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| Name | Last modified | Size | Description |
|---|---|---|---|---|
| Parent Directory | - | ||
| BAMbinSortByCoordinate.cpp | 2017-03-17 20:22 | 2.4K | |
| BAMbinSortByCoordinate.h | 2017-03-17 20:22 | 269 | |
| BAMbinSortUnmapped.cpp | 2017-03-17 20:22 | 2.8K | |
| BAMbinSortUnmapped.h | 2017-03-17 20:22 | 251 | |
| BAMfunctions.cpp | 2017-03-17 20:22 | 3.5K | |
| BAMfunctions.h | 2017-03-17 20:22 | 355 | |
| BAMoutput.cpp | 2017-03-17 20:22 | 7.0K | |
| BAMoutput.h | 2017-03-17 20:22 | 1.2K | |
| Chain.cpp | 2017-03-17 20:22 | 5.1K | |
| Chain.h | 2017-03-17 20:22 | 725 | |
| ErrorWarning.cpp | 2017-03-17 20:22 | 649 | |
| ErrorWarning.h | 2017-03-17 20:22 | 213 | |
| Genome.cpp | 2017-03-17 20:22 | 27K | |
| Genome.h | 2017-03-17 20:22 | 842 | |
| Genome_insertSequences.cpp | 2017-03-17 20:22 | 1.3K | |
| GlobalVariables.cpp | 2017-03-17 20:22 | 105 | |
| GlobalVariables.h | 2017-03-17 20:22 | 157 | |
| InOutStreams.cpp | 2017-03-17 20:22 | 905 | |
| InOutStreams.h | 2017-03-17 20:22 | 540 | |
| IncludeDefine.h | 2017-03-17 20:22 | 5.3K | |
| Makefile | 2017-03-17 20:22 | 5.9K | |
| OutSJ.cpp | 2017-03-17 20:22 | 4.4K | |
| OutSJ.h | 2017-03-17 20:22 | 1.3K | |
| PackedArray.cpp | 2017-03-17 20:22 | 1.1K | |
| PackedArray.h | 2017-03-17 20:22 | 788 | |
| ParameterInfo.h | 2017-03-17 20:22 | 3.2K | |
| Parameters.cpp | 2017-03-17 20:22 | 72K | |
| Parameters.h | 2017-03-17 20:22 | 13K | |
| Parameters_closeReadsFiles.cpp | 2017-03-17 20:22 | 391 | |
| Parameters_openReadsFiles.cpp | 2017-03-17 20:22 | 5.9K | |
| Quantifications.cpp | 2017-03-17 20:22 | 1.1K | |
| Quantifications.h | 2017-03-17 20:22 | 662 | |
| ReadAlign.cpp | 2017-03-17 20:22 | 4.6K | |
| ReadAlign.h | 2017-03-17 20:22 | 6.6K | |
| ReadAlignChunk.cpp | 2017-03-17 20:22 | 5.2K | |
| ReadAlignChunk.h | 2017-03-17 20:22 | 1.4K | |
| ReadAlignChunk_mapChunk.cpp | 2017-03-17 20:22 | 5.9K | |
| ReadAlignChunk_processChunks.cpp | 2017-03-17 20:22 | 10K | |
| ReadAlign_alignBAM.cpp | 2017-03-17 20:22 | 20K | |
| ReadAlign_assignAlignToWindow.cpp | 2017-03-17 20:22 | 5.2K | |
| ReadAlign_chimericDetection.cpp | 2017-03-17 20:22 | 26K | |
| ReadAlign_createExtendWindowsWithAlign.cpp | 2017-03-17 20:22 | 3.5K | |
| ReadAlign_mapOneRead.cpp | 2017-03-17 20:22 | 4.4K | |
| ReadAlign_maxMappableLength2strands.cpp | 2017-03-17 20:22 | 4.1K | |
| ReadAlign_multMapSelect.cpp | 2017-03-17 20:22 | 4.7K | |
| ReadAlign_oneRead.cpp | 2017-03-17 20:22 | 3.5K | |
| ReadAlign_outputAlignments.cpp | 2017-03-17 20:22 | 13K | |
| ReadAlign_outputTranscriptCIGARp.cpp | 2017-03-17 20:22 | 2.7K | |
| ReadAlign_outputTranscriptSAM.cpp | 2017-03-17 20:22 | 13K | |
| ReadAlign_outputTranscriptSJ.cpp | 2017-03-17 20:22 | 3.1K | |
| ReadAlign_quantTranscriptome.cpp | 2017-03-17 20:22 | 4.4K | |
| ReadAlign_stitchPieces.cpp | 2017-03-17 20:22 | 14K | |
| ReadAlign_stitchWindowSeeds.cpp | 2017-03-17 20:22 | 12K | |
| ReadAlign_storeAligns.cpp | 2017-03-17 20:22 | 5.6K | |
| STAR.cpp | 2017-03-17 20:22 | 17K | |
| SequenceFuns.cpp | 2017-03-17 20:22 | 6.0K | |
| SequenceFuns.h | 2017-03-17 20:22 | 743 | |
| SharedMemory.cpp | 2017-03-17 20:22 | 6.3K | |
| SharedMemory.h | 2017-03-17 20:22 | 3.4K | |
| SjdbClass.h | 2017-03-17 20:22 | 242 | |
| Stats.cpp | 2017-03-17 20:22 | 8.0K | |
| Stats.h | 2017-03-17 20:22 | 1.1K | |
| SuffixArrayFuns.cpp | 2017-03-17 20:22 | 14K | |
| SuffixArrayFuns.h | 2017-03-17 20:22 | 1.0K | |
| ThreadControl.cpp | 2017-03-17 20:22 | 159 | |
| ThreadControl.h | 2017-03-17 20:22 | 664 | |
| TimeFunctions.cpp | 2017-03-17 20:22 | 581 | |
| TimeFunctions.h | 2017-03-17 20:22 | 168 | |
| Transcript.cpp | 2017-03-17 20:22 | 748 | |
| Transcript.h | 2017-03-17 20:22 | 2.4K | |
| Transcript_alignScore.cpp | 2017-03-17 20:22 | 2.0K | |
| Transcriptome.cpp | 2017-03-17 20:22 | 4.1K | |
| Transcriptome.h | 2017-03-17 20:22 | 1.5K | |
| Transcriptome_geneCountsAddAlign.cpp | 2017-03-17 20:22 | 2.8K | |
| Transcriptome_quantAlign.cpp | 2017-03-17 20:22 | 5.1K | |
| VERSION | 2017-03-17 20:22 | 35 | |
| alignSmithWaterman.cpp | 2017-03-17 20:22 | 4.2K | |
| alignSmithWaterman.h | 2017-03-17 20:22 | 217 | |
| bamRemoveDuplicates.cpp | 2017-03-17 20:22 | 9.2K | |
| bamRemoveDuplicates.h | 2017-03-17 20:22 | 241 | |
| bam_cat.c | 2017-03-17 20:22 | 4.6K | |
| bam_cat.h | 2017-03-17 20:22 | 163 | |
| binarySearch2.cpp | 2017-03-17 20:22 | 928 | |
| binarySearch2.h | 2017-03-17 20:22 | 150 | |
| blocksOverlap.cpp | 2017-03-17 20:22 | 1.3K | |
| blocksOverlap.h | 2017-03-17 20:22 | 168 | |
| extendAlign.cpp | 2017-03-17 20:22 | 2.4K | |
| extendAlign.h | 2017-03-17 20:22 | 263 | |
| funCompareUintAndSuffixes.cpp | 2017-03-17 20:22 | 1.3K | |
| funCompareUintAndSuffixes.h | 2017-03-17 20:22 | 263 | |
| funCompareUintAndSuffixesMemcmp.cpp | 2017-03-17 20:22 | 1.2K | |
| funCompareUintAndSuffixesMemcmp.h | 2017-03-17 20:22 | 291 | |
| genomeGenerate.cpp | 2017-03-17 20:22 | 18K | |
| genomeGenerate.h | 2017-03-17 20:22 | 62 | |
| genomeParametersWrite.cpp | 2017-03-17 20:22 | 1.6K | |
| genomeParametersWrite.h | 2017-03-17 20:22 | 179 | |
| genomeSAindex.cpp | 2017-03-17 20:22 | 10K | |
| genomeSAindex.h | 2017-03-17 20:22 | 429 | |
| genomeScanFastaFiles.cpp | 2017-03-17 20:22 | 4.4K | |
| genomeScanFastaFiles.h | 2017-03-17 20:22 | 195 | |
| htslib/ | 2017-03-17 20:22 | - | |
| insertSeqSA.cpp | 2017-03-17 20:22 | 12K | |
| insertSeqSA.h | 2017-03-17 20:22 | 282 | |
| loadGTF.cpp | 2017-03-17 20:22 | 15K | |
| loadGTF.h | 2017-03-17 20:22 | 160 | |
| mapThreadsSpawn.cpp | 2017-03-17 20:22 | 1.7K | |
| mapThreadsSpawn.h | 2017-03-17 20:22 | 181 | |
| outputSJ.cpp | 2017-03-17 20:22 | 6.8K | |
| outputSJ.h | 2017-03-17 20:22 | 105 | |
| parametersDefault | 2017-03-17 20:22 | 30K | |
| parametersDefault.xxd | 2017-03-17 20:22 | 185K | |
| readLoad.cpp | 2017-03-17 20:22 | 6.9K | |
| readLoad.h | 2017-03-17 20:22 | 422 | |
| serviceFuns.cpp | 2017-03-17 20:22 | 2.1K | |
| signalFromBAM.cpp | 2017-03-17 20:22 | 8.3K | |
| signalFromBAM.h | 2017-03-17 20:22 | 283 | |
| sjSplitAlign.cpp | 2017-03-17 20:22 | 556 | |
| sjdbBuildIndex.cpp | 2017-03-17 20:22 | 12K | |
| sjdbBuildIndex.h | 2017-03-17 20:22 | 241 | |
| sjdbInsertJunctions.cpp | 2017-03-17 20:22 | 5.9K | |
| sjdbInsertJunctions.h | 2017-03-17 20:22 | 241 | |
| sjdbLoadFromFiles.cpp | 2017-03-17 20:22 | 1.0K | |
| sjdbLoadFromFiles.h | 2017-03-17 20:22 | 198 | |
| sjdbLoadFromStream.cpp | 2017-03-17 20:22 | 896 | |
| sjdbLoadFromStream.h | 2017-03-17 20:22 | 185 | |
| sjdbPrepare.cpp | 2017-03-17 20:22 | 9.7K | |
| sjdbPrepare.h | 2017-03-17 20:22 | 214 | |
| sortSuffixesBucket.cpp | 2017-03-17 20:22 | 3.3K | |
| sortSuffixesBucket.h | 2017-03-17 20:22 | 88 | |
| stitchAlignToTranscript.cpp | 2017-03-17 20:22 | 19K | |
| stitchAlignToTranscript.h | 2017-03-17 20:22 | 288 | |
| stitchGapIndel.cpp | 2017-03-17 20:22 | 1.9K | |
| stitchWindowAligns.cpp | 2017-03-17 20:22 | 16K | |
| stitchWindowAligns.h | 2017-03-17 20:22 | 546 | |
| streamFuns.cpp | 2017-03-17 20:22 | 4.3K | |
| streamFuns.h | 2017-03-17 20:22 | 643 | |
| stringSubstituteAll.cpp | 2017-03-17 20:22 | 413 | |
| stringSubstituteAll.h | 2017-03-17 20:22 | 178 | |
| sysRemoveDir.cpp | 2017-03-17 20:22 | 586 | |
| sysRemoveDir.h | 2017-03-17 20:22 | 117 | |