#ifndef PARAMETERS_DEF #define PARAMETERS_DEF #include "IncludeDefine.h" #include "InOutStreams.h" #include "ParameterInfo.h" #include #include "TimeFunctions.h" #include #include class Parameters { public: vector parArray, parArrayInitial; vector parameterInputName; string commandLine, commandLineFull; //version uint versionSTAR; vector versionGenome; //system parameters string sysShell; //shell for executing system commands // run parameters string runMode; int runThreadN; mode_t runDirPerm; string runDirPermIn; //permission for directores created at run-time int runRNGseed; //random number generator seed //parameters vector parametersFiles; //input string inputBAMfile; //genome, SA, ... vector chrStart, chrLength, chrLengthAll; string genomeDir,genomeLoad; vector genomeFastaFiles, genomeChainFiles; uint genomeSAsparseD;//sparsity=distance between indices uint genomeInsertL; //total length of the sequence to be inserted on the fly uint genomeInsertChrIndFirst; //index of the first inserted chromosome uint genomeSuffixLengthMax; //maximum length of the suffixes, has to be longer than read length vector genomeFileSizes; //size of the genome files //binning,windows,anchors uint genomeChrBinNbits, genomeChrBinNbases, chrBinN, *chrBin; uint winBinChrNbits, winBinNbits, winAnchorDistNbins, winFlankNbins, winBinN; uint winAnchorMultimapNmax; //max number of alignments for anchors double winReadCoverageRelativeMin; uint winReadCoverageBasesMin; uint genomeSAindexNbases; //length of the SA pre-index strings uint *genomeSAindexStart;//starts of the L-mer indices in the SAindex, 1<=L<=genomeSAindexNbases char genomeNumToNT[6]; //read parameters uint readMapNumber; uint iReadAll; int readFilesIndex; uint32 readFilesN; vector readFilesIn, readFilesInTmp; vector > readFilesNames; uint readNmates; string readMatesLengthsIn; vector readFilesCommand; pid_t readFilesCommandPID[MAX_N_MATES]; vector readNameSeparator; vector readNameSeparatorChar; string outSAMreadID; vector clip5pNbases, clip3pNbases, clip3pAfterAdapterNbases; vector clip3pAdapterMMp; vector clip3pAdapterSeq; char *clip3pAdapterSeqNum[MAX_N_MATES];//adapter sequence - numerical bool readMatesEqualLengths; //whether or not the read mates have the same length, true if onyl one mate //align parameters uint alignSJoverhangMin,alignSJDBoverhangMin,alignSplicedMateMapLmin; //min SJ donor/acceptor length double alignSplicedMateMapLminOverLmate; uint alignWindowsPerReadNmax; //max number of alignment windows per read uint alignTranscriptsPerWindowNmax; //maximum number of transcripts recorded per window uint alignTranscriptsPerReadNmax; //max number of alignments per read uint alignIntronMin;//min length to call a gap an intron uint alignIntronMax;//max length to call uint alignMatesGapMax;//max gap between the mates (if paired-end) string alignSoftClipAtReferenceEnds; vector alignSJstitchMismatchNmax; struct { string in; bool ext[2][2]; } alignEndsType; struct { vector in; int nBasesMax; bool concordantPair; } alignEndsProtrude; //seed parameters uint seedMultimapNmax; //max number of multiple alignments per piece uint seedSearchLmax; //max length of the seed uint seedPerReadNmax; //max number of pieces per Read uint seedPerWindowNmax; //max number of aligns per window uint seedNoneLociPerWindow; //max number of aligns from one piece per window uint seedSearchStartLmax; double seedSearchStartLmaxOverLread; //length of split start points //chunk parameters uint chunkInSizeBytes,chunkInSizeBytesArray,chunkOutBAMsizeBytes; //output string outFileNamePrefix, outStd; string outTmpDir, outTmpKeep; //SAM output string outBAMfileCoordName, outBAMfileUnsortedName, outQuantBAMfileName; string samHeader, samHeaderHD, samHeaderSortedCoord; string outSAMmode, outSAMstrandField, outSAMorder, outSAMprimaryFlag; vector outSAMattributes, outSAMheaderHD, outSAMheaderPG; vector outSAMattrRGline,outSAMattrRGlineSplit,outSAMattrRG; uint outSAMmultNmax,outSAMattrIHstart; string outSAMheaderCommentFile; int outSAMmapqUnique; struct {bool NH,HI,AS,NM,MD,nM,jM,jI,RG,XS,ch;} outSAMattrPresent, outSAMattrPresentQuant; vector outSAMattrOrder, outSAMattrOrderQuant; int outBAMcompression; vector outSAMtype; bool outBAMunsorted, outBAMcoord, outSAMbool; uint32 outBAMcoordNbins; string outBAMsortTmpDir; // string bamRemoveDuplicatesType; // uint bamRemoveDuplicatesMate2basesN; struct { string mode; bool yes; bool markMulti; uint mate2basesN; } removeDuplicates; int outBAMsortingThreadN, outBAMsortingThreadNactual; uint64 *outBAMsortingBinStart; //genomic starts for bins for sorting BAM files uint16 outSAMflagOR, outSAMflagAND; struct { vector mode; bool yes; bool within;//output unmapped reads within SAM/BAM files bool keepPairs;//keep mates together } outSAMunmapped; struct { vector mode; bool yes; bool KeepOnlyAddedReferences; bool KeepAllAddedReferences; } outSAMfilter; struct { string mode; bool random; } outMultimapperOrder; string outReadsUnmapped; int outQSconversionAdd; string outFileTmp; //output filtering uint outFilterMismatchNmax; double outFilterMismatchNoverLmax, outFilterMismatchNoverReadLmax; //max proportion of all MM within all bases uint outFilterMatchNmin,outFilterMultimapNmax;//min number of matches double outFilterScoreMinOverLread, outFilterMatchNminOverLread;//normalzied to read length intScore outFilterScoreMin,outFilterMultimapScoreRange;//min score to output string outFilterIntronMotifs; string outFilterType; //type of filtering int outFilterBySJoutStage; //indicates the stage of filtering by SJout //output filtering SJs string outSJfilterReads; vector outSJfilterCountUniqueMin, outSJfilterCountTotalMin; vector outSJfilterOverhangMin; vector outSJfilterDistToOtherSJmin; //min allowed distance to other SJ's donor/acceptor vector outSJfilterIntronMaxVsReadN; //wiggle output vector outWigType, outWigStrand, outWigNorm; string outWigReferencesPrefix; struct { bool yes; bool strand; int type; int format; int norm; } outWigFlags; //2-pass // uint twoPass.pass1readsN, twoPass.sjLimit; // string twoPass.dir,twopassSJpass1file; struct { bool yes; //true in 2-pass mode bool pass2; //true if now running the 2nd pass uint pass1readsN; int pass1readsN_par; string dir; string pass1sjFile; string mode; } twoPass; //inserting junctions on the fly struct { bool yes; //insert? bool pass1;//insert on the 1st pass? bool pass2;//insert on the 2nd pass? string save; string outDir; } sjdbInsert; //storage limits uint limitGenomeGenerateRAM; uint limitIObufferSize; //max size of the in/out buffer, bytes uint limitOutSAMoneReadBytes; uint limitOutSJoneRead, limitOutSJcollapsed; uint limitBAMsortRAM; uint limitSjdbInsertNsj; // penalties intScore scoreGap, scoreGapNoncan, scoreGapGCAG, scoreGapATAC, scoreDelBase, scoreDelOpen, scoreInsBase, scoreInsOpen; intScore scoreStitchSJshift;//Max negative score when double scoreGenomicLengthLog2scale; //old variables: CLEAN-up needed char outputBED[MAX_OUTPUT_FLAG]; //output flags //SW search uint swMode, swWinCoverageMinP; //SW penalties uint swPeoutFilterMatchNmin, swPenMismatch, swPenGapOpen, swPenGapExtend; uint swHsize; int annotScoreScale;//overall multiplication factor for the annotation string annotSignalFile;//binary file with annotation signal //SJ database parameters vector sjdbFileChrStartEnd; string sjdbGTFfile, sjdbGTFchrPrefix, sjdbGTFfeatureExon, sjdbGTFtagExonParentTranscript, sjdbGTFtagExonParentGene; uint sjdbOverhang,sjdbLength; //length of the donor/acceptor, length of the sj "chromosome" =2*sjdbOverhang+1 including spacer int sjdbOverhang_par; int sjdbScore; uint sjChrStart,sjdbN; //first sj-db chr uint sjGstart; //start of the sj-db genome sequence uint *sjDstart,*sjAstart,*sjStr, *sjdbStart, *sjdbEnd; //sjdb loci uint8 *sjdbMotif; //motifs of annotated junctions uint8 *sjdbShiftLeft, *sjdbShiftRight; //shifts of junctions uint8 *sjdbStrand; //junctions strand, not used yet uint sjNovelN, *sjNovelStart, *sjNovelEnd; //novel junctions collapased and filtered //quantification parameters //input struct { bool yes; //if any quantification is done vector mode; //quantification mode input string struct { bool yes; bool indel; bool softClip; bool singleEnd; int bamCompression; string ban; } trSAM; struct { bool yes; string outFile; } geCount; } quant; //chimeric uint chimSegmentMin, chimJunctionOverhangMin; //min chimeric donor/acceptor length uint chimSegmentReadGapMax; //max read gap for stitching chimeric windows int chimScoreMin,chimScoreDropMax,chimScoreSeparation, chimScoreJunctionNonGTAG; //min chimeric score uint chimMainSegmentMultNmax; vector chimFilter; struct { struct { bool genomicN; } filter; struct { vector type; bool bam; bool bamHardClip; } out; } chim; //splitting char Qsplit; uint maxNsplit, minLsplit, minLmap; //limits ////////////////////// CLEAN-UP needed InOutStreams *inOut; //main input output streams uint Lread; //Genome parameters uint nGenome, nSA, nSAbyte, nChrReal;//genome length, SA length, # of chromosomes, vector of chromosome start loci uint nGenome2, nSA2, nSAbyte2, nChrReal2; //same for the 2nd pass uint nSAi; //size of the SAindex vector chrName, chrNameAll; map chrNameIndex; unsigned char GstrandBit, SAiMarkNbit, SAiMarkAbsentBit; //SA index bit for strand information uint GstrandMask, SAiMarkAbsentMask, SAiMarkAbsentMaskC, SAiMarkNmask, SAiMarkNmaskC;//maske to remove strand bit from SA index, to remove mark from SAi index Parameters(); void chrInfoLoad(); //find nChr and chrStart from genome void chrBinFill();//file chrBin array int readParsFromFile(ifstream*, ofstream*, int); //read parameters from one file int readPars(); // read parameters from all files int scanOneLine (string &lineIn, int inputLevel, int inputLevelRequested); void scanAllLines (istream &streamIn, int inputLevel, int inputLevelRequested); void inputParameters (int argInN, char* argIn[]); //input parameters: default, from files, from command line void openReadsFiles(); void closeReadsFiles(); }; #endif // Parameters.h