotation;-DGA" "--drop-info-annotation;-DA" "--exclude-ids;-xl-ids" "--exclude-sample-expressions;-xl-se" "--exclude-sample-name;-xl-sn" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--invertSelect;-invert-select" "--keep-ids;-ids" "--pedigree;-ped" "--reference;-R" "--sample-expressions;-se" "--sample-name;-sn" "--selectExpressions;-select" "--select-random-fraction;-fraction" "--select-type-to-exclude;-xl-select-type" "--select-type-to-include;-select-type" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--output --variant --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --concordance --disable-bam-index-caching --disable-sequence-dictionary-validation --discordance --drop-genotype-annotation --drop-info-annotation --exclude-filtered --exclude-ids --exclude-non-variants --exclude-sample-expressions --exclude-sample-name --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --invert-mendelian-violation --invertSelect --keep-ids --keep-original-ac --keep-original-dp --max-filtered-genotypes --max-fraction-filtered-genotypes --max-indel-size --max-nocall-fraction --max-nocall-number --mendelian-violation --mendelian-violation-qual-threshold --min-filtered-genotypes --min-fraction-filtered-genotypes --min-indel-size --pedigree --preserve-alleles --reference --remove-fraction-genotypes --remove-unused-alternates --restrict-alleles-to --sample-expressions --sample-name --selectExpressions --select-random-fraction --select-type-to-exclude --select-type-to-include --set-filtered-gt-to-nocall --sites-only-vcf-output --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "String" "boolean" "boolean" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "List[String]" "int" "int" "IntervalSetRule" "boolean" "Boolean" "List[String]" "List[String]" "ValidationStringency" "double" "String" "String" "boolean" "boolean" "LogLevel" "List[File]" "int" "int" "FeatureInput[VariantContext]" "boolean" "boolean" "FeatureInput[VariantContext]" "List[String]" "List[String]" "boolean" "Set[String]" "boolean" "Set[String]" "Set[String]" "int" "String" "boolean" "IntervalMergingRule" "List[String]" "Boolean" "boolean" "Set[String]" "boolean" "boolean" "int" "double" "int" "double" "int" "Boolean" "double" "int" "double" "int" "File" "boolean" "String" "double" "boolean" "NumberAlleleRestriction" "Set[String]" "Set[String]" "ArrayList[String]" "double" "List[Type]" "List[Type]" "boolean" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "AnalyzeCovariates" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--gatk-config-file --QUIET --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --after-report-file --arguments_file --before-report-file --bqsr-recal-file --gcs-max-retries --gcs-project-for-requester-pays --help --ignore-last-modification-times --intermediate-csv-file --plots-report-file --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--after-report-file;-after" "--before-report-file;-before" "--bqsr-recal-file;-bqsr" "--gcs-max-retries;-gcs-retries" "--help;-h" "--intermediate-csv-file;-csv" "--plots-report-file;-plots" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--gatk-config-file --QUIET --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --after-report-file --arguments_file --before-report-file --bqsr-recal-file --gcs-max-retries --gcs-project-for-requester-pays --help --ignore-last-modification-times --intermediate-csv-file --plots-report-file --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("String" "Boolean" "String" "boolean" "boolean" "LogLevel" "File" "List[File]" "File" "File" "int" "String" "boolean" "boolean" "File" "File" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "PathSeqBuildReferenceTaxonomy" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--output --reference --tax-dump --gatk-config-file --QUIET --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --gcs-max-retries --gcs-project-for-requester-pays --genbank-catalog --help --min-non-virus-contig-length --refseq-catalog --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--output;-O" "--reference;-R" "--tax-dump;-TD" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--gcs-max-retries;-gcs-retries" "--genbank-catalog;-GC" "--help;-h" "--min-non-virus-contig-length;-min-non-virus-contig-length" "--refseq-catalog;-RC" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--output --reference --tax-dump --gatk-config-file --QUIET --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --gcs-max-retries --gcs-project-for-requester-pays --genbank-catalog --help --min-non-virus-contig-length --refseq-catalog --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("String" "String" "String" "String" "Boolean" "String" "boolean" "boolean" "LogLevel" "List[File]" "int" "String" "String" "boolean" "int" "String" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "FilterAlignmentArtifacts" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--bwa-mem-index-image --input --output --variant --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --dont-skip-filtered-variants --dont-use-mates --drop-ratio --fragment-size --gcs-max-retries --gcs-project-for-requester-pays --help --indel-start-tolerance --interval-merging-rule --intervals --max-failed-realignments --max-reasonable-fragment-length --min-aligner-score-difference --minimum-seed-length --min-mismatch-ratio --num-regular-contigs --reference --seed-split-factor --sites-only-vcf-output --sufficient-good-realignments --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--bwa-mem-index-image;-index" "--input;-I" "--output;-O" "--variant;-V" "--add-output-sam-program-record;-add-output-sam-program-record" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-bam-md5;-OBM" "--create-output-variant-index;-OVI" "--create-output-variant-md5;-OVM" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--lenient;-LE" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--seconds-between-progress-updates;-seconds-between-progress-updates" "--sequence-dictionary;-sequence-dictionary" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--cloud-index-prefetch-buffer;-CIPB" "--cloud-prefetch-buffer;-CPB" "--disable-bam-index-caching;-DBIC" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--drop-ratio;-drop-ratio" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--minimum-seed-length;-min-seed-length" "--reference;-R" "--seed-split-factor;-split-factor" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--bwa-mem-index-image --input --output --variant --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --dont-skip-filtered-variants --dont-use-mates --drop-ratio --fragment-size --gcs-max-retries --gcs-project-for-requester-pays --help --indel-start-tolerance --interval-merging-rule --intervals --max-failed-realignments --max-reasonable-fragment-length --min-aligner-score-difference --minimum-seed-length --min-mismatch-ratio --num-regular-contigs --reference --seed-split-factor --sites-only-vcf-output --sufficient-good-realignments --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("String" "List[String]" "String" "String" "boolean" "boolean" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "int" "int" "IntervalSetRule" "boolean" "Boolean" "List[String]" "List[String]" "ValidationStringency" "double" "String" "String" "boolean" "boolean" "LogLevel" "List[File]" "int" "int" "boolean" "boolean" "boolean" "boolean" "double" "int" "int" "String" "boolean" "int" "IntervalMergingRule" "List[String]" "int" "int" "int" "int" "double" "int" "String" "double" "boolean" "int" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "PrintReads" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--input --output --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --reference --sites-only-vcf-output --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--input;-I" "--output;-O" "--add-output-sam-program-record;-add-output-sam-program-record" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-bam-md5;-OBM" "--create-output-variant-index;-OVI" "--create-output-variant-md5;-OVM" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--lenient;-LE" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--seconds-between-progress-updates;-seconds-between-progress-updates" "--sequence-dictionary;-sequence-dictionary" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--cloud-index-prefetch-buffer;-CIPB" "--cloud-prefetch-buffer;-CPB" "--disable-bam-index-caching;-DBIC" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--reference;-R" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--input --output --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --reference --sites-only-vcf-output --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("List[String]" "String" "boolean" "boolean" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "int" "int" "IntervalSetRule" "boolean" "Boolean" "List[String]" "List[String]" "ValidationStringency" "double" "String" "String" "boolean" "boolean" "LogLevel" "List[File]" "int" "int" "boolean" "boolean" "int" "String" "boolean" "IntervalMergingRule" "List[String]" "String" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "CalculateReadGroupChecksum" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--INPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --OUTPUT --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--INPUT;-I" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--help;-h" "--OUTPUT;-O" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--INPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --OUTPUT --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "List[File]" "boolean" "File" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "CollectRnaSeqMetrics" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--IGNORE_SEQUENCE --INPUT --OUTPUT --REF_FLAT --STRAND_SPECIFICITY --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --ASSUME_SORTED --CHART_OUTPUT --help --METRIC_ACCUMULATION_LEVEL --MINIMUM_LENGTH --RIBOSOMAL_INTERVALS --RRNA_FRAGMENT_PERCENTAGE --STOP_AFTER --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--INPUT;-I" "--OUTPUT;-O" "--STRAND_SPECIFICITY;-STRAND" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--ASSUME_SORTED;-AS" "--CHART_OUTPUT;-CHART" "--help;-h" "--METRIC_ACCUMULATION_LEVEL;-LEVEL" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--IGNORE_SEQUENCE --INPUT --OUTPUT --REF_FLAT --STRAND_SPECIFICITY --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --ASSUME_SORTED --CHART_OUTPUT --help --METRIC_ACCUMULATION_LEVEL --MINIMUM_LENGTH --RIBOSOMAL_INTERVALS --RRNA_FRAGMENT_PERCENTAGE --STOP_AFTER --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("Set[String]" "File" "File" "File" "StrandSpecificity" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "List[File]" "boolean" "File" "boolean" "Set[MetricAccumulationLevel]" "int" "File" "double" "long" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "GetSampleName" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--input --output --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --reference --sites-only-vcf-output --use-url-encoding --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--input;-I" "--output;-O" "--add-output-sam-program-record;-add-output-sam-program-record" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-bam-md5;-OBM" "--create-output-variant-index;-OVI" "--create-output-variant-md5;-OVM" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--lenient;-LE" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--seconds-between-progress-updates;-seconds-between-progress-updates" "--sequence-dictionary;-sequence-dictionary" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--cloud-index-prefetch-buffer;-CIPB" "--cloud-prefetch-buffer;-CPB" "--disable-bam-index-caching;-DBIC" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--reference;-R" "--use-url-encoding;-encode" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--input --output --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --reference --sites-only-vcf-output --use-url-encoding --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("List[String]" "File" "boolean" "boolean" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "int" "int" "IntervalSetRule" "boolean" "Boolean" "List[String]" "List[String]" "ValidationStringency" "double" "String" "String" "boolean" "boolean" "LogLevel" "List[File]" "int" "int" "boolean" "boolean" "int" "String" "boolean" "IntervalMergingRule" "List[String]" "String" "boolean" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "CompareBaseQualities" ]] ; then # Set up the completion information for this tool: NUM_POSITIONAL_ARGUMENTS=2 POSITIONAL_ARGUMENT_TYPE=("List[File]") DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --gatk-config-file --MAX_RECORDS_IN_RAM --QUIET --reference --tmp-dir --use-jdk-deflater --use-jdk-inflater --VALIDATION_STRINGENCY --verbosity --arguments_file --gcs-max-retries --gcs-project-for-requester-pays --help --output --throw-on-diff --version --round-down-quantized --showHidden --static-quantized-quals ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--reference;-R" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--gcs-max-retries;-gcs-retries" "--help;-h" "--output;-O" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --gatk-config-file --MAX_RECORDS_IN_RAM --QUIET --reference --tmp-dir --use-jdk-deflater --use-jdk-inflater --VALIDATION_STRINGENCY --verbosity --arguments_file --gcs-max-retries --gcs-project-for-requester-pays --help --output --throw-on-diff --version --round-down-quantized --showHidden --static-quantized-quals ) ALL_ARGUMENT_VALUE_TYPES=("int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "String" "boolean" "boolean" "ValidationStringency" "LogLevel" "List[File]" "int" "String" "boolean" "String" "boolean" "boolean" "boolean" "boolean" "List[Integer]" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "BamIndexStats" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--INPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--INPUT;-I" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--help;-h" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--INPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "List[File]" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "CollectOxoGMetrics" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--INPUT --OUTPUT --REFERENCE_SEQUENCE --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --CONTEXT_SIZE --CONTEXTS --DB_SNP --help --INCLUDE_NON_PF_READS --INTERVALS --MAXIMUM_INSERT_SIZE --MINIMUM_INSERT_SIZE --MINIMUM_MAPPING_QUALITY --MINIMUM_QUALITY_SCORE --STOP_AFTER --USE_OQ --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--INPUT;-I" "--OUTPUT;-O" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--help;-h" "--INCLUDE_NON_PF_READS;-NON_PF" "--MAXIMUM_INSERT_SIZE;-MAX_INS" "--MINIMUM_INSERT_SIZE;-MIN_INS" "--MINIMUM_MAPPING_QUALITY;-MQ" "--MINIMUM_QUALITY_SCORE;-Q" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--INPUT --OUTPUT --REFERENCE_SEQUENCE --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --CONTEXT_SIZE --CONTEXTS --DB_SNP --help --INCLUDE_NON_PF_READS --INTERVALS --MAXIMUM_INSERT_SIZE --MINIMUM_INSERT_SIZE --MINIMUM_MAPPING_QUALITY --MINIMUM_QUALITY_SCORE --STOP_AFTER --USE_OQ --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "File" "File" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "List[File]" "int" "Set[String]" "File" "boolean" "boolean" "File" "int" "int" "int" "int" "int" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "VariantEval" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--eval --output --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --ancestral-alignments --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --comp --dbsnp --disable-bam-index-caching --disable-sequence-dictionary-validation --do-not-use-all-standard-modules --do-not-use-all-standard-stratifications --eval-module --gcs-max-retries --gcs-project-for-requester-pays --gold-standard --help --interval-merging-rule --intervals --keep-ac0 --KNOWN_NAMES --known-cnvs --list --mendelian-violation-qual-threshold --merge-evals --min-phase-quality --pedigree --reference --require-strict-allele-match --sample --sample-ploidy --SELECT_EXPS --SELECT_NAMES --sites-only-vcf-output --stratification-module --strat-intervals --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--eval;-eval" "--output;-O" "--add-output-sam-program-record;-add-output-sam-program-record" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-bam-md5;-OBM" "--create-output-variant-index;-OVI" "--create-output-variant-md5;-OVM" "--exclude-intervals;-XL" "--input;-I" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--lenient;-LE" "--read-index;-read-index" "--read-validation-stringency;-VS" "--seconds-between-progress-updates;-seconds-between-progress-updates" "--sequence-dictionary;-sequence-dictionary" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--ancestral-alignments;-aa" "--cloud-index-prefetch-buffer;-CIPB" "--cloud-prefetch-buffer;-CPB" "--comp;-comp" "--dbsnp;-D" "--disable-bam-index-caching;-DBIC" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--do-not-use-all-standard-modules;-no-ev" "--do-not-use-all-standard-stratifications;-no-st" "--eval-module;-EV" "--gcs-max-retries;-gcs-retries" "--gold-standard;-gold" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--keep-ac0;-keep-ac0" "--KNOWN_NAMES;-known-name" "--known-cnvs;-known-cnvs" "--list;-ls" "--mendelian-violation-qual-threshold;-mvq" "--merge-evals;-merge-evals" "--min-phase-quality;-mpq" "--pedigree;-ped" "--reference;-R" "--require-strict-allele-match;-strict" "--sample;-sn" "--sample-ploidy;-ploidy" "--SELECT_EXPS;-select" "--SELECT_NAMES;-select-name" "--stratification-module;-ST" "--strat-intervals;-strat-intervals" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--eval --output --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --ancestral-alignments --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --comp --dbsnp --disable-bam-index-caching --disable-sequence-dictionary-validation --do-not-use-all-standard-modules --do-not-use-all-standard-stratifications --eval-module --gcs-max-retries --gcs-project-for-requester-pays --gold-standard --help --interval-merging-rule --intervals --keep-ac0 --KNOWN_NAMES --known-cnvs --list --mendelian-violation-qual-threshold --merge-evals --min-phase-quality --pedigree --reference --require-strict-allele-match --sample --sample-ploidy --SELECT_EXPS --SELECT_NAMES --sites-only-vcf-output --stratification-module --strat-intervals --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("List[FeatureInput[VariantContext]]" "File" "boolean" "boolean" "boolean" "boolean" "boolean" "boolean" "List[String]" "String" "List[String]" "int" "int" "IntervalSetRule" "boolean" "Boolean" "List[String]" "ValidationStringency" "double" "String" "String" "boolean" "boolean" "LogLevel" "File" "List[File]" "int" "int" "List[FeatureInput[VariantContext]]" "FeatureInput[VariantContext]" "boolean" "boolean" "Boolean" "Boolean" "List[String]" "int" "String" "FeatureInput[VariantContext]" "boolean" "IntervalMergingRule" "List[String]" "boolean" "HashSet[String]" "FeatureInput[Feature]" "Boolean" "double" "boolean" "double" "File" "String" "boolean" "Set[String]" "int" "ArrayList[String]" "ArrayList[String]" "boolean" "List[String]" "FeatureInput[Feature]" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "MarkDuplicatesWithMateCigar" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--INPUT --METRICS_FILE --OUTPUT --ADD_PG_TAG_TO_READS --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --ASSUME_SORT_ORDER --BLOCK_SIZE --COMMENT --DUPLICATE_SCORING_STRATEGY --help --MAX_OPTICAL_DUPLICATE_SET_SIZE --MINIMUM_DISTANCE --OPTICAL_DUPLICATE_PIXEL_DISTANCE --PROGRAM_GROUP_COMMAND_LINE --PROGRAM_GROUP_NAME --PROGRAM_GROUP_VERSION --PROGRAM_RECORD_ID --READ_NAME_REGEX --REMOVE_DUPLICATES --SKIP_PAIRS_WITH_NO_MATE_CIGAR --version --showHidden --ASSUME_SORTED ) MUTUALLY_EXCLUSIVE_ARGS=("--ASSUME_SORT_ORDER;ASSUME_SORTED" "--ASSUME_SORTED;ASSUME_SORT_ORDER,ASO" ) SYNONYMOUS_ARGS=("--INPUT;-I" "--METRICS_FILE;-M" "--OUTPUT;-O" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--ASSUME_SORT_ORDER;-ASO" "--COMMENT;-CO" "--DUPLICATE_SCORING_STRATEGY;-DS" "--help;-h" "--PROGRAM_GROUP_COMMAND_LINE;-PG_COMMAND" "--PROGRAM_GROUP_NAME;-PG_NAME" "--PROGRAM_GROUP_VERSION;-PG_VERSION" "--PROGRAM_RECORD_ID;-PG" "--showHidden;-showHidden" "--ASSUME_SORTED;-AS" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--INPUT --METRICS_FILE --OUTPUT --ADD_PG_TAG_TO_READS --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --ASSUME_SORT_ORDER --BLOCK_SIZE --COMMENT --DUPLICATE_SCORING_STRATEGY --help --MAX_OPTICAL_DUPLICATE_SET_SIZE --MINIMUM_DISTANCE --OPTICAL_DUPLICATE_PIXEL_DISTANCE --PROGRAM_GROUP_COMMAND_LINE --PROGRAM_GROUP_NAME --PROGRAM_GROUP_VERSION --PROGRAM_RECORD_ID --READ_NAME_REGEX --REMOVE_DUPLICATES --SKIP_PAIRS_WITH_NO_MATE_CIGAR --version --showHidden --ASSUME_SORTED ) ALL_ARGUMENT_VALUE_TYPES=("List[String]" "File" "File" "boolean" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "List[File]" "SortOrder" "int" "List[String]" "ScoringStrategy" "boolean" "long" "int" "int" "String" "String" "String" "String" "String" "boolean" "boolean" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "GatherBQSRReports" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--input --output --gatk-config-file --QUIET --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --gcs-max-retries --gcs-project-for-requester-pays --help --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--input;-I" "--output;-O" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--gcs-max-retries;-gcs-retries" "--help;-h" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--input --output --gatk-config-file --QUIET --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --gcs-max-retries --gcs-project-for-requester-pays --help --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("List[File]" "File" "String" "Boolean" "String" "boolean" "boolean" "LogLevel" "List[File]" "int" "String" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "GenotypeConcordance" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--CALL_VCF --OUTPUT --TRUTH_VCF --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --CALL_SAMPLE --help --IGNORE_FILTER_STATUS --INTERSECT_INTERVALS --INTERVALS --MIN_DP --MIN_GQ --MISSING_SITES_HOM_REF --OUTPUT_ALL_ROWS --OUTPUT_VCF --TRUTH_SAMPLE --USE_VCF_INDEX --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--CALL_VCF;-CV" "--OUTPUT;-O" "--TRUTH_VCF;-TV" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--CALL_SAMPLE;-CS" "--help;-h" "--MISSING_SITES_HOM_REF;-MISSING_HOM" "--TRUTH_SAMPLE;-TS" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--CALL_VCF --OUTPUT --TRUTH_VCF --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --CALL_SAMPLE --help --IGNORE_FILTER_STATUS --INTERSECT_INTERVALS --INTERVALS --MIN_DP --MIN_GQ --MISSING_SITES_HOM_REF --OUTPUT_ALL_ROWS --OUTPUT_VCF --TRUTH_SAMPLE --USE_VCF_INDEX --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "File" "File" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "List[File]" "String" "boolean" "boolean" "boolean" "List[File]" "int" "int" "boolean" "boolean" "boolean" "String" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "CompareDuplicatesSpark" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--input --input2 --add-output-vcf-command-line --create-output-bam-index --create-output-bam-splitting-index --create-output-variant-index --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --read-filter --read-index --read-validation-stringency --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --bam-partition-size --conf --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --num-reducers --output --output2 --output-shard-tmp-dir --print-summary --program-name --reference --sharded-output --spark-master --throw-on-diff --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=("--output-shard-tmp-dir;sharded-output" "--sharded-output;output-shard-tmp-dir" ) SYNONYMOUS_ARGS=("--input;-I" "--input2;-I2" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-variant-index;-OVI" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--conf;-conf" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--output;-O" "--output2;-O2" "--reference;-R" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--input --input2 --add-output-vcf-command-line --create-output-bam-index --create-output-bam-splitting-index --create-output-variant-index --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --read-filter --read-index --read-validation-stringency --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --bam-partition-size --conf --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --num-reducers --output --output2 --output-shard-tmp-dir --print-summary --program-name --reference --sharded-output --spark-master --throw-on-diff --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("List[String]" "String" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "int" "int" "IntervalSetRule" "Boolean" "List[String]" "List[String]" "ValidationStringency" "String" "boolean" "boolean" "LogLevel" "List[File]" "long" "List[String]" "boolean" "int" "String" "boolean" "IntervalMergingRule" "List[String]" "int" "String" "String" "String" "boolean" "String" "String" "boolean" "String" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "BaseQualityRankSumTest" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=() MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=() MAX_OCCURRENCES=() ALL_LEGAL_ARGUMENTS=() ALL_ARGUMENT_VALUE_TYPES=() # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "CountNs" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=() MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=() MAX_OCCURRENCES=() ALL_LEGAL_ARGUMENTS=() ALL_ARGUMENT_VALUE_TYPES=() # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "MateOnSameContigOrNoMappedMateReadFilter" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=() MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=() MAX_OCCURRENCES=() ALL_LEGAL_ARGUMENTS=() ALL_ARGUMENT_VALUE_TYPES=() # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "BaseRecalibrator" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--input --known-sites --output --reference --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --binary-tag-name --bqsr-baq-gap-open-penalty --cloud-index-prefetch-buffer --cloud-prefetch-buffer --default-base-qualities --deletions-default-quality --disable-bam-index-caching --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --indels-context-size --insertions-default-quality --interval-merging-rule --intervals --low-quality-tail --maximum-cycle-value --mismatches-context-size --mismatches-default-quality --preserve-qscores-less-than --quantizing-levels --sites-only-vcf-output --use-original-qualities --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--input;-I" "--output;-O" "--reference;-R" "--add-output-sam-program-record;-add-output-sam-program-record" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-bam-md5;-OBM" "--create-output-variant-index;-OVI" "--create-output-variant-md5;-OVM" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--lenient;-LE" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--seconds-between-progress-updates;-seconds-between-progress-updates" "--sequence-dictionary;-sequence-dictionary" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--cloud-index-prefetch-buffer;-CIPB" "--cloud-prefetch-buffer;-CPB" "--disable-bam-index-caching;-DBIC" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--gcs-max-retries;-gcs-retries" "--help;-h" "--indels-context-size;-ics" "--interval-merging-rule;-imr" "--intervals;-L" "--maximum-cycle-value;-max-cycle" "--mismatches-context-size;-mcs" "--use-original-qualities;-OQ" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--input --known-sites --output --reference --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --binary-tag-name --bqsr-baq-gap-open-penalty --cloud-index-prefetch-buffer --cloud-prefetch-buffer --default-base-qualities --deletions-default-quality --disable-bam-index-caching --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --indels-context-size --insertions-default-quality --interval-merging-rule --intervals --low-quality-tail --maximum-cycle-value --mismatches-context-size --mismatches-default-quality --preserve-qscores-less-than --quantizing-levels --sites-only-vcf-output --use-original-qualities --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("List[String]" "List[FeatureInput[Feature]]" "File" "String" "boolean" "boolean" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "int" "int" "IntervalSetRule" "boolean" "Boolean" "List[String]" "List[String]" "ValidationStringency" "double" "String" "String" "boolean" "boolean" "LogLevel" "List[File]" "String" "double" "int" "int" "byte" "byte" "boolean" "boolean" "int" "String" "boolean" "int" "byte" "IntervalMergingRule" "List[String]" "byte" "int" "int" "byte" "int" "int" "boolean" "Boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "PlatformUnitReadFilter" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--black-listed-lanes ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=(0 ) MAX_OCCURRENCES=(2147483647 ) ALL_LEGAL_ARGUMENTS=(--black-listed-lanes ) ALL_ARGUMENT_VALUE_TYPES=("Set[String]" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "SortSamSpark" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--input --output --add-output-vcf-command-line --create-output-bam-index --create-output-bam-splitting-index --create-output-variant-index --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --read-filter --read-index --read-validation-stringency --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --bam-partition-size --conf --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --num-reducers --output-shard-tmp-dir --program-name --reference --sharded-output --sort-order --spark-master --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=("--output-shard-tmp-dir;sharded-output" "--sharded-output;output-shard-tmp-dir" ) SYNONYMOUS_ARGS=("--input;-I" "--output;-O" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-variant-index;-OVI" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--conf;-conf" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--reference;-R" "--sort-order;-SO" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--input --output --add-output-vcf-command-line --create-output-bam-index --create-output-bam-splitting-index --create-output-variant-index --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --read-filter --read-index --read-validation-stringency --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --bam-partition-size --conf --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --num-reducers --output-shard-tmp-dir --program-name --reference --sharded-output --sort-order --spark-master --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("List[String]" "String" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "int" "int" "IntervalSetRule" "Boolean" "List[String]" "List[String]" "ValidationStringency" "String" "boolean" "boolean" "LogLevel" "List[File]" "long" "List[String]" "boolean" "int" "String" "boolean" "IntervalMergingRule" "List[String]" "int" "String" "String" "String" "boolean" "SparkSortOrder" "String" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "SetNmAndUqTags" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--INPUT --OUTPUT --REFERENCE_SEQUENCE --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --IS_BISULFITE_SEQUENCE --SET_ONLY_UQ --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--INPUT;-I" "--OUTPUT;-O" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--help;-h" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--INPUT --OUTPUT --REFERENCE_SEQUENCE --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --IS_BISULFITE_SEQUENCE --SET_ONLY_UQ --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "File" "File" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "List[File]" "boolean" "boolean" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "OxoGReadCounts" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=() MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=() MAX_OCCURRENCES=() ALL_LEGAL_ARGUMENTS=() ALL_ARGUMENT_VALUE_TYPES=() # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "VariantRecalibrator" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--output --resource --tranches-file --use-annotation --variant --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --aggregate --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --ignore-all-filters --ignore-filter --input-model --interval-merging-rule --intervals --mode --output-model --reference --rscript-file --sites-only-vcf-output --target-titv --truth-sensitivity-tranche --use-allele-specific-annotations --version --bad-lod-score-cutoff --dirichlet --k-means-iterations --max-attempts --max-gaussians --maximum-training-variants --max-iterations --max-negative-gaussians --minimum-bad-variants --mq-cap-for-logit-jitter-transform --prior-counts --showHidden --shrinkage --standard-deviation-threshold --trust-all-polymorphic ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--output;-O" "--resource;-resource" "--use-annotation;-an" "--variant;-V" "--add-output-sam-program-record;-add-output-sam-program-record" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-bam-md5;-OBM" "--create-output-variant-index;-OVI" "--create-output-variant-md5;-OVM" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--input;-I" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--lenient;-LE" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--seconds-between-progress-updates;-seconds-between-progress-updates" "--sequence-dictionary;-sequence-dictionary" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--aggregate;-aggregate" "--cloud-index-prefetch-buffer;-CIPB" "--cloud-prefetch-buffer;-CPB" "--disable-bam-index-caching;-DBIC" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--mode;-mode" "--reference;-R" "--target-titv;-titv" "--truth-sensitivity-tranche;-tranche" "--use-allele-specific-annotations;-AS" "--bad-lod-score-cutoff;-bad-lod-cutoff" "--mq-cap-for-logit-jitter-transform;-mq-cap" "--showHidden;-showHidden" "--standard-deviation-threshold;-std" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--output --resource --tranches-file --use-annotation --variant --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --aggregate --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --ignore-all-filters --ignore-filter --input-model --interval-merging-rule --intervals --mode --output-model --reference --rscript-file --sites-only-vcf-output --target-titv --truth-sensitivity-tranche --use-allele-specific-annotations --version --bad-lod-score-cutoff --dirichlet --k-means-iterations --max-attempts --max-gaussians --maximum-training-variants --max-iterations --max-negative-gaussians --minimum-bad-variants --mq-cap-for-logit-jitter-transform --prior-counts --showHidden --shrinkage --standard-deviation-threshold --trust-all-polymorphic ) ALL_ARGUMENT_VALUE_TYPES=("String" "List[FeatureInput[VariantContext]]" "String" "List[String]" "List[String]" "boolean" "boolean" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "List[String]" "int" "int" "IntervalSetRule" "boolean" "Boolean" "List[String]" "List[String]" "ValidationStringency" "double" "String" "String" "boolean" "boolean" "LogLevel" "List[FeatureInput[VariantContext]]" "List[File]" "int" "int" "boolean" "boolean" "int" "String" "boolean" "boolean" "List[String]" "String" "IntervalMergingRule" "List[String]" "Mode" "String" "String" "String" "boolean" "double" "List[Double]" "boolean" "boolean" "double" "double" "int" "int" "int" "int" "int" "int" "int" "int" "double" "boolean" "double" "double" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "ValidateBasicSomaticShortMutations" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--discovery-sample-name --input --output --reference --val-case-sample-name --val-control-sample-name --variant --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --annotated-vcf --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --max-validation-normal-count --min-base-quality-cutoff --min-power --sites-only-vcf-output --summary --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--input;-I" "--output;-O" "--reference;-R" "--variant;-V" "--add-output-sam-program-record;-add-output-sam-program-record" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-bam-md5;-OBM" "--create-output-variant-index;-OVI" "--create-output-variant-md5;-OVM" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--lenient;-LE" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--seconds-between-progress-updates;-seconds-between-progress-updates" "--sequence-dictionary;-sequence-dictionary" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--cloud-index-prefetch-buffer;-CIPB" "--cloud-prefetch-buffer;-CPB" "--disable-bam-index-caching;-DBIC" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--discovery-sample-name --input --output --reference --val-case-sample-name --val-control-sample-name --variant --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --annotated-vcf --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --max-validation-normal-count --min-base-quality-cutoff --min-power --sites-only-vcf-output --summary --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("String" "List[String]" "String" "String" "String" "String" "String" "boolean" "boolean" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "int" "int" "IntervalSetRule" "boolean" "Boolean" "List[String]" "List[String]" "ValidationStringency" "double" "String" "String" "boolean" "boolean" "LogLevel" "File" "List[File]" "int" "int" "boolean" "boolean" "int" "String" "boolean" "IntervalMergingRule" "List[String]" "int" "int" "double" "boolean" "File" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "OverclippedReadFilter" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--dont-require-soft-clips-both-ends --filter-too-short ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=(0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--dont-require-soft-clips-both-ends --filter-too-short ) ALL_ARGUMENT_VALUE_TYPES=("boolean" "int" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "FragmentLength" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=() MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=() MAX_OCCURRENCES=() ALL_LEGAL_ARGUMENTS=() ALL_ARGUMENT_VALUE_TYPES=() # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "CountBases" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--input --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --reference --sites-only-vcf-output --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--input;-I" "--add-output-sam-program-record;-add-output-sam-program-record" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-bam-md5;-OBM" "--create-output-variant-index;-OVI" "--create-output-variant-md5;-OVM" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--lenient;-LE" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--seconds-between-progress-updates;-seconds-between-progress-updates" "--sequence-dictionary;-sequence-dictionary" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--cloud-index-prefetch-buffer;-CIPB" "--cloud-prefetch-buffer;-CPB" "--disable-bam-index-caching;-DBIC" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--reference;-R" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--input --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --reference --sites-only-vcf-output --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("List[String]" "boolean" "boolean" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "int" "int" "IntervalSetRule" "boolean" "Boolean" "List[String]" "List[String]" "ValidationStringency" "double" "String" "String" "boolean" "boolean" "LogLevel" "List[File]" "int" "int" "boolean" "boolean" "int" "String" "boolean" "IntervalMergingRule" "List[String]" "String" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "PlatformReadFilter" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--platform-filter-name ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=(0 ) MAX_OCCURRENCES=(2147483647 ) ALL_LEGAL_ARGUMENTS=(--platform-filter-name ) ALL_ARGUMENT_VALUE_TYPES=("Set[String]" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "LiftOverIntervalList" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--CHAIN --INPUT --OUTPUT --SEQUENCE_DICTIONARY --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --MIN_LIFTOVER_PCT --REJECT --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--INPUT;-I" "--OUTPUT;-O" "--SEQUENCE_DICTIONARY;-SD" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--help;-h" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--CHAIN --INPUT --OUTPUT --SEQUENCE_DICTIONARY --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --MIN_LIFTOVER_PCT --REJECT --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "File" "File" "File" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "List[File]" "boolean" "double" "File" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "PassesVendorQualityCheckReadFilter" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=() MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=() MAX_OCCURRENCES=() ALL_LEGAL_ARGUMENTS=() ALL_ARGUMENT_VALUE_TYPES=() # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "PrimaryLineReadFilter" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=() MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=() MAX_OCCURRENCES=() ALL_LEGAL_ARGUMENTS=() ALL_ARGUMENT_VALUE_TYPES=() # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "CollectBaseDistributionByCycle" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--CHART_OUTPUT --INPUT --OUTPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --ALIGNED_READS_ONLY --arguments_file --ASSUME_SORTED --help --PF_READS_ONLY --STOP_AFTER --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--CHART_OUTPUT;-CHART" "--INPUT;-I" "--OUTPUT;-O" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--ASSUME_SORTED;-AS" "--help;-h" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--CHART_OUTPUT --INPUT --OUTPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --ALIGNED_READS_ONLY --arguments_file --ASSUME_SORTED --help --PF_READS_ONLY --STOP_AFTER --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "File" "File" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "boolean" "List[File]" "boolean" "boolean" "boolean" "long" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "PrintReadsSpark" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--input --output --add-output-vcf-command-line --create-output-bam-index --create-output-bam-splitting-index --create-output-variant-index --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --read-filter --read-index --read-validation-stringency --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --bam-partition-size --conf --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --num-reducers --output-shard-tmp-dir --program-name --reference --sharded-output --spark-master --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=("--output-shard-tmp-dir;sharded-output" "--sharded-output;output-shard-tmp-dir" ) SYNONYMOUS_ARGS=("--input;-I" "--output;-O" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-variant-index;-OVI" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--conf;-conf" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--reference;-R" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--input --output --add-output-vcf-command-line --create-output-bam-index --create-output-bam-splitting-index --create-output-variant-index --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --read-filter --read-index --read-validation-stringency --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --bam-partition-size --conf --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --num-reducers --output-shard-tmp-dir --program-name --reference --sharded-output --spark-master --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("List[String]" "String" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "int" "int" "IntervalSetRule" "Boolean" "List[String]" "List[String]" "ValidationStringency" "String" "boolean" "boolean" "LogLevel" "List[File]" "long" "List[String]" "boolean" "int" "String" "boolean" "IntervalMergingRule" "List[String]" "int" "String" "String" "String" "boolean" "String" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "PathSeqBuildKmers" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--output --reference --gatk-config-file --QUIET --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --bloom-false-positive-probability --gcs-max-retries --gcs-project-for-requester-pays --help --kmer-mask --kmer-size --kmer-spacing --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--output;-O" "--reference;-R" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--bloom-false-positive-probability;-P" "--gcs-max-retries;-gcs-retries" "--help;-h" "--kmer-mask;-M" "--kmer-size;-SZ" "--kmer-spacing;-SP" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--output --reference --gatk-config-file --QUIET --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --bloom-false-positive-probability --gcs-max-retries --gcs-project-for-requester-pays --help --kmer-mask --kmer-size --kmer-spacing --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("String" "String" "String" "Boolean" "String" "boolean" "boolean" "LogLevel" "List[File]" "double" "int" "String" "boolean" "String" "int" "int" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "VariantFiltration" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--output --variant --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --cluster-size --cluster-window-size --disable-bam-index-caching --disable-sequence-dictionary-validation --filter-expression --filter-name --filter-not-in-mask --gcs-max-retries --gcs-project-for-requester-pays --genotype-filter-expression --genotype-filter-name --help --interval-merging-rule --intervals --invalidate-previous-filters --invert-filter-expression --invert-genotype-filter-expression --mask --mask-extension --mask-name --missing-values-evaluate-as-failing --reference --set-filtered-genotype-to-no-call --sites-only-vcf-output --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--output;-O" "--variant;-V" "--add-output-sam-program-record;-add-output-sam-program-record" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-bam-md5;-OBM" "--create-output-variant-index;-OVI" "--create-output-variant-md5;-OVM" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--input;-I" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--lenient;-LE" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--seconds-between-progress-updates;-seconds-between-progress-updates" "--sequence-dictionary;-sequence-dictionary" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--cloud-index-prefetch-buffer;-CIPB" "--cloud-prefetch-buffer;-CPB" "--cluster-size;-cluster" "--cluster-window-size;-window" "--disable-bam-index-caching;-DBIC" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--filter-expression;-filter" "--gcs-max-retries;-gcs-retries" "--genotype-filter-expression;-G-filter" "--genotype-filter-name;-G-filter-name" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--invert-filter-expression;-invfilter" "--invert-genotype-filter-expression;-invG-filter" "--mask;-mask" "--reference;-R" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--output --variant --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --cluster-size --cluster-window-size --disable-bam-index-caching --disable-sequence-dictionary-validation --filter-expression --filter-name --filter-not-in-mask --gcs-max-retries --gcs-project-for-requester-pays --genotype-filter-expression --genotype-filter-name --help --interval-merging-rule --intervals --invalidate-previous-filters --invert-filter-expression --invert-genotype-filter-expression --mask --mask-extension --mask-name --missing-values-evaluate-as-failing --reference --set-filtered-genotype-to-no-call --sites-only-vcf-output --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("String" "String" "boolean" "boolean" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "List[String]" "int" "int" "IntervalSetRule" "boolean" "Boolean" "List[String]" "List[String]" "ValidationStringency" "double" "String" "String" "boolean" "boolean" "LogLevel" "List[File]" "int" "int" "Integer" "Integer" "boolean" "boolean" "List[String]" "List[String]" "boolean" "int" "String" "List[String]" "List[String]" "boolean" "IntervalMergingRule" "List[String]" "boolean" "boolean" "boolean" "FeatureInput[Feature]" "Integer" "String" "Boolean" "String" "boolean" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "InbreedingCoeff" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=() MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=() MAX_OCCURRENCES=() ALL_LEGAL_ARGUMENTS=() ALL_ARGUMENT_VALUE_TYPES=() # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "MetricsReadFilter" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=() MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=() MAX_OCCURRENCES=() ALL_LEGAL_ARGUMENTS=() ALL_ARGUMENT_VALUE_TYPES=() # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "FilterIntervals" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--intervals --output --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --annotated-intervals --arguments_file --extreme-count-filter-maximum-percentile --extreme-count-filter-minimum-percentile --extreme-count-filter-percentage-of-samples --gcs-max-retries --gcs-project-for-requester-pays --help --input --interval-merging-rule --low-count-filter-count-threshold --low-count-filter-percentage-of-samples --maximum-gc-content --maximum-mappability --maximum-segmental-duplication-content --minimum-gc-content --minimum-mappability --minimum-segmental-duplication-content --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--intervals;-L" "--output;-O" "--exclude-intervals;-XL" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--gcs-max-retries;-gcs-retries" "--help;-h" "--input;-I" "--interval-merging-rule;-imr" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--intervals --output --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --annotated-intervals --arguments_file --extreme-count-filter-maximum-percentile --extreme-count-filter-minimum-percentile --extreme-count-filter-percentage-of-samples --gcs-max-retries --gcs-project-for-requester-pays --help --input --interval-merging-rule --low-count-filter-count-threshold --low-count-filter-percentage-of-samples --maximum-gc-content --maximum-mappability --maximum-segmental-duplication-content --minimum-gc-content --minimum-mappability --minimum-segmental-duplication-content --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("List[String]" "File" "List[String]" "String" "int" "int" "IntervalSetRule" "Boolean" "String" "boolean" "boolean" "LogLevel" "File" "List[File]" "double" "double" "double" "int" "String" "boolean" "List[File]" "IntervalMergingRule" "int" "double" "double" "double" "double" "double" "double" "double" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "RevertSam" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--INPUT --OUTPUT --OUTPUT_MAP --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --ATTRIBUTE_TO_CLEAR --help --KEEP_FIRST_DUPLICATE --LIBRARY_NAME --MAX_DISCARD_FRACTION --OUTPUT_BY_READGROUP --OUTPUT_BY_READGROUP_FILE_FORMAT --REMOVE_ALIGNMENT_INFORMATION --REMOVE_DUPLICATE_INFORMATION --RESTORE_ORIGINAL_QUALITIES --SAMPLE_ALIAS --SANITIZE --SORT_ORDER --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=("--OUTPUT;OUTPUT_MAP,OM" "--OUTPUT_MAP;OUTPUT" ) SYNONYMOUS_ARGS=("--INPUT;-I" "--OUTPUT;-O" "--OUTPUT_MAP;-OM" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--help;-h" "--LIBRARY_NAME;-LIB" "--OUTPUT_BY_READGROUP;-OBR" "--OUTPUT_BY_READGROUP_FILE_FORMAT;-OBRFF" "--RESTORE_ORIGINAL_QUALITIES;-OQ" "--SAMPLE_ALIAS;-ALIAS" "--SORT_ORDER;-SO" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--INPUT --OUTPUT --OUTPUT_MAP --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --ATTRIBUTE_TO_CLEAR --help --KEEP_FIRST_DUPLICATE --LIBRARY_NAME --MAX_DISCARD_FRACTION --OUTPUT_BY_READGROUP --OUTPUT_BY_READGROUP_FILE_FORMAT --REMOVE_ALIGNMENT_INFORMATION --REMOVE_DUPLICATE_INFORMATION --RESTORE_ORIGINAL_QUALITIES --SAMPLE_ALIAS --SANITIZE --SORT_ORDER --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "File" "File" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "List[File]" "List[String]" "boolean" "boolean" "String" "double" "boolean" "FileType" "boolean" "boolean" "boolean" "String" "boolean" "SortOrder" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "CountReads" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--input --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --reference --sites-only-vcf-output --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--input;-I" "--add-output-sam-program-record;-add-output-sam-program-record" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-bam-md5;-OBM" "--create-output-variant-index;-OVI" "--create-output-variant-md5;-OVM" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--lenient;-LE" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--seconds-between-progress-updates;-seconds-between-progress-updates" "--sequence-dictionary;-sequence-dictionary" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--cloud-index-prefetch-buffer;-CIPB" "--cloud-prefetch-buffer;-CPB" "--disable-bam-index-caching;-DBIC" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--reference;-R" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--input --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --reference --sites-only-vcf-output --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("List[String]" "boolean" "boolean" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "int" "int" "IntervalSetRule" "boolean" "Boolean" "List[String]" "List[String]" "ValidationStringency" "double" "String" "String" "boolean" "boolean" "LogLevel" "List[File]" "int" "int" "boolean" "boolean" "int" "String" "boolean" "IntervalMergingRule" "List[String]" "String" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "UniqueAltReadCount" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=() MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=() MAX_OCCURRENCES=() ALL_LEGAL_ARGUMENTS=() ALL_ARGUMENT_VALUE_TYPES=() # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "MeanQualityByCycle" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--CHART_OUTPUT --INPUT --OUTPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --ALIGNED_READS_ONLY --arguments_file --ASSUME_SORTED --help --PF_READS_ONLY --STOP_AFTER --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--CHART_OUTPUT;-CHART" "--INPUT;-I" "--OUTPUT;-O" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--ASSUME_SORTED;-AS" "--help;-h" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--CHART_OUTPUT --INPUT --OUTPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --ALIGNED_READS_ONLY --arguments_file --ASSUME_SORTED --help --PF_READS_ONLY --STOP_AFTER --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "File" "File" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "boolean" "List[File]" "boolean" "boolean" "boolean" "long" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "VcfFormatConverter" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--INPUT --OUTPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --REQUIRE_INDEX --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--INPUT;-I" "--OUTPUT;-O" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--help;-h" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--INPUT --OUTPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --REQUIRE_INDEX --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "File" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "List[File]" "boolean" "Boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "FilterByOrientationBias" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--output --pre-adapter-detail-file --variant --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --artifact-modes --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --reference --sites-only-vcf-output --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--output;-O" "--pre-adapter-detail-file;-P" "--variant;-V" "--add-output-sam-program-record;-add-output-sam-program-record" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-bam-md5;-OBM" "--create-output-variant-index;-OVI" "--create-output-variant-md5;-OVM" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--input;-I" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--lenient;-LE" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--seconds-between-progress-updates;-seconds-between-progress-updates" "--sequence-dictionary;-sequence-dictionary" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--artifact-modes;-AM" "--cloud-index-prefetch-buffer;-CIPB" "--cloud-prefetch-buffer;-CPB" "--disable-bam-index-caching;-DBIC" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--reference;-R" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--output --pre-adapter-detail-file --variant --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --artifact-modes --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --reference --sites-only-vcf-output --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "File" "String" "boolean" "boolean" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "List[String]" "int" "int" "IntervalSetRule" "boolean" "Boolean" "List[String]" "List[String]" "ValidationStringency" "double" "String" "String" "boolean" "boolean" "LogLevel" "List[File]" "List[String]" "int" "int" "boolean" "boolean" "int" "String" "boolean" "IntervalMergingRule" "List[String]" "String" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "VariantsToTable" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--output --variant --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --fields --gcs-max-retries --gcs-project-for-requester-pays --genotype-fields --help --interval-merging-rule --intervals --reference --sites-only-vcf-output --split-multi-allelic --version --error-if-missing-data --moltenize --show-filtered --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--output;-O" "--variant;-V" "--add-output-sam-program-record;-add-output-sam-program-record" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-bam-md5;-OBM" "--create-output-variant-index;-OVI" "--create-output-variant-md5;-OVM" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--input;-I" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--lenient;-LE" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--seconds-between-progress-updates;-seconds-between-progress-updates" "--sequence-dictionary;-sequence-dictionary" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--cloud-index-prefetch-buffer;-CIPB" "--cloud-prefetch-buffer;-CPB" "--disable-bam-index-caching;-DBIC" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--fields;-F" "--gcs-max-retries;-gcs-retries" "--genotype-fields;-GF" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--reference;-R" "--split-multi-allelic;-SMA" "--error-if-missing-data;-EMD" "--moltenize;-moltenize" "--show-filtered;-raw" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--output --variant --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --fields --gcs-max-retries --gcs-project-for-requester-pays --genotype-fields --help --interval-merging-rule --intervals --reference --sites-only-vcf-output --split-multi-allelic --version --error-if-missing-data --moltenize --show-filtered --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("String" "String" "boolean" "boolean" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "List[String]" "int" "int" "IntervalSetRule" "boolean" "Boolean" "List[String]" "List[String]" "ValidationStringency" "double" "String" "String" "boolean" "boolean" "LogLevel" "List[File]" "int" "int" "boolean" "boolean" "List[String]" "int" "String" "List[String]" "boolean" "IntervalMergingRule" "List[String]" "String" "boolean" "boolean" "boolean" "boolean" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "CollectRrbsMetrics" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--INPUT --METRICS_FILE_PREFIX --REFERENCE --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --ASSUME_SORTED --C_QUALITY_THRESHOLD --help --MAX_MISMATCH_RATE --METRIC_ACCUMULATION_LEVEL --MINIMUM_READ_LENGTH --NEXT_BASE_QUALITY_THRESHOLD --SEQUENCE_NAMES --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--INPUT;-I" "--METRICS_FILE_PREFIX;-M" "--REFERENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--ASSUME_SORTED;-AS" "--help;-h" "--METRIC_ACCUMULATION_LEVEL;-LEVEL" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--INPUT --METRICS_FILE_PREFIX --REFERENCE --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --ASSUME_SORTED --C_QUALITY_THRESHOLD --help --MAX_MISMATCH_RATE --METRIC_ACCUMULATION_LEVEL --MINIMUM_READ_LENGTH --NEXT_BASE_QUALITY_THRESHOLD --SEQUENCE_NAMES --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "String" "File" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "List[File]" "boolean" "int" "boolean" "double" "Set[MetricAccumulationLevel]" "int" "int" "Set[String]" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "CheckTerminatorBlock" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--INPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--INPUT;-I" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--help;-h" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--INPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "List[File]" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "GatherTranches" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--input --output --gatk-config-file --QUIET --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --gcs-max-retries --gcs-project-for-requester-pays --help --mode --truth-sensitivity-tranche --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--input;-I" "--output;-O" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--gcs-max-retries;-gcs-retries" "--help;-h" "--mode;-mode" "--truth-sensitivity-tranche;-tranche" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--input --output --gatk-config-file --QUIET --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --gcs-max-retries --gcs-project-for-requester-pays --help --mode --truth-sensitivity-tranche --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("List[File]" "File" "String" "Boolean" "String" "boolean" "boolean" "LogLevel" "List[File]" "int" "String" "boolean" "Mode" "List[Double]" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "AlleleFraction" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=() MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=() MAX_OCCURRENCES=() ALL_LEGAL_ARGUMENTS=() ALL_ARGUMENT_VALUE_TYPES=() # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "QualityScoreDistribution" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--CHART_OUTPUT --INPUT --OUTPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --ALIGNED_READS_ONLY --arguments_file --ASSUME_SORTED --help --INCLUDE_NO_CALLS --PF_READS_ONLY --STOP_AFTER --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--CHART_OUTPUT;-CHART" "--INPUT;-I" "--OUTPUT;-O" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--ASSUME_SORTED;-AS" "--help;-h" "--PF_READS_ONLY;-PF" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--CHART_OUTPUT --INPUT --OUTPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --ALIGNED_READS_ONLY --arguments_file --ASSUME_SORTED --help --INCLUDE_NO_CALLS --PF_READS_ONLY --STOP_AFTER --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "File" "File" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "boolean" "List[File]" "boolean" "boolean" "boolean" "boolean" "long" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "FlagStatSpark" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--input --add-output-vcf-command-line --create-output-bam-index --create-output-bam-splitting-index --create-output-variant-index --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --read-filter --read-index --read-validation-stringency --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --bam-partition-size --conf --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --num-reducers --output --output-shard-tmp-dir --program-name --reference --sharded-output --spark-master --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=("--output-shard-tmp-dir;sharded-output" "--sharded-output;output-shard-tmp-dir" ) SYNONYMOUS_ARGS=("--input;-I" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-variant-index;-OVI" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--conf;-conf" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--output;-O" "--reference;-R" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--input --add-output-vcf-command-line --create-output-bam-index --create-output-bam-splitting-index --create-output-variant-index --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --read-filter --read-index --read-validation-stringency --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --bam-partition-size --conf --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --num-reducers --output --output-shard-tmp-dir --program-name --reference --sharded-output --spark-master --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("List[String]" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "int" "int" "IntervalSetRule" "Boolean" "List[String]" "List[String]" "ValidationStringency" "String" "boolean" "boolean" "LogLevel" "List[File]" "long" "List[String]" "boolean" "int" "String" "boolean" "IntervalMergingRule" "List[String]" "int" "String" "String" "String" "String" "boolean" "String" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "NormalizeFasta" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--INPUT --OUTPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --LINE_LENGTH --TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--INPUT;-I" "--OUTPUT;-O" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--help;-h" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--INPUT --OUTPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --LINE_LENGTH --TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "File" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "List[File]" "boolean" "int" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "ValidAlignmentStartReadFilter" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=() MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=() MAX_OCCURRENCES=() ALL_LEGAL_ARGUMENTS=() ALL_ARGUMENT_VALUE_TYPES=() # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "HasReadGroupReadFilter" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=() MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=() MAX_OCCURRENCES=() ALL_LEGAL_ARGUMENTS=() ALL_ARGUMENT_VALUE_TYPES=() # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "MakeSitesOnlyVcf" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--INPUT --OUTPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --SAMPLE --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--INPUT;-I" "--OUTPUT;-O" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--help;-h" "--SAMPLE;-S" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--INPUT --OUTPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --SAMPLE --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "File" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "List[File]" "boolean" "Set[String]" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "BaseQuality" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=() MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=() MAX_OCCURRENCES=() ALL_LEGAL_ARGUMENTS=() ALL_ARGUMENT_VALUE_TYPES=() # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "SplitSamByNumberOfReads" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--INPUT --OUTPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --OUT_PREFIX --SPLIT_TO_N_FILES --SPLIT_TO_N_READS --TOTAL_READS_IN_INPUT --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=("--SPLIT_TO_N_FILES;SPLIT_TO_N_READS" "--SPLIT_TO_N_READS;SPLIT_TO_N_FILES,N_FILES" ) SYNONYMOUS_ARGS=("--INPUT;-I" "--OUTPUT;-O" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--help;-h" "--OUT_PREFIX;-OUT_PREFIX" "--SPLIT_TO_N_FILES;-N_FILES" "--SPLIT_TO_N_READS;-N_READS" "--TOTAL_READS_IN_INPUT;-TOTAL_READS" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--INPUT --OUTPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --OUT_PREFIX --SPLIT_TO_N_FILES --SPLIT_TO_N_READS --TOTAL_READS_IN_INPUT --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "File" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "List[File]" "boolean" "String" "int" "int" "long" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "ExtractIlluminaBarcodes" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--BARCODE --BARCODE_FILE --BASECALLS_DIR --LANE --METRICS_FILE --READ_STRUCTURE --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --COMPRESS_OUTPUTS --help --MAX_MISMATCHES --MAX_NO_CALLS --MIN_MISMATCH_DELTA --MINIMUM_BASE_QUALITY --MINIMUM_QUALITY --NUM_PROCESSORS --OUTPUT_DIR --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=("--BARCODE;BARCODE_FILE" "--BARCODE_FILE;BARCODE" ) SYNONYMOUS_ARGS=("--BASECALLS_DIR;-B" "--LANE;-L" "--METRICS_FILE;-M" "--READ_STRUCTURE;-RS" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--COMPRESS_OUTPUTS;-GZIP" "--help;-h" "--MINIMUM_BASE_QUALITY;-Q" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--BARCODE --BARCODE_FILE --BASECALLS_DIR --LANE --METRICS_FILE --READ_STRUCTURE --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --COMPRESS_OUTPUTS --help --MAX_MISMATCHES --MAX_NO_CALLS --MIN_MISMATCH_DELTA --MINIMUM_BASE_QUALITY --MINIMUM_QUALITY --NUM_PROCESSORS --OUTPUT_DIR --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("List[String]" "File" "File" "Integer" "File" "String" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "List[File]" "boolean" "boolean" "int" "int" "int" "int" "int" "int" "File" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "FindBreakpointEvidenceSpark" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--aligner-index-image --input --kmers-to-ignore --output --add-output-vcf-command-line --create-output-bam-index --create-output-bam-splitting-index --create-output-variant-index --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --read-filter --read-index --read-validation-stringency --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --adapter-sequence --allowed-short-fragment-overhang --arguments_file --assembled-contigs-output-order --assembly-to-mapped-size-ratio-guess --bam-partition-size --breakpoint-evidence-dir --breakpoint-intervals --cleaner-max-copy-number --cleaner-max-intervals --cleaner-min-kmer-count --conf --cross-contigs-to-ignore --disable-sequence-dictionary-validation --exclusion-interval-padding --exclusion-intervals --external-evidence --external-evidence-uncertainty --external-evidence-weight --fastq-dir --gcs-max-retries --gcs-project-for-requester-pays --help --high-coverage-intervals --high-depth-coverage-factor --high-depth-coverage-peak-factor --include-mapping-location --interval-merging-rule --interval-only-assembly --intervals --kmer-intervals --kmer-max-dust-score --k-size --max-fastq-size --max-tracked-fragment-length --min-coherent-evidence-coverage-ratio --min-evidence-coverage-ratio --min-evidence-mapq --min-evidence-match-length --min-kmers-per-interval --num-reducers --output-shard-tmp-dir --program-name --qname-intervals-for-assembly --qname-intervals-mapped --read-metadata --reference --run-without-gaps-annotation --run-without-umap-s100-annotation --sharded-output --spark-master --sv-evidence-filter-model-file --sv-evidence-filter-threshold-probability --sv-evidence-filter-type --sv-genome-gaps-file --sv-genome-umap-s100-file --target-link-file --unfiltered-breakpoint-evidence-dir --version --write-gfas --expand-assembly-graph --pop-variant-bubbles --remove-shadowed-contigs --showHidden --z-dropoff ) MUTUALLY_EXCLUSIVE_ARGS=("--output-shard-tmp-dir;sharded-output" "--sharded-output;output-shard-tmp-dir" ) SYNONYMOUS_ARGS=("--input;-I" "--output;-O" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-variant-index;-OVI" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--assembled-contigs-output-order;-sort" "--conf;-conf" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--reference;-R" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--aligner-index-image --input --kmers-to-ignore --output --add-output-vcf-command-line --create-output-bam-index --create-output-bam-splitting-index --create-output-variant-index --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --read-filter --read-index --read-validation-stringency --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --adapter-sequence --allowed-short-fragment-overhang --arguments_file --assembled-contigs-output-order --assembly-to-mapped-size-ratio-guess --bam-partition-size --breakpoint-evidence-dir --breakpoint-intervals --cleaner-max-copy-number --cleaner-max-intervals --cleaner-min-kmer-count --conf --cross-contigs-to-ignore --disable-sequence-dictionary-validation --exclusion-interval-padding --exclusion-intervals --external-evidence --external-evidence-uncertainty --external-evidence-weight --fastq-dir --gcs-max-retries --gcs-project-for-requester-pays --help --high-coverage-intervals --high-depth-coverage-factor --high-depth-coverage-peak-factor --include-mapping-location --interval-merging-rule --interval-only-assembly --intervals --kmer-intervals --kmer-max-dust-score --k-size --max-fastq-size --max-tracked-fragment-length --min-coherent-evidence-coverage-ratio --min-evidence-coverage-ratio --min-evidence-mapq --min-evidence-match-length --min-kmers-per-interval --num-reducers --output-shard-tmp-dir --program-name --qname-intervals-for-assembly --qname-intervals-mapped --read-metadata --reference --run-without-gaps-annotation --run-without-umap-s100-annotation --sharded-output --spark-master --sv-evidence-filter-model-file --sv-evidence-filter-threshold-probability --sv-evidence-filter-type --sv-genome-gaps-file --sv-genome-umap-s100-file --target-link-file --unfiltered-breakpoint-evidence-dir --version --write-gfas --expand-assembly-graph --pop-variant-bubbles --remove-shadowed-contigs --showHidden --z-dropoff ) ALL_ARGUMENT_VALUE_TYPES=("String" "List[String]" "String" "String" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "int" "int" "IntervalSetRule" "Boolean" "List[String]" "List[String]" "ValidationStringency" "String" "boolean" "boolean" "LogLevel" "String" "int" "List[File]" "SortOrder" "int" "long" "String" "String" "int" "int" "int" "List[String]" "String" "boolean" "int" "String" "String" "int" "int" "String" "int" "String" "boolean" "String" "int" "int" "boolean" "IntervalMergingRule" "boolean" "List[String]" "String" "int" "int" "int" "int" "double" "double" "int" "int" "int" "int" "String" "String" "String" "String" "String" "String" "boolean" "boolean" "boolean" "String" "String" "double" "SvEvidenceFilterType" "String" "String" "String" "String" "boolean" "boolean" "boolean" "boolean" "boolean" "boolean" "int" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "CalculateContamination" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--input --output --gatk-config-file --QUIET --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --gcs-max-retries --gcs-project-for-requester-pays --help --high-coverage-ratio-threshold --low-coverage-ratio-threshold --matched-normal --tumor-segmentation --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--input;-I" "--output;-O" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--gcs-max-retries;-gcs-retries" "--help;-h" "--matched-normal;-matched" "--tumor-segmentation;-segments" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--input --output --gatk-config-file --QUIET --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --gcs-max-retries --gcs-project-for-requester-pays --help --high-coverage-ratio-threshold --low-coverage-ratio-threshold --matched-normal --tumor-segmentation --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "File" "String" "Boolean" "String" "boolean" "boolean" "LogLevel" "List[File]" "int" "String" "boolean" "double" "double" "File" "File" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "CombineGVCFs" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--output --reference --variant --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --annotation --annotation-group --annotations-to-exclude --arguments_file --break-bands-at-multiples-of --cloud-index-prefetch-buffer --cloud-prefetch-buffer --convert-to-base-pair-resolution --dbsnp --disable-bam-index-caching --disable-sequence-dictionary-validation --founder-id --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --pedigree --sites-only-vcf-output --version --disable-tool-default-annotations --enable-all-annotations --ignore-variants-starting-outside-interval --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--output;-O" "--reference;-R" "--variant;-V" "--add-output-sam-program-record;-add-output-sam-program-record" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-bam-md5;-OBM" "--create-output-variant-index;-OVI" "--create-output-variant-md5;-OVM" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--input;-I" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--lenient;-LE" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--seconds-between-progress-updates;-seconds-between-progress-updates" "--sequence-dictionary;-sequence-dictionary" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--annotation;-A" "--annotation-group;-G" "--annotations-to-exclude;-AX" "--cloud-index-prefetch-buffer;-CIPB" "--cloud-prefetch-buffer;-CPB" "--dbsnp;-D" "--disable-bam-index-caching;-DBIC" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--founder-id;-founder-id" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--pedigree;-ped" "--disable-tool-default-annotations;-disable-tool-default-annotations" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--output --reference --variant --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --annotation --annotation-group --annotations-to-exclude --arguments_file --break-bands-at-multiples-of --cloud-index-prefetch-buffer --cloud-prefetch-buffer --convert-to-base-pair-resolution --dbsnp --disable-bam-index-caching --disable-sequence-dictionary-validation --founder-id --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --pedigree --sites-only-vcf-output --version --disable-tool-default-annotations --enable-all-annotations --ignore-variants-starting-outside-interval --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "String" "List[String]" "boolean" "boolean" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "List[String]" "int" "int" "IntervalSetRule" "boolean" "Boolean" "List[String]" "List[String]" "ValidationStringency" "double" "String" "String" "boolean" "boolean" "LogLevel" "List[String]" "List[String]" "List[String]" "List[File]" "int" "int" "int" "boolean" "FeatureInput[VariantContext]" "boolean" "boolean" "List[String]" "int" "String" "boolean" "IntervalMergingRule" "List[String]" "File" "boolean" "boolean" "boolean" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "FixMisencodedBaseQualityReads" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--input --output --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --reference --sites-only-vcf-output --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--input;-I" "--output;-O" "--add-output-sam-program-record;-add-output-sam-program-record" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-bam-md5;-OBM" "--create-output-variant-index;-OVI" "--create-output-variant-md5;-OVM" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--lenient;-LE" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--seconds-between-progress-updates;-seconds-between-progress-updates" "--sequence-dictionary;-sequence-dictionary" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--cloud-index-prefetch-buffer;-CIPB" "--cloud-prefetch-buffer;-CPB" "--disable-bam-index-caching;-DBIC" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--reference;-R" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--input --output --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --reference --sites-only-vcf-output --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("List[String]" "File" "boolean" "boolean" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "int" "int" "IntervalSetRule" "boolean" "Boolean" "List[String]" "List[String]" "ValidationStringency" "double" "String" "String" "boolean" "boolean" "LogLevel" "List[File]" "int" "int" "boolean" "boolean" "int" "String" "boolean" "IntervalMergingRule" "List[String]" "String" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "RevertOriginalBaseQualitiesAndAddMateCigar" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--INPUT --OUTPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --MAX_RECORDS_TO_EXAMINE --RESTORE_ORIGINAL_QUALITIES --SORT_ORDER --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--INPUT;-I" "--OUTPUT;-O" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--help;-h" "--RESTORE_ORIGINAL_QUALITIES;-OQ" "--SORT_ORDER;-SO" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--INPUT --OUTPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --MAX_RECORDS_TO_EXAMINE --RESTORE_ORIGINAL_QUALITIES --SORT_ORDER --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "File" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "List[File]" "boolean" "int" "boolean" "SortOrder" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "BwaAndMarkDuplicatesPipelineSpark" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--input --output --reference --add-output-vcf-command-line --create-output-bam-index --create-output-bam-splitting-index --create-output-variant-index --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --read-filter --read-index --read-validation-stringency --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --bam-partition-size --bwa-mem-index-image --conf --do-not-mark-unmapped-mates --duplicate-scoring-strategy --duplicate-tagging-policy --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --num-reducers --output-shard-tmp-dir --program-name --remove-all-duplicates --remove-sequencing-duplicates --sharded-output --single-end-alignment --spark-master --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=("--duplicate-tagging-policy;remove-all-duplicates,remove-sequencing-duplicates" "--output-shard-tmp-dir;sharded-output" "--remove-all-duplicates;duplicate-tagging-policy,remove-sequencing-duplicates" "--remove-sequencing-duplicates;duplicate-tagging-policy,remove-all-duplicates" "--sharded-output;output-shard-tmp-dir" ) SYNONYMOUS_ARGS=("--input;-I" "--output;-O" "--reference;-R" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-variant-index;-OVI" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--bwa-mem-index-image;-image" "--conf;-conf" "--duplicate-scoring-strategy;-DS" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--single-end-alignment;-se" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--input --output --reference --add-output-vcf-command-line --create-output-bam-index --create-output-bam-splitting-index --create-output-variant-index --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --read-filter --read-index --read-validation-stringency --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --bam-partition-size --bwa-mem-index-image --conf --do-not-mark-unmapped-mates --duplicate-scoring-strategy --duplicate-tagging-policy --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --num-reducers --output-shard-tmp-dir --program-name --remove-all-duplicates --remove-sequencing-duplicates --sharded-output --single-end-alignment --spark-master --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("List[String]" "String" "String" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "int" "int" "IntervalSetRule" "Boolean" "List[String]" "List[String]" "ValidationStringency" "String" "boolean" "boolean" "LogLevel" "List[File]" "long" "String" "List[String]" "boolean" "MarkDuplicatesScoringStrategy" "DuplicateTaggingPolicy" "int" "String" "boolean" "IntervalMergingRule" "List[String]" "int" "String" "String" "boolean" "boolean" "boolean" "boolean" "String" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "AddOATag" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--INPUT --OUTPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --INTERVAL_LIST --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--INPUT;-I" "--OUTPUT;-O" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--help;-h" "--INTERVAL_LIST;-L" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--INPUT --OUTPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --INTERVAL_LIST --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("String" "String" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "List[File]" "boolean" "File" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "Funcotator" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--data-sources-path --output --output-file-format --reference --ref-version --variant --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --annotation-default --annotation-override --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --exclude-field --five-prime-flank-size --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --lookahead-cache-bp --remove-filtered-variants --sites-only-vcf-output --three-prime-flank-size --transcript-list --transcript-selection-mode --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--output;-O" "--reference;-R" "--variant;-V" "--add-output-sam-program-record;-add-output-sam-program-record" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-bam-md5;-OBM" "--create-output-variant-index;-OVI" "--create-output-variant-md5;-OVM" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--input;-I" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--lenient;-LE" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--seconds-between-progress-updates;-seconds-between-progress-updates" "--sequence-dictionary;-sequence-dictionary" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--cloud-index-prefetch-buffer;-CIPB" "--cloud-prefetch-buffer;-CPB" "--disable-bam-index-caching;-DBIC" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--data-sources-path --output --output-file-format --reference --ref-version --variant --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --annotation-default --annotation-override --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --exclude-field --five-prime-flank-size --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --lookahead-cache-bp --remove-filtered-variants --sites-only-vcf-output --three-prime-flank-size --transcript-list --transcript-selection-mode --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("List[String]" "File" "OutputFormatType" "String" "String" "String" "boolean" "boolean" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "List[String]" "int" "int" "IntervalSetRule" "boolean" "Boolean" "List[String]" "List[String]" "ValidationStringency" "double" "String" "String" "boolean" "boolean" "LogLevel" "List[String]" "List[String]" "List[File]" "int" "int" "boolean" "boolean" "Set[String]" "int" "int" "String" "boolean" "IntervalMergingRule" "List[String]" "int" "boolean" "boolean" "int" "Set[String]" "TranscriptSelectionMode" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "MappingQualityAvailableReadFilter" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=() MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=() MAX_OCCURRENCES=() ALL_LEGAL_ARGUMENTS=() ALL_ARGUMENT_VALUE_TYPES=() # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "PathSeqPipelineSpark" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--input --microbe-bwa-image --microbe-fasta --scores-output --taxonomy-file --add-output-vcf-command-line --create-output-bam-index --create-output-bam-splitting-index --create-output-variant-index --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --read-filter --read-index --read-validation-stringency --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --bam-partition-size --bwa-score-threshold --conf --disable-sequence-dictionary-validation --divide-by-genome-length --dust-mask-quality --dust-t --dust-window --filter-bwa-image --filter-bwa-seed-length --filter-duplicates --filter-metrics --gcs-max-retries --gcs-project-for-requester-pays --help --host-kmer-thresh --host-min-identity --identity-margin --interval-merging-rule --intervals --is-host-aligned --kmer-file --max-adapter-mismatches --max-alternate-hits --max-masked-bases --microbe-min-seed-length --min-adapter-length --min-base-quality --min-clipped-read-length --min-score-identity --not-normalized-by-kingdom --num-reducers --output --output-shard-tmp-dir --pipeline-reads-per-partition --program-name --quality-threshold --readsPerPartitionOutput --reference --score-metrics --score-warnings --sharded-output --skip-quality-filters --spark-master --version --filter-reads-per-partition --score-reads-per-partition-estimate --showHidden --skip-pre-bwa-repartition ) MUTUALLY_EXCLUSIVE_ARGS=("--output-shard-tmp-dir;sharded-output" "--sharded-output;output-shard-tmp-dir" ) SYNONYMOUS_ARGS=("--input;-I" "--microbe-bwa-image;-MI" "--microbe-fasta;-MF" "--scores-output;-SO" "--taxonomy-file;-T" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-variant-index;-OVI" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--bwa-score-threshold;-bwa-score-threshold" "--conf;-conf" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--divide-by-genome-length;-divide-by-genome-length" "--dust-mask-quality;-dust-mask-quality" "--dust-t;-dust-t" "--dust-window;-dust-window" "--filter-bwa-image;-FI" "--filter-bwa-seed-length;-filter-bwa-seed-length" "--filter-duplicates;-filter-duplicates" "--filter-metrics;-FM" "--gcs-max-retries;-gcs-retries" "--help;-h" "--host-kmer-thresh;-host-kmer-thresh" "--host-min-identity;-host-min-identity" "--identity-margin;-identity-margin" "--interval-merging-rule;-imr" "--intervals;-L" "--is-host-aligned;-is-host-aligned" "--kmer-file;-K" "--max-adapter-mismatches;-max-adapter-mismatches" "--max-alternate-hits;-max-alternate-hits" "--max-masked-bases;-max-masked-bases" "--microbe-min-seed-length;-microbe-min-seed-length" "--min-adapter-length;-min-adapter-length" "--min-base-quality;-min-base-quality" "--min-clipped-read-length;-min-clipped-read-length" "--min-score-identity;-min-score-identity" "--not-normalized-by-kingdom;-not-normalized-by-kingdom" "--output;-O" "--pipeline-reads-per-partition;-pipeline-reads-per-partition" "--quality-threshold;-quality-threshold" "--reference;-R" "--score-metrics;-SM" "--score-warnings;-SW" "--skip-quality-filters;-skip-quality-filters" "--filter-reads-per-partition;-filter-reads-per-partition" "--score-reads-per-partition-estimate;-score-reads-per-partition-estimate" "--showHidden;-showHidden" "--skip-pre-bwa-repartition;-skip-pre-bwa-repartition" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--input --microbe-bwa-image --microbe-fasta --scores-output --taxonomy-file --add-output-vcf-command-line --create-output-bam-index --create-output-bam-splitting-index --create-output-variant-index --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --read-filter --read-index --read-validation-stringency --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --bam-partition-size --bwa-score-threshold --conf --disable-sequence-dictionary-validation --divide-by-genome-length --dust-mask-quality --dust-t --dust-window --filter-bwa-image --filter-bwa-seed-length --filter-duplicates --filter-metrics --gcs-max-retries --gcs-project-for-requester-pays --help --host-kmer-thresh --host-min-identity --identity-margin --interval-merging-rule --intervals --is-host-aligned --kmer-file --max-adapter-mismatches --max-alternate-hits --max-masked-bases --microbe-min-seed-length --min-adapter-length --min-base-quality --min-clipped-read-length --min-score-identity --not-normalized-by-kingdom --num-reducers --output --output-shard-tmp-dir --pipeline-reads-per-partition --program-name --quality-threshold --readsPerPartitionOutput --reference --score-metrics --score-warnings --sharded-output --skip-quality-filters --spark-master --version --filter-reads-per-partition --score-reads-per-partition-estimate --showHidden --skip-pre-bwa-repartition ) ALL_ARGUMENT_VALUE_TYPES=("List[String]" "String" "String" "String" "String" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "int" "int" "IntervalSetRule" "Boolean" "List[String]" "List[String]" "ValidationStringency" "String" "boolean" "boolean" "LogLevel" "List[File]" "long" "int" "List[String]" "boolean" "boolean" "int" "double" "int" "String" "int" "boolean" "String" "int" "String" "boolean" "int" "int" "double" "IntervalMergingRule" "List[String]" "boolean" "String" "int" "int" "int" "int" "int" "int" "int" "double" "boolean" "int" "String" "String" "int" "String" "int" "int" "String" "String" "String" "boolean" "boolean" "String" "boolean" "int" "int" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "CollectHsMetrics" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--BAIT_INTERVALS --INPUT --OUTPUT --TARGET_INTERVALS --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --ALLELE_FRACTION --arguments_file --BAIT_SET_NAME --CLIP_OVERLAPPING_READS --COVERAGE_CAP --help --METRIC_ACCUMULATION_LEVEL --MINIMUM_BASE_QUALITY --MINIMUM_MAPPING_QUALITY --NEAR_DISTANCE --PER_BASE_COVERAGE --PER_TARGET_COVERAGE --SAMPLE_SIZE --THEORETICAL_SENSITIVITY_OUTPUT --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--BAIT_INTERVALS;-BI" "--INPUT;-I" "--OUTPUT;-O" "--TARGET_INTERVALS;-TI" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--BAIT_SET_NAME;-N" "--COVERAGE_CAP;-covMax" "--help;-h" "--METRIC_ACCUMULATION_LEVEL;-LEVEL" "--MINIMUM_BASE_QUALITY;-Q" "--MINIMUM_MAPPING_QUALITY;-MQ" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--BAIT_INTERVALS --INPUT --OUTPUT --TARGET_INTERVALS --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --ALLELE_FRACTION --arguments_file --BAIT_SET_NAME --CLIP_OVERLAPPING_READS --COVERAGE_CAP --help --METRIC_ACCUMULATION_LEVEL --MINIMUM_BASE_QUALITY --MINIMUM_MAPPING_QUALITY --NEAR_DISTANCE --PER_BASE_COVERAGE --PER_TARGET_COVERAGE --SAMPLE_SIZE --THEORETICAL_SENSITIVITY_OUTPUT --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("List[File]" "File" "File" "List[File]" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "List[Double]" "List[File]" "String" "boolean" "int" "boolean" "Set[MetricAccumulationLevel]" "int" "int" "int" "File" "File" "int" "File" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "ValidateVariants" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--variant --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --dbsnp --disable-bam-index-caching --disable-sequence-dictionary-validation --do-not-validate-filtered-records --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --reference --sites-only-vcf-output --validate-GVCF --validation-type-to-exclude --version --warn-on-errors --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=("--do-not-validate-filtered-records;validate-GVCF" "--validate-GVCF;do-not-validate-filtered-records" ) SYNONYMOUS_ARGS=("--variant;-V" "--add-output-sam-program-record;-add-output-sam-program-record" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-bam-md5;-OBM" "--create-output-variant-index;-OVI" "--create-output-variant-md5;-OVM" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--input;-I" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--lenient;-LE" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--seconds-between-progress-updates;-seconds-between-progress-updates" "--sequence-dictionary;-sequence-dictionary" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--cloud-index-prefetch-buffer;-CIPB" "--cloud-prefetch-buffer;-CPB" "--dbsnp;-D" "--disable-bam-index-caching;-DBIC" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--do-not-validate-filtered-records;-do-not-validate-filtered-records" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--reference;-R" "--validate-GVCF;-gvcf" "--validation-type-to-exclude;-Xtype" "--warn-on-errors;-warn-on-errors" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--variant --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --dbsnp --disable-bam-index-caching --disable-sequence-dictionary-validation --do-not-validate-filtered-records --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --reference --sites-only-vcf-output --validate-GVCF --validation-type-to-exclude --version --warn-on-errors --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("String" "boolean" "boolean" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "List[String]" "int" "int" "IntervalSetRule" "boolean" "Boolean" "List[String]" "List[String]" "ValidationStringency" "double" "String" "String" "boolean" "boolean" "LogLevel" "List[File]" "int" "int" "FeatureInput[VariantContext]" "boolean" "boolean" "Boolean" "int" "String" "boolean" "IntervalMergingRule" "List[String]" "String" "boolean" "Boolean" "List[ValidationType]" "boolean" "Boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "FilterMutectCalls" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--output --variant --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --contamination-estimate --contamination-table --disable-bam-index-caching --disable-sequence-dictionary-validation --distance-on-haplotype --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --lod-divided-by-depth --log-somatic-prior --long-indel-length --max-alt-allele-count --max-contamination-probability --max-events-in-region --max-germline-posterior --max-median-fragment-length-difference --max-strand-artifact-probability --min-median-base-quality --min-median-mapping-quality --min-median-read-position --min-pcr-slippage-size --min-strand-artifact-allele-fraction --mitochondria-mode --non-mt-alts-divided-by-alts --normal-artifact-lod --normal-p-value-threshold --n-ratio --orientation-bias-fdr --pcr-slippage-p-value --pcr-slippage-rate --reference --sites-only-vcf-output --stats --strict-strand-bias --tumor-lod --tumor-segmentation --unique-alt-read-count --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--output;-O" "--variant;-V" "--add-output-sam-program-record;-add-output-sam-program-record" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-bam-md5;-OBM" "--create-output-variant-index;-OVI" "--create-output-variant-md5;-OVM" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--input;-I" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--lenient;-LE" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--seconds-between-progress-updates;-seconds-between-progress-updates" "--sequence-dictionary;-sequence-dictionary" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--cloud-index-prefetch-buffer;-CIPB" "--cloud-prefetch-buffer;-CPB" "--disable-bam-index-caching;-DBIC" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--max-strand-artifact-probability;-strand-prob" "--min-strand-artifact-allele-fraction;-strand-af" "--reference;-R" "--unique-alt-read-count;-unique" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--output --variant --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --contamination-estimate --contamination-table --disable-bam-index-caching --disable-sequence-dictionary-validation --distance-on-haplotype --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --lod-divided-by-depth --log-somatic-prior --long-indel-length --max-alt-allele-count --max-contamination-probability --max-events-in-region --max-germline-posterior --max-median-fragment-length-difference --max-strand-artifact-probability --min-median-base-quality --min-median-mapping-quality --min-median-read-position --min-pcr-slippage-size --min-strand-artifact-allele-fraction --mitochondria-mode --non-mt-alts-divided-by-alts --normal-artifact-lod --normal-p-value-threshold --n-ratio --orientation-bias-fdr --pcr-slippage-p-value --pcr-slippage-rate --reference --sites-only-vcf-output --stats --strict-strand-bias --tumor-lod --tumor-segmentation --unique-alt-read-count --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("String" "String" "boolean" "boolean" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "List[String]" "int" "int" "IntervalSetRule" "boolean" "Boolean" "List[String]" "List[String]" "ValidationStringency" "double" "String" "String" "boolean" "boolean" "LogLevel" "List[File]" "int" "int" "double" "List[File]" "boolean" "boolean" "int" "int" "String" "boolean" "IntervalMergingRule" "List[String]" "double" "double" "int" "int" "double" "int" "double" "int" "double" "int" "int" "int" "int" "double" "boolean" "double" "double" "double" "double" "double" "double" "double" "String" "boolean" "File" "boolean" "double" "List[File]" "int" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "CrosscheckFingerprints" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--HAPLOTYPE_MAP --INPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --ALLOW_DUPLICATE_READS --arguments_file --CALCULATE_TUMOR_AWARE_RESULTS --CROSSCHECK_BY --CROSSCHECK_MODE --EXIT_CODE_WHEN_MISMATCH --EXPECT_ALL_GROUPS_TO_MATCH --GENOTYPING_ERROR_RATE --help --INPUT_SAMPLE_MAP --LOD_THRESHOLD --LOSS_OF_HET_RATE --MATRIX_OUTPUT --NUM_THREADS --OUTPUT --OUTPUT_ERRORS_ONLY --SECOND_INPUT --SECOND_INPUT_SAMPLE_MAP --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=("--MATRIX_OUTPUT;SECOND_INPUT" "--SECOND_INPUT;MATRIX_OUTPUT,MO" ) SYNONYMOUS_ARGS=("--HAPLOTYPE_MAP;-H" "--INPUT;-I" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--help;-h" "--LOD_THRESHOLD;-LOD" "--MATRIX_OUTPUT;-MO" "--OUTPUT;-O" "--SECOND_INPUT;-SI" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--HAPLOTYPE_MAP --INPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --ALLOW_DUPLICATE_READS --arguments_file --CALCULATE_TUMOR_AWARE_RESULTS --CROSSCHECK_BY --CROSSCHECK_MODE --EXIT_CODE_WHEN_MISMATCH --EXPECT_ALL_GROUPS_TO_MATCH --GENOTYPING_ERROR_RATE --help --INPUT_SAMPLE_MAP --LOD_THRESHOLD --LOSS_OF_HET_RATE --MATRIX_OUTPUT --NUM_THREADS --OUTPUT --OUTPUT_ERRORS_ONLY --SECOND_INPUT --SECOND_INPUT_SAMPLE_MAP --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "List[String]" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "boolean" "List[File]" "boolean" "DataType" "CrosscheckMode" "int" "boolean" "double" "boolean" "File" "double" "double" "File" "int" "File" "boolean" "List[String]" "File" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "SplitIntervals" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--output --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --extension --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --reference --scatter-count --sites-only-vcf-output --subdivision-mode --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--output;-O" "--add-output-sam-program-record;-add-output-sam-program-record" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-bam-md5;-OBM" "--create-output-variant-index;-OVI" "--create-output-variant-md5;-OVM" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--input;-I" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--lenient;-LE" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--seconds-between-progress-updates;-seconds-between-progress-updates" "--sequence-dictionary;-sequence-dictionary" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--cloud-index-prefetch-buffer;-CIPB" "--cloud-prefetch-buffer;-CPB" "--disable-bam-index-caching;-DBIC" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--reference;-R" "--scatter-count;-scatter" "--subdivision-mode;-mode" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--output --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --extension --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --reference --scatter-count --sites-only-vcf-output --subdivision-mode --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "boolean" "boolean" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "List[String]" "int" "int" "IntervalSetRule" "boolean" "Boolean" "List[String]" "List[String]" "ValidationStringency" "double" "String" "String" "boolean" "boolean" "LogLevel" "List[File]" "int" "int" "boolean" "boolean" "String" "int" "String" "boolean" "IntervalMergingRule" "List[String]" "String" "int" "boolean" "IntervalListScatterMode" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "FragmentLengthReadFilter" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--max-fragment-length ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=(0 ) MAX_OCCURRENCES=(2147483647 ) ALL_LEGAL_ARGUMENTS=(--max-fragment-length ) ALL_ARGUMENT_VALUE_TYPES=("int" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "AmbiguousBaseReadFilter" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--ambig-filter-bases --ambig-filter-frac ) MUTUALLY_EXCLUSIVE_ARGS=("--ambig-filter-bases;ambig-filter-frac" "--ambig-filter-frac;ambig-filter-bases" ) SYNONYMOUS_ARGS=() MIN_OCCURRENCES=(0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--ambig-filter-bases --ambig-filter-frac ) ALL_ARGUMENT_VALUE_TYPES=("Integer" "double" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "ApplyBQSRSpark" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--bqsr-recal-file --input --output --add-output-vcf-command-line --create-output-bam-index --create-output-bam-splitting-index --create-output-variant-index --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --read-filter --read-index --read-validation-stringency --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --bam-partition-size --conf --disable-sequence-dictionary-validation --emit-original-quals --gcs-max-retries --gcs-project-for-requester-pays --global-qscore-prior --help --interval-merging-rule --intervals --num-reducers --output-shard-tmp-dir --preserve-qscores-less-than --program-name --quantize-quals --reference --sharded-output --spark-master --use-original-qualities --version --round-down-quantized --showHidden --static-quantized-quals ) MUTUALLY_EXCLUSIVE_ARGS=("--output-shard-tmp-dir;sharded-output" "--quantize-quals;static-quantized-quals,round-down-quantized" "--sharded-output;output-shard-tmp-dir" "--round-down-quantized;quantize-quals" "--static-quantized-quals;quantize-quals" ) SYNONYMOUS_ARGS=("--bqsr-recal-file;-bqsr" "--input;-I" "--output;-O" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-variant-index;-OVI" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--conf;-conf" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--reference;-R" "--use-original-qualities;-OQ" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--bqsr-recal-file --input --output --add-output-vcf-command-line --create-output-bam-index --create-output-bam-splitting-index --create-output-variant-index --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --read-filter --read-index --read-validation-stringency --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --bam-partition-size --conf --disable-sequence-dictionary-validation --emit-original-quals --gcs-max-retries --gcs-project-for-requester-pays --global-qscore-prior --help --interval-merging-rule --intervals --num-reducers --output-shard-tmp-dir --preserve-qscores-less-than --program-name --quantize-quals --reference --sharded-output --spark-master --use-original-qualities --version --round-down-quantized --showHidden --static-quantized-quals ) ALL_ARGUMENT_VALUE_TYPES=("String" "List[String]" "String" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "int" "int" "IntervalSetRule" "Boolean" "List[String]" "List[String]" "ValidationStringency" "String" "boolean" "boolean" "LogLevel" "List[File]" "long" "List[String]" "boolean" "boolean" "int" "String" "double" "boolean" "IntervalMergingRule" "List[String]" "int" "String" "int" "String" "int" "String" "boolean" "String" "Boolean" "boolean" "boolean" "boolean" "List[Integer]" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "CalcMetadataSpark" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--input --output --add-output-vcf-command-line --create-output-bam-index --create-output-bam-splitting-index --create-output-variant-index --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --read-filter --read-index --read-validation-stringency --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --bam-partition-size --conf --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --num-reducers --output-shard-tmp-dir --program-name --reference --sharded-output --spark-master --version --write-as-binary --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=("--output-shard-tmp-dir;sharded-output" "--sharded-output;output-shard-tmp-dir" ) SYNONYMOUS_ARGS=("--input;-I" "--output;-O" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-variant-index;-OVI" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--conf;-conf" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--reference;-R" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--input --output --add-output-vcf-command-line --create-output-bam-index --create-output-bam-splitting-index --create-output-variant-index --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --read-filter --read-index --read-validation-stringency --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --bam-partition-size --conf --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --num-reducers --output-shard-tmp-dir --program-name --reference --sharded-output --spark-master --version --write-as-binary --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("List[String]" "String" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "int" "int" "IntervalSetRule" "Boolean" "List[String]" "List[String]" "ValidationStringency" "String" "boolean" "boolean" "LogLevel" "List[File]" "long" "List[String]" "boolean" "int" "String" "boolean" "IntervalMergingRule" "List[String]" "int" "String" "String" "String" "boolean" "String" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "SortSam" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--INPUT --OUTPUT --SORT_ORDER --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--INPUT;-I" "--OUTPUT;-O" "--SORT_ORDER;-SO" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--help;-h" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--INPUT --OUTPUT --SORT_ORDER --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "File" "SortOrder" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "List[File]" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "OriginalAlignment" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=() MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=() MAX_OCCURRENCES=() ALL_LEGAL_ARGUMENTS=() ALL_ARGUMENT_VALUE_TYPES=() # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "StructuralVariationDiscoveryPipelineSpark" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--aligner-index-image --contig-sam-file --input --kmers-to-ignore --output --reference --add-output-vcf-command-line --create-output-bam-index --create-output-bam-splitting-index --create-output-variant-index --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --read-filter --read-index --read-validation-stringency --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --adapter-sequence --allowed-short-fragment-overhang --arguments_file --assembled-contigs-output-order --assembly-imprecise-evidence-overlap-uncertainty --assembly-to-mapped-size-ratio-guess --bam-partition-size --breakpoint-evidence-dir --breakpoint-intervals --cleaner-max-copy-number --cleaner-max-intervals --cleaner-min-kmer-count --cnv-calls --conf --cross-contigs-to-ignore --disable-sequence-dictionary-validation --exclusion-interval-padding --exclusion-intervals --external-evidence --external-evidence-uncertainty --external-evidence-weight --fastq-dir --gcs-max-retries --gcs-project-for-requester-pays --help --high-coverage-intervals --high-depth-coverage-factor --high-depth-coverage-peak-factor --imprecise-variant-evidence-threshold --include-mapping-location --interval-merging-rule --interval-only-assembly --intervals --kmer-intervals --kmer-max-dust-score --k-size --max-callable-imprecise-deletion-size --max-fastq-size --max-tracked-fragment-length --min-align-length --min-coherent-evidence-coverage-ratio --min-evidence-coverage-ratio --min-evidence-mapq --min-evidence-match-length --min-kmers-per-interval --min-mq --num-reducers --output-shard-tmp-dir --program-name --qname-intervals-for-assembly --qname-intervals-mapped --read-metadata --run-without-gaps-annotation --run-without-umap-s100-annotation --sharded-output --spark-master --sv-evidence-filter-model-file --sv-evidence-filter-threshold-probability --sv-evidence-filter-type --sv-genome-gaps-file --sv-genome-umap-s100-file --target-link-file --truth-interval-padding --unfiltered-breakpoint-evidence-dir --version --write-gfas --debug-mode --expand-assembly-graph --exp-interpret --pop-variant-bubbles --remove-shadowed-contigs --showHidden --z-dropoff ) MUTUALLY_EXCLUSIVE_ARGS=("--output-shard-tmp-dir;sharded-output" "--sharded-output;output-shard-tmp-dir" ) SYNONYMOUS_ARGS=("--input;-I" "--output;-O" "--reference;-R" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-variant-index;-OVI" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--assembled-contigs-output-order;-sort" "--conf;-conf" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--min-mq;-mq" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--aligner-index-image --contig-sam-file --input --kmers-to-ignore --output --reference --add-output-vcf-command-line --create-output-bam-index --create-output-bam-splitting-index --create-output-variant-index --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --read-filter --read-index --read-validation-stringency --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --adapter-sequence --allowed-short-fragment-overhang --arguments_file --assembled-contigs-output-order --assembly-imprecise-evidence-overlap-uncertainty --assembly-to-mapped-size-ratio-guess --bam-partition-size --breakpoint-evidence-dir --breakpoint-intervals --cleaner-max-copy-number --cleaner-max-intervals --cleaner-min-kmer-count --cnv-calls --conf --cross-contigs-to-ignore --disable-sequence-dictionary-validation --exclusion-interval-padding --exclusion-intervals --external-evidence --external-evidence-uncertainty --external-evidence-weight --fastq-dir --gcs-max-retries --gcs-project-for-requester-pays --help --high-coverage-intervals --high-depth-coverage-factor --high-depth-coverage-peak-factor --imprecise-variant-evidence-threshold --include-mapping-location --interval-merging-rule --interval-only-assembly --intervals --kmer-intervals --kmer-max-dust-score --k-size --max-callable-imprecise-deletion-size --max-fastq-size --max-tracked-fragment-length --min-align-length --min-coherent-evidence-coverage-ratio --min-evidence-coverage-ratio --min-evidence-mapq --min-evidence-match-length --min-kmers-per-interval --min-mq --num-reducers --output-shard-tmp-dir --program-name --qname-intervals-for-assembly --qname-intervals-mapped --read-metadata --run-without-gaps-annotation --run-without-umap-s100-annotation --sharded-output --spark-master --sv-evidence-filter-model-file --sv-evidence-filter-threshold-probability --sv-evidence-filter-type --sv-genome-gaps-file --sv-genome-umap-s100-file --target-link-file --truth-interval-padding --unfiltered-breakpoint-evidence-dir --version --write-gfas --debug-mode --expand-assembly-graph --exp-interpret --pop-variant-bubbles --remove-shadowed-contigs --showHidden --z-dropoff ) ALL_ARGUMENT_VALUE_TYPES=("String" "String" "List[String]" "String" "String" "String" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "int" "int" "IntervalSetRule" "Boolean" "List[String]" "List[String]" "ValidationStringency" "String" "boolean" "boolean" "LogLevel" "String" "int" "List[File]" "SortOrder" "int" "int" "long" "String" "String" "int" "int" "int" "String" "List[String]" "String" "boolean" "int" "String" "String" "int" "int" "String" "int" "String" "boolean" "String" "int" "int" "int" "boolean" "IntervalMergingRule" "boolean" "List[String]" "String" "int" "int" "int" "int" "int" "Integer" "double" "double" "int" "int" "int" "Integer" "int" "String" "String" "String" "String" "String" "boolean" "boolean" "boolean" "String" "String" "double" "SvEvidenceFilterType" "String" "String" "String" "int" "String" "boolean" "boolean" "Boolean" "boolean" "Boolean" "boolean" "boolean" "boolean" "int" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "NonZeroReferenceLengthAlignmentReadFilter" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=() MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=() MAX_OCCURRENCES=() ALL_LEGAL_ARGUMENTS=() ALL_ARGUMENT_VALUE_TYPES=() # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "ValidateSamFile" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--INPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --IGNORE --IGNORE_WARNINGS --INDEX_VALIDATION_STRINGENCY --IS_BISULFITE_SEQUENCED --MAX_OPEN_TEMP_FILES --MAX_OUTPUT --MODE --OUTPUT --SKIP_MATE_VALIDATION --VALIDATE_INDEX --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--INPUT;-I" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--help;-h" "--IS_BISULFITE_SEQUENCED;-BISULFITE" "--MAX_OUTPUT;-MO" "--MODE;-M" "--OUTPUT;-O" "--SKIP_MATE_VALIDATION;-SMV" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--INPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --IGNORE --IGNORE_WARNINGS --INDEX_VALIDATION_STRINGENCY --IS_BISULFITE_SEQUENCED --MAX_OPEN_TEMP_FILES --MAX_OUTPUT --MODE --OUTPUT --SKIP_MATE_VALIDATION --VALIDATE_INDEX --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "List[File]" "boolean" "List[Type]" "boolean" "IndexValidationStringency" "boolean" "int" "Integer" "Mode" "File" "boolean" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "CollectGcBiasMetrics" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--CHART_OUTPUT --INPUT --OUTPUT --SUMMARY_OUTPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --ALSO_IGNORE_DUPLICATES --arguments_file --ASSUME_SORTED --help --IS_BISULFITE_SEQUENCED --METRIC_ACCUMULATION_LEVEL --MINIMUM_GENOME_FRACTION --SCAN_WINDOW_SIZE --STOP_AFTER --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--CHART_OUTPUT;-CHART" "--INPUT;-I" "--OUTPUT;-O" "--SUMMARY_OUTPUT;-S" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--ALSO_IGNORE_DUPLICATES;-ALSO_IGNORE_DUPLICATES" "--ASSUME_SORTED;-AS" "--help;-h" "--IS_BISULFITE_SEQUENCED;-BS" "--METRIC_ACCUMULATION_LEVEL;-LEVEL" "--MINIMUM_GENOME_FRACTION;-MGF" "--SCAN_WINDOW_SIZE;-WINDOW_SIZE" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--CHART_OUTPUT --INPUT --OUTPUT --SUMMARY_OUTPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --ALSO_IGNORE_DUPLICATES --arguments_file --ASSUME_SORTED --help --IS_BISULFITE_SEQUENCED --METRIC_ACCUMULATION_LEVEL --MINIMUM_GENOME_FRACTION --SCAN_WINDOW_SIZE --STOP_AFTER --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "File" "File" "File" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "boolean" "List[File]" "boolean" "boolean" "boolean" "Set[MetricAccumulationLevel]" "double" "int" "long" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "SplitVcfs" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--INDEL_OUTPUT --INPUT --SNP_OUTPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --SEQUENCE_DICTIONARY --STRICT --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--INPUT;-I" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--help;-h" "--SEQUENCE_DICTIONARY;-D" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--INDEL_OUTPUT --INPUT --SNP_OUTPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --arguments_file --help --SEQUENCE_DICTIONARY --STRICT --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "File" "File" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "List[File]" "boolean" "File" "Boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "LeftAlignIndels" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--input --output --reference --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --sites-only-vcf-output --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--input;-I" "--output;-O" "--reference;-R" "--add-output-sam-program-record;-add-output-sam-program-record" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-bam-md5;-OBM" "--create-output-variant-index;-OVI" "--create-output-variant-md5;-OVM" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--lenient;-LE" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--seconds-between-progress-updates;-seconds-between-progress-updates" "--sequence-dictionary;-sequence-dictionary" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--cloud-index-prefetch-buffer;-CIPB" "--cloud-prefetch-buffer;-CPB" "--disable-bam-index-caching;-DBIC" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--input --output --reference --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --sites-only-vcf-output --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("List[String]" "String" "String" "boolean" "boolean" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "int" "int" "IntervalSetRule" "boolean" "Boolean" "List[String]" "List[String]" "ValidationStringency" "double" "String" "String" "boolean" "boolean" "LogLevel" "List[File]" "int" "int" "boolean" "boolean" "int" "String" "boolean" "IntervalMergingRule" "List[String]" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "CreateHadoopBamSplittingIndex" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--input --gatk-config-file --QUIET --read-validation-stringency --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --create-bai --gcs-max-retries --gcs-project-for-requester-pays --help --output --splitting-index-granularity --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--input;-I" "--read-validation-stringency;-VS" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--gcs-max-retries;-gcs-retries" "--help;-h" "--output;-O" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--input --gatk-config-file --QUIET --read-validation-stringency --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --create-bai --gcs-max-retries --gcs-project-for-requester-pays --help --output --splitting-index-granularity --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "String" "Boolean" "ValidationStringency" "String" "boolean" "boolean" "LogLevel" "List[File]" "boolean" "int" "String" "boolean" "File" "long" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "CrosscheckReadGroupFingerprints" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--HAPLOTYPE_MAP --INPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --ALLOW_DUPLICATE_READS --arguments_file --CALCULATE_TUMOR_AWARE_RESULTS --CROSSCHECK_BY --CROSSCHECK_LIBRARIES --CROSSCHECK_MODE --CROSSCHECK_SAMPLES --EXIT_CODE_WHEN_MISMATCH --EXPECT_ALL_GROUPS_TO_MATCH --EXPECT_ALL_READ_GROUPS_TO_MATCH --GENOTYPING_ERROR_RATE --help --INPUT_SAMPLE_MAP --LOD_THRESHOLD --LOSS_OF_HET_RATE --MATRIX_OUTPUT --NUM_THREADS --OUTPUT --OUTPUT_ERRORS_ONLY --SECOND_INPUT --SECOND_INPUT_SAMPLE_MAP --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=("--EXPECT_ALL_READ_GROUPS_TO_MATCH;EXPECT_ALL_GROUPS_TO_MATCH" "--MATRIX_OUTPUT;SECOND_INPUT" "--SECOND_INPUT;MATRIX_OUTPUT,MO" ) SYNONYMOUS_ARGS=("--HAPLOTYPE_MAP;-H" "--INPUT;-I" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--help;-h" "--LOD_THRESHOLD;-LOD" "--MATRIX_OUTPUT;-MO" "--OUTPUT;-O" "--SECOND_INPUT;-SI" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--HAPLOTYPE_MAP --INPUT --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --ALLOW_DUPLICATE_READS --arguments_file --CALCULATE_TUMOR_AWARE_RESULTS --CROSSCHECK_BY --CROSSCHECK_LIBRARIES --CROSSCHECK_MODE --CROSSCHECK_SAMPLES --EXIT_CODE_WHEN_MISMATCH --EXPECT_ALL_GROUPS_TO_MATCH --EXPECT_ALL_READ_GROUPS_TO_MATCH --GENOTYPING_ERROR_RATE --help --INPUT_SAMPLE_MAP --LOD_THRESHOLD --LOSS_OF_HET_RATE --MATRIX_OUTPUT --NUM_THREADS --OUTPUT --OUTPUT_ERRORS_ONLY --SECOND_INPUT --SECOND_INPUT_SAMPLE_MAP --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "List[String]" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "boolean" "List[File]" "boolean" "DataType" "boolean" "CrosscheckMode" "boolean" "int" "boolean" "boolean" "double" "boolean" "File" "double" "double" "File" "int" "File" "boolean" "List[String]" "File" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "CollectBaseDistributionByCycleSpark" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--add-output-vcf-command-line --create-output-bam-index --create-output-bam-splitting-index --create-output-variant-index --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --read-filter --read-index --read-validation-stringency --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --aligned-reads-only --arguments_file --bam-partition-size --chart --conf --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --num-reducers --output --output-shard-tmp-dir --pf-reads-only --program-name --reference --sharded-output --spark-master --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=("--output-shard-tmp-dir;sharded-output" "--sharded-output;output-shard-tmp-dir" ) SYNONYMOUS_ARGS=("--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-variant-index;-OVI" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--input;-I" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--aligned-reads-only;-A" "--chart;-C" "--conf;-conf" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--output;-O" "--pf-reads-only;-F" "--reference;-R" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--add-output-vcf-command-line --create-output-bam-index --create-output-bam-splitting-index --create-output-variant-index --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --QUIET --read-filter --read-index --read-validation-stringency --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --aligned-reads-only --arguments_file --bam-partition-size --chart --conf --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --num-reducers --output --output-shard-tmp-dir --pf-reads-only --program-name --reference --sharded-output --spark-master --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "List[String]" "int" "int" "IntervalSetRule" "Boolean" "List[String]" "List[String]" "ValidationStringency" "String" "boolean" "boolean" "LogLevel" "boolean" "List[File]" "long" "File" "List[String]" "boolean" "int" "String" "boolean" "IntervalMergingRule" "List[String]" "int" "String" "String" "boolean" "String" "String" "boolean" "String" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "FilterVariantTranches" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--output --resource --variant --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --indel-tranche --info-key --interval-merging-rule --intervals --invalidate-previous-filters --reference --sites-only-vcf-output --snp-tranche --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--output;-O" "--resource;-resource" "--variant;-V" "--add-output-sam-program-record;-add-output-sam-program-record" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-bam-md5;-OBM" "--create-output-variant-index;-OVI" "--create-output-variant-md5;-OVM" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--input;-I" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--lenient;-LE" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--seconds-between-progress-updates;-seconds-between-progress-updates" "--sequence-dictionary;-sequence-dictionary" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--cloud-index-prefetch-buffer;-CIPB" "--cloud-prefetch-buffer;-CPB" "--disable-bam-index-caching;-DBIC" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--gcs-max-retries;-gcs-retries" "--help;-h" "--indel-tranche;-indel-tranche" "--info-key;-info-key" "--interval-merging-rule;-imr" "--intervals;-L" "--reference;-R" "--snp-tranche;-snp-tranche" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--output --resource --variant --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --indel-tranche --info-key --interval-merging-rule --intervals --invalidate-previous-filters --reference --sites-only-vcf-output --snp-tranche --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("String" "List[FeatureInput[VariantContext]]" "String" "boolean" "boolean" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "List[String]" "int" "int" "IntervalSetRule" "boolean" "Boolean" "List[String]" "List[String]" "ValidationStringency" "double" "String" "String" "boolean" "boolean" "LogLevel" "List[File]" "int" "int" "boolean" "boolean" "int" "String" "boolean" "List[Double]" "String" "IntervalMergingRule" "List[String]" "boolean" "String" "boolean" "List[Double]" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "CalculateGenotypePosteriors" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--output --variant --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --default-to-allele-count --de-novo-prior --disable-bam-index-caching --disable-sequence-dictionary-validation --discovered-allele-count-priors-off --gcs-max-retries --gcs-project-for-requester-pays --global-prior-indel --global-prior-snp --help --ignore-input-samples --interval-merging-rule --intervals --num-reference-samples-if-no-call --pedigree --reference --sites-only-vcf-output --skip-family-priors --skip-population-priors --supporting-callsets --use-flat-priors-for-indels --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--output;-O" "--variant;-V" "--add-output-sam-program-record;-add-output-sam-program-record" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-bam-md5;-OBM" "--create-output-variant-index;-OVI" "--create-output-variant-md5;-OVM" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--input;-I" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--lenient;-LE" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--seconds-between-progress-updates;-seconds-between-progress-updates" "--sequence-dictionary;-sequence-dictionary" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--cloud-index-prefetch-buffer;-CIPB" "--cloud-prefetch-buffer;-CPB" "--disable-bam-index-caching;-DBIC" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--pedigree;-ped" "--reference;-R" "--supporting-callsets;-supporting" "--use-flat-priors-for-indels;-skipIndels" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--output --variant --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --default-to-allele-count --de-novo-prior --disable-bam-index-caching --disable-sequence-dictionary-validation --discovered-allele-count-priors-off --gcs-max-retries --gcs-project-for-requester-pays --global-prior-indel --global-prior-snp --help --ignore-input-samples --interval-merging-rule --intervals --num-reference-samples-if-no-call --pedigree --reference --sites-only-vcf-output --skip-family-priors --skip-population-priors --supporting-callsets --use-flat-priors-for-indels --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "String" "boolean" "boolean" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "List[String]" "int" "int" "IntervalSetRule" "boolean" "Boolean" "List[String]" "List[String]" "ValidationStringency" "double" "String" "String" "boolean" "boolean" "LogLevel" "List[File]" "int" "int" "boolean" "double" "boolean" "boolean" "boolean" "int" "String" "double" "double" "boolean" "boolean" "IntervalMergingRule" "List[String]" "int" "File" "String" "boolean" "boolean" "boolean" "List[FeatureInput[VariantContext]]" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "NonZeroFragmentLengthReadFilter" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=() MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=() MAX_OCCURRENCES=() ALL_LEGAL_ARGUMENTS=() ALL_ARGUMENT_VALUE_TYPES=() # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "GenotypeSummaries" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=() MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=() MAX_OCCURRENCES=() ALL_LEGAL_ARGUMENTS=() ALL_ARGUMENT_VALUE_TYPES=() # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "CollectTargetedPcrMetrics" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--AMPLICON_INTERVALS --INPUT --OUTPUT --TARGET_INTERVALS --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --ALLELE_FRACTION --arguments_file --CLIP_OVERLAPPING_READS --COVERAGE_CAP --CUSTOM_AMPLICON_SET_NAME --help --METRIC_ACCUMULATION_LEVEL --MINIMUM_BASE_QUALITY --MINIMUM_MAPPING_QUALITY --NEAR_DISTANCE --PER_BASE_COVERAGE --PER_TARGET_COVERAGE --SAMPLE_SIZE --THEORETICAL_SENSITIVITY_OUTPUT --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--AMPLICON_INTERVALS;-AI" "--INPUT;-I" "--OUTPUT;-O" "--TARGET_INTERVALS;-TI" "--REFERENCE_SEQUENCE;-R" "--USE_JDK_DEFLATER;-use_jdk_deflater" "--USE_JDK_INFLATER;-use_jdk_inflater" "--COVERAGE_CAP;-covMax" "--CUSTOM_AMPLICON_SET_NAME;-N" "--help;-h" "--METRIC_ACCUMULATION_LEVEL;-LEVEL" "--MINIMUM_BASE_QUALITY;-Q" "--MINIMUM_MAPPING_QUALITY;-MQ" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--AMPLICON_INTERVALS --INPUT --OUTPUT --TARGET_INTERVALS --COMPRESSION_LEVEL --CREATE_INDEX --CREATE_MD5_FILE --GA4GH_CLIENT_SECRETS --MAX_RECORDS_IN_RAM --QUIET --REFERENCE_SEQUENCE --TMP_DIR --USE_JDK_DEFLATER --USE_JDK_INFLATER --VALIDATION_STRINGENCY --VERBOSITY --ALLELE_FRACTION --arguments_file --CLIP_OVERLAPPING_READS --COVERAGE_CAP --CUSTOM_AMPLICON_SET_NAME --help --METRIC_ACCUMULATION_LEVEL --MINIMUM_BASE_QUALITY --MINIMUM_MAPPING_QUALITY --NEAR_DISTANCE --PER_BASE_COVERAGE --PER_TARGET_COVERAGE --SAMPLE_SIZE --THEORETICAL_SENSITIVITY_OUTPUT --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "File" "File" "List[File]" "int" "Boolean" "boolean" "String" "Integer" "Boolean" "File" "List[File]" "Boolean" "Boolean" "ValidationStringency" "LogLevel" "List[Double]" "List[File]" "boolean" "int" "String" "boolean" "Set[MetricAccumulationLevel]" "int" "int" "int" "File" "File" "int" "File" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "CollectAllelicCounts" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--input --intervals --output --reference --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --maxDepthPerSample --minimum-base-quality --sites-only-vcf-output --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--input;-I" "--intervals;-L" "--output;-O" "--reference;-R" "--add-output-sam-program-record;-add-output-sam-program-record" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-bam-md5;-OBM" "--create-output-variant-index;-OVI" "--create-output-variant-md5;-OVM" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--lenient;-LE" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--seconds-between-progress-updates;-seconds-between-progress-updates" "--sequence-dictionary;-sequence-dictionary" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--cloud-index-prefetch-buffer;-CIPB" "--cloud-prefetch-buffer;-CPB" "--disable-bam-index-caching;-DBIC" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--maxDepthPerSample;-maxDepthPerSample" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--input --intervals --output --reference --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --maxDepthPerSample --minimum-base-quality --sites-only-vcf-output --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("List[String]" "List[String]" "File" "String" "boolean" "boolean" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "int" "int" "IntervalSetRule" "boolean" "Boolean" "List[String]" "List[String]" "ValidationStringency" "double" "String" "String" "boolean" "boolean" "LogLevel" "List[File]" "int" "int" "boolean" "boolean" "int" "String" "boolean" "IntervalMergingRule" "int" "int" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "StrandOddsRatio" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=() MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=() MAX_OCCURRENCES=() ALL_LEGAL_ARGUMENTS=() ALL_ARGUMENT_VALUE_TYPES=() # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "BwaMemIndexImageCreator" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--input --gatk-config-file --QUIET --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --gcs-max-retries --gcs-project-for-requester-pays --help --output --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--input;-I" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--gcs-max-retries;-gcs-retries" "--help;-h" "--output;-O" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--input --gatk-config-file --QUIET --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --gcs-max-retries --gcs-project-for-requester-pays --help --output --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("String" "String" "Boolean" "String" "boolean" "boolean" "LogLevel" "List[File]" "int" "String" "boolean" "String" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "PlotModeledSegments" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--output --output-prefix --segments --sequence-dictionary --gatk-config-file --QUIET --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --allelic-counts --arguments_file --denoised-copy-ratios --gcs-max-retries --gcs-project-for-requester-pays --help --minimum-contig-length --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--output;-O" "--sequence-dictionary;-sequence-dictionary" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--gcs-max-retries;-gcs-retries" "--help;-h" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--output --output-prefix --segments --sequence-dictionary --gatk-config-file --QUIET --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --allelic-counts --arguments_file --denoised-copy-ratios --gcs-max-retries --gcs-project-for-requester-pays --help --minimum-contig-length --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("String" "String" "File" "File" "String" "Boolean" "String" "boolean" "boolean" "LogLevel" "File" "List[File]" "File" "int" "String" "boolean" "int" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "RemoveNearbyIndels" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--output --variant --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --min-indel-spacing --reference --sites-only-vcf-output --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--output;-O" "--variant;-V" "--add-output-sam-program-record;-add-output-sam-program-record" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-bam-md5;-OBM" "--create-output-variant-index;-OVI" "--create-output-variant-md5;-OVM" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--input;-I" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--lenient;-LE" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--seconds-between-progress-updates;-seconds-between-progress-updates" "--sequence-dictionary;-sequence-dictionary" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--cloud-index-prefetch-buffer;-CIPB" "--cloud-prefetch-buffer;-CPB" "--disable-bam-index-caching;-DBIC" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--min-indel-spacing;-min-indel-spacing" "--reference;-R" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--output --variant --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --min-indel-spacing --reference --sites-only-vcf-output --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("String" "String" "boolean" "boolean" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "List[String]" "int" "int" "IntervalSetRule" "boolean" "Boolean" "List[String]" "List[String]" "ValidationStringency" "double" "String" "String" "boolean" "boolean" "LogLevel" "List[File]" "int" "int" "boolean" "boolean" "int" "String" "boolean" "IntervalMergingRule" "List[String]" "int" "String" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "PreprocessIntervals" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=(--output --reference --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --bin-length --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --padding --sites-only-vcf-output --version --showHidden ) MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=("--output;-O" "--reference;-R" "--add-output-sam-program-record;-add-output-sam-program-record" "--add-output-vcf-command-line;-add-output-vcf-command-line" "--create-output-bam-index;-OBI" "--create-output-bam-md5;-OBM" "--create-output-variant-index;-OVI" "--create-output-variant-md5;-OVM" "--disable-read-filter;-DF" "--disable-tool-default-read-filters;-disable-tool-default-read-filters" "--exclude-intervals;-XL" "--input;-I" "--interval-exclusion-padding;-ixp" "--interval-padding;-ip" "--interval-set-rule;-isr" "--lenient;-LE" "--read-filter;-RF" "--read-index;-read-index" "--read-validation-stringency;-VS" "--seconds-between-progress-updates;-seconds-between-progress-updates" "--sequence-dictionary;-sequence-dictionary" "--use-jdk-deflater;-jdk-deflater" "--use-jdk-inflater;-jdk-inflater" "--verbosity;-verbosity" "--cloud-index-prefetch-buffer;-CIPB" "--cloud-prefetch-buffer;-CPB" "--disable-bam-index-caching;-DBIC" "--disable-sequence-dictionary-validation;-disable-sequence-dictionary-validation" "--gcs-max-retries;-gcs-retries" "--help;-h" "--interval-merging-rule;-imr" "--intervals;-L" "--showHidden;-showHidden" ) MIN_OCCURRENCES=(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ) MAX_OCCURRENCES=(2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 2147483647 ) ALL_LEGAL_ARGUMENTS=(--output --reference --add-output-sam-program-record --add-output-vcf-command-line --create-output-bam-index --create-output-bam-md5 --create-output-variant-index --create-output-variant-md5 --disable-read-filter --disable-tool-default-read-filters --exclude-intervals --gatk-config-file --input --interval-exclusion-padding --interval-padding --interval-set-rule --lenient --QUIET --read-filter --read-index --read-validation-stringency --seconds-between-progress-updates --sequence-dictionary --tmp-dir --use-jdk-deflater --use-jdk-inflater --verbosity --arguments_file --bin-length --cloud-index-prefetch-buffer --cloud-prefetch-buffer --disable-bam-index-caching --disable-sequence-dictionary-validation --gcs-max-retries --gcs-project-for-requester-pays --help --interval-merging-rule --intervals --padding --sites-only-vcf-output --version --showHidden ) ALL_ARGUMENT_VALUE_TYPES=("File" "String" "boolean" "boolean" "boolean" "boolean" "boolean" "boolean" "List[String]" "boolean" "List[String]" "String" "List[String]" "int" "int" "IntervalSetRule" "boolean" "Boolean" "List[String]" "List[String]" "ValidationStringency" "double" "String" "String" "boolean" "boolean" "LogLevel" "List[File]" "int" "int" "int" "boolean" "boolean" "int" "String" "boolean" "IntervalMergingRule" "List[String]" "int" "boolean" "boolean" "boolean" ) # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "GoodCigarReadFilter" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=() MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=() MAX_OCCURRENCES=() ALL_LEGAL_ARGUMENTS=() ALL_ARGUMENT_VALUE_TYPES=() # Complete the arguments for this tool: _gatk_handleArgs elif [[ ${toolName} == "PolymorphicNuMT" ]] ; then # Set up the completion information for this tool: DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=() MUTUALLY_EXCLUSIVE_ARGS=() SYNONYMOUS_ARGS=() MIN_OCCURRENCES=() MAX_OCCURRENCES=() ALL_LEGAL_ARGUMENTS=() ALL_ARGUMENT_VALUE_TYPES=() # Complete the arguments for this tool: _gatk_handleArgs # We have no postfix options or tool options. # We now must complete any prefix options and the tools themselves. # These are defined at the top. else NUM_POSITIONAL_ARGUMENTS=0 POSITIONAL_ARGUMENT_TYPE=() DEPENDENT_ARGUMENTS=() NORMAL_COMPLETION_ARGUMENTS=("${CS_PREFIX_OPTIONS_NORMAL_COMPLETION_ARGUMENTS[@]}") MUTUALLY_EXCLUSIVE_ARGS=("${CS_PREFIX_OPTIONS_MUTUALLY_EXCLUSIVE_ARGS[@]}") SYNONYMOUS_ARGS=("${CS_PREFIX_OPTIONS_SYNONYMOUS_ARGS[@]}") MIN_OCCURRENCES=("${CS_PREFIX_OPTIONS_MIN_OCCURRENCES[@]}") MAX_OCCURRENCES=("${CS_PREFIX_OPTIONS_MAX_OCCURRENCES[@]}") ALL_LEGAL_ARGUMENTS=("${CS_PREFIX_OPTIONS_ALL_LEGAL_ARGUMENTS[@]}") ALL_ARGUMENT_VALUE_TYPES=("${CS_PREFIX_OPTIONS_ALL_ARGUMENT_VALUE_TYPES[@]}") # Complete the arguments for the prefix arguments and tools: _gatk_handleArgs PREFIX_OPTIONS fi } complete -o default -F _gatk_masterCompletionFunction ${CALLER_SCRIPT_NAME}