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Parameters.cpp
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#include <stdexcept>
#include "IncludeDefine.h"
#include "Parameters.h"
#include "ErrorWarning.h"
#include "SequenceFuns.h"
#include "OutSJ.h"
#include "sysRemoveDir.h"
#include "stringSubstituteAll.h"
#include SAMTOOLS_BGZF_H
#include "GlobalVariables.h"
//for mkfifo
#include <sys/stat.h>
#define PAR_NAME_PRINT_WIDTH 30
ParameterInfoBase::ParameterInfoBase(const char* nameStringIn, int inputLevelIn, int inputLevelAllowedIn)
: nameString(nameStringIn), inputLevel(inputLevelIn), inputLevelAllowed(inputLevelAllowedIn) {}
Parameters::Parameters() {//initalize parameters info
inOut = new InOutStreams;
//versions
parArray.push_back(new ParameterInfoScalar <string> (-1, -1, "versionGenome", &versionGenome));
//parameters
parArray.push_back(new ParameterInfoVector <string> (-1, 2, "parametersFiles", ¶metersFiles));
//system
parArray.push_back(new ParameterInfoScalar <string> (-1, -1, "sysShell", &sysShell));
//run
parArray.push_back(new ParameterInfoScalar <string> (-1, -1, "runMode", &runMode));
parArray.push_back(new ParameterInfoScalar <int> (-1, -1, "runThreadN", &runThreadN));
parArray.push_back(new ParameterInfoScalar <string> (-1, -1, "runDirPerm", &runDirPermIn));
parArray.push_back(new ParameterInfoScalar <int> (-1, -1, "runRNGseed", &runRNGseed));
//genome
parArray.push_back(new ParameterInfoScalar <string> (-1, -1, "genomeDir", &pGe.gDir));
parArray.push_back(new ParameterInfoScalar <string> (-1, -1, "genomeLoad", &pGe.gLoad));
parArray.push_back(new ParameterInfoVector <string> (-1, -1, "genomeFastaFiles", &pGe.gFastaFiles));
parArray.push_back(new ParameterInfoVector <string> (-1, -1, "genomeChainFiles", &pGe.gChainFiles));
parArray.push_back(new ParameterInfoScalar <uint> (-1, -1, "genomeSAindexNbases", &pGe.gSAindexNbases));
parArray.push_back(new ParameterInfoScalar <uint> (-1, -1, "genomeChrBinNbits", &pGe.gChrBinNbits));
parArray.push_back(new ParameterInfoScalar <uint> (-1, -1, "genomeSAsparseD", &pGe.gSAsparseD));
parArray.push_back(new ParameterInfoScalar <uint> (-1, -1, "genomeSuffixLengthMax", &pGe.gSuffixLengthMax));
parArray.push_back(new ParameterInfoVector <uint> (-1, -1, "genomeFileSizes", &pGe.gFileSizes));
parArray.push_back(new ParameterInfoScalar <string> (-1, -1, "genomeConsensusFile", &pGe.gConsensusFile));
//read
parArray.push_back(new ParameterInfoVector <string> (-1, -1, "readFilesType", &readFilesType));
parArray.push_back(new ParameterInfoVector <string> (-1, -1, "readFilesIn", &readFilesIn));
parArray.push_back(new ParameterInfoScalar <string> (-1, -1, "readFilesPrefix", &readFilesPrefix));
parArray.push_back(new ParameterInfoVector <string> (-1, -1, "readFilesCommand", &readFilesCommand));
parArray.push_back(new ParameterInfoScalar <string> (-1, -1, "readMatesLengthsIn", &readMatesLengthsIn));
parArray.push_back(new ParameterInfoScalar <uint> (-1, -1, "readMapNumber", &readMapNumber));
parArray.push_back(new ParameterInfoVector <string> (-1, -1, "readNameSeparator", &readNameSeparator));
//parArray.push_back(new ParameterInfoScalar <string> (-1, -1, "readStrand", &pReads.strandString));
parArray.push_back(new ParameterInfoScalar <string> (-1, -1, "inputBAMfile", &inputBAMfile));
parArray.push_back(new ParameterInfoScalar <string> (-1, -1, "bamRemoveDuplicatesType", &removeDuplicates.mode));
parArray.push_back(new ParameterInfoScalar <uint> (-1, -1, "bamRemoveDuplicatesMate2basesN", &removeDuplicates.mate2basesN));
//limits
parArray.push_back(new ParameterInfoScalar <uint> (-1, -1, "limitGenomeGenerateRAM", &limitGenomeGenerateRAM));
parArray.push_back(new ParameterInfoScalar <uint> (-1, -1, "limitIObufferSize", &limitIObufferSize));
parArray.push_back(new ParameterInfoScalar <uint> (-1, -1, "limitOutSAMoneReadBytes", &limitOutSAMoneReadBytes));
parArray.push_back(new ParameterInfoScalar <uint> (-1, -1, "limitOutSJcollapsed", &limitOutSJcollapsed));
parArray.push_back(new ParameterInfoScalar <uint> (-1, -1, "limitOutSJoneRead", &limitOutSJoneRead));
parArray.push_back(new ParameterInfoScalar <uint> (-1, -1, "limitBAMsortRAM", &limitBAMsortRAM));
parArray.push_back(new ParameterInfoScalar <uint> (-1, -1, "limitSjdbInsertNsj", &limitSjdbInsertNsj));
parArray.push_back(new ParameterInfoScalar <uint> (-1, -1, "limitNreadsSoft", &limitNreadsSoft));
//output
parArray.push_back(new ParameterInfoScalar <string> (-1, 2, "outFileNamePrefix", &outFileNamePrefix));
parArray.push_back(new ParameterInfoScalar <string> (-1, 2, "outTmpDir", &outTmpDir));
parArray.push_back(new ParameterInfoScalar <string> (-1, 2, "outTmpKeep", &outTmpKeep));
parArray.push_back(new ParameterInfoScalar <string> (-1, 2, "outStd", &outStd));
parArray.push_back(new ParameterInfoScalar <string> (-1, -1, "outReadsUnmapped", &outReadsUnmapped));
parArray.push_back(new ParameterInfoScalar <int> (-1, -1, "outQSconversionAdd", &outQSconversionAdd));
parArray.push_back(new ParameterInfoScalar <string> (-1, -1, "outMultimapperOrder", &outMultimapperOrder.mode));
//outSAM
parArray.push_back(new ParameterInfoVector <string> (-1, -1, "outSAMtype", &outSAMtype));
parArray.push_back(new ParameterInfoScalar <string> (-1, -1, "outSAMmode", &outSAMmode));
parArray.push_back(new ParameterInfoScalar <string> (-1, -1, "outSAMstrandField", &outSAMstrandField.in));
parArray.push_back(new ParameterInfoVector <string> (-1, -1, "outSAMattributes", &outSAMattributes));
parArray.push_back(new ParameterInfoVector <string> (-1, -1, "outSAMunmapped", &outSAMunmapped.mode));
parArray.push_back(new ParameterInfoScalar <string> (-1, -1, "outSAMorder", &outSAMorder));
parArray.push_back(new ParameterInfoScalar <string> (-1, -1, "outSAMprimaryFlag", &outSAMprimaryFlag));
parArray.push_back(new ParameterInfoScalar <string> (-1, -1, "outSAMreadID", &outSAMreadID));
parArray.push_back(new ParameterInfoScalar <int> (-1, -1, "outSAMmapqUnique", &outSAMmapqUnique));
parArray.push_back(new ParameterInfoScalar <uint16> (-1, -1, "outSAMflagOR", &outSAMflagOR));
parArray.push_back(new ParameterInfoScalar <uint16> (-1, -1, "outSAMflagAND", &outSAMflagAND));
parArray.push_back(new ParameterInfoVector <string> (-1, -1, "outSAMattrRGline", &outSAMattrRGline));
parArray.push_back(new ParameterInfoVector <string> (-1, -1, "outSAMheaderHD", &outSAMheaderHD));
parArray.push_back(new ParameterInfoVector <string> (-1, -1, "outSAMheaderPG", &outSAMheaderPG));
parArray.push_back(new ParameterInfoScalar <string> (-1, -1, "outSAMheaderCommentFile", &outSAMheaderCommentFile));
parArray.push_back(new ParameterInfoScalar <int> (-1, -1, "outBAMcompression", &outBAMcompression));
parArray.push_back(new ParameterInfoScalar <int> (-1, -1, "outBAMsortingThreadN", &outBAMsortingThreadN));
parArray.push_back(new ParameterInfoScalar <uint32> (-1, -1, "outBAMsortingBinsN", &outBAMsortingBinsN));
parArray.push_back(new ParameterInfoVector <string> (-1, -1, "outSAMfilter", &outSAMfilter.mode));
parArray.push_back(new ParameterInfoScalar <uint> (-1, -1, "outSAMmultNmax", &outSAMmultNmax));
parArray.push_back(new ParameterInfoScalar <uint> (-1, -1, "outSAMattrIHstart", &outSAMattrIHstart));
parArray.push_back(new ParameterInfoScalar <int> (-1, -1, "outSAMtlen", &outSAMtlen));
//output SJ filtering
parArray.push_back(new ParameterInfoScalar <string> (-1, -1, "outSJfilterReads", &outSJfilterReads));
parArray.push_back(new ParameterInfoVector <int32> (-1, -1, "outSJfilterCountUniqueMin", &outSJfilterCountUniqueMin));
parArray.push_back(new ParameterInfoVector <int32> (-1, -1, "outSJfilterCountTotalMin", &outSJfilterCountTotalMin));
parArray.push_back(new ParameterInfoVector <int32> (-1, -1, "outSJfilterOverhangMin", &outSJfilterOverhangMin));
parArray.push_back(new ParameterInfoVector <int32> (-1, -1, "outSJfilterDistToOtherSJmin", &outSJfilterDistToOtherSJmin));
parArray.push_back(new ParameterInfoVector <int32> (-1, -1, "outSJfilterIntronMaxVsReadN", &outSJfilterIntronMaxVsReadN));
//output wiggle
parArray.push_back(new ParameterInfoVector <string> (-1, -1, "outWigType", &outWigType));
parArray.push_back(new ParameterInfoVector <string> (-1, -1, "outWigStrand", &outWigStrand));
parArray.push_back(new ParameterInfoScalar <string> (-1, -1, "outWigReferencesPrefix", &outWigReferencesPrefix));
parArray.push_back(new ParameterInfoVector <string> (-1, -1, "outWigNorm", &outWigNorm));
//output filtering
parArray.push_back(new ParameterInfoScalar <string> (-1, -1, "outFilterType", &outFilterType) );
parArray.push_back(new ParameterInfoScalar <uint> (-1, -1, "outFilterMultimapNmax", &outFilterMultimapNmax));
parArray.push_back(new ParameterInfoScalar <intScore> (-1, -1, "outFilterMultimapScoreRange", &outFilterMultimapScoreRange));
parArray.push_back(new ParameterInfoScalar <intScore> (-1, -1, "outFilterScoreMin", &outFilterScoreMin));
parArray.push_back(new ParameterInfoScalar <double> (-1, -1, "outFilterScoreMinOverLread", &outFilterScoreMinOverLread));
parArray.push_back(new ParameterInfoScalar <uint> (-1, -1, "outFilterMatchNmin", &outFilterMatchNmin));
parArray.push_back(new ParameterInfoScalar <double> (-1, -1, "outFilterMatchNminOverLread", &outFilterMatchNminOverLread));
parArray.push_back(new ParameterInfoScalar <uint> (-1, -1, "outFilterMismatchNmax", &outFilterMismatchNmax));
parArray.push_back(new ParameterInfoScalar <double> (-1, -1, "outFilterMismatchNoverLmax", &outFilterMismatchNoverLmax));
parArray.push_back(new ParameterInfoScalar <double> (-1, -1, "outFilterMismatchNoverReadLmax", &outFilterMismatchNoverReadLmax));
parArray.push_back(new ParameterInfoScalar <string> (-1, -1, "outFilterIntronMotifs", &outFilterIntronMotifs));
parArray.push_back(new ParameterInfoScalar <string> (-1, -1, "outFilterIntronStrands", &outFilterIntronStrands));
//clipping
parArray.push_back(new ParameterInfoVector <uint> (-1, -1, "clip5pNbases", &clip5pNbases));
parArray.push_back(new ParameterInfoVector <uint> (-1, -1, "clip3pNbases", &clip3pNbases));
parArray.push_back(new ParameterInfoVector <uint> (-1, -1, "clip3pAfterAdapterNbases", &clip3pAfterAdapterNbases));
parArray.push_back(new ParameterInfoVector <string> (-1, -1, "clip3pAdapterSeq", &clip3pAdapterSeq));
parArray.push_back(new ParameterInfoVector <double> (-1, -1, "clip3pAdapterMMp", &clip3pAdapterMMp));
//binning, anchors, windows
parArray.push_back(new ParameterInfoScalar <uint> (-1, -1, "winBinNbits", &winBinNbits));
parArray.push_back(new ParameterInfoScalar <uint> (-1, -1, "winAnchorDistNbins", &winAnchorDistNbins));
parArray.push_back(new ParameterInfoScalar <uint> (-1, -1, "winFlankNbins", &winFlankNbins));
parArray.push_back(new ParameterInfoScalar <uint> (-1, -1, "winAnchorMultimapNmax", &winAnchorMultimapNmax));
parArray.push_back(new ParameterInfoScalar <double> (-1, -1, "winReadCoverageRelativeMin", &winReadCoverageRelativeMin));
parArray.push_back(new ParameterInfoScalar <uint> (-1, -1, "winReadCoverageBasesMin", &winReadCoverageBasesMin));
//scoring
parArray.push_back(new ParameterInfoScalar <intScore> (-1, -1, "scoreGap", &scoreGap));
parArray.push_back(new ParameterInfoScalar <intScore> (-1, -1, "scoreGapNoncan", &scoreGapNoncan));
parArray.push_back(new ParameterInfoScalar <intScore> (-1, -1, "scoreGapGCAG", &scoreGapGCAG));
parArray.push_back(new ParameterInfoScalar <intScore> (-1, -1, "scoreGapATAC", &scoreGapATAC));
parArray.push_back(new ParameterInfoScalar <intScore> (-1, -1, "scoreStitchSJshift", &scoreStitchSJshift));
parArray.push_back(new ParameterInfoScalar <double> (-1, -1, "scoreGenomicLengthLog2scale", &scoreGenomicLengthLog2scale));
parArray.push_back(new ParameterInfoScalar <intScore> (-1, -1, "scoreDelBase", &scoreDelBase));
parArray.push_back(new ParameterInfoScalar <intScore> (-1, -1, "scoreDelOpen", &scoreDelOpen));
parArray.push_back(new ParameterInfoScalar <intScore> (-1, -1, "scoreInsOpen", &scoreInsOpen));
parArray.push_back(new ParameterInfoScalar <intScore> (-1, -1, "scoreInsBase", &scoreInsBase));
//alignment
parArray.push_back(new ParameterInfoScalar <uint> (-1, -1, "seedSearchLmax", &seedSearchLmax));
parArray.push_back(new ParameterInfoScalar <uint> (-1, -1, "seedSearchStartLmax", &seedSearchStartLmax));
parArray.push_back(new ParameterInfoScalar <double> (-1, -1, "seedSearchStartLmaxOverLread", &seedSearchStartLmaxOverLread));
parArray.push_back(new ParameterInfoScalar <uint> (-1, -1, "seedPerReadNmax", &seedPerReadNmax));
parArray.push_back(new ParameterInfoScalar <uint> (-1, -1, "seedPerWindowNmax", &seedPerWindowNmax));
parArray.push_back(new ParameterInfoScalar <uint> (-1, -1, "seedNoneLociPerWindow", &seedNoneLociPerWindow));
parArray.push_back(new ParameterInfoScalar <uint> (-1, -1, "seedMultimapNmax", &seedMultimapNmax));
parArray.push_back(new ParameterInfoScalar <uint> (-1, -1, "seedSplitMin", &seedSplitMin));
parArray.push_back(new ParameterInfoScalar <uint> (-1, -1, "alignIntronMin", &alignIntronMin));
parArray.push_back(new ParameterInfoScalar <uint> (-1, -1, "alignIntronMax", &alignIntronMax));
parArray.push_back(new ParameterInfoScalar <uint> (-1, -1, "alignMatesGapMax", &alignMatesGapMax));
parArray.push_back(new ParameterInfoScalar <uint> (-1, -1, "alignTranscriptsPerReadNmax", &alignTranscriptsPerReadNmax));
parArray.push_back(new ParameterInfoScalar <uint> (-1, -1, "alignSJoverhangMin", &alignSJoverhangMin));
parArray.push_back(new ParameterInfoScalar <uint> (-1, -1, "alignSJDBoverhangMin", &alignSJDBoverhangMin));
parArray.push_back(new ParameterInfoVector <int32> (-1, -1, "alignSJstitchMismatchNmax", &alignSJstitchMismatchNmax));
parArray.push_back(new ParameterInfoScalar <uint> (-1, -1, "alignSplicedMateMapLmin", &alignSplicedMateMapLmin));
parArray.push_back(new ParameterInfoScalar <double> (-1, -1, "alignSplicedMateMapLminOverLmate", &alignSplicedMateMapLminOverLmate));
parArray.push_back(new ParameterInfoScalar <uint> (-1, -1, "alignWindowsPerReadNmax", &alignWindowsPerReadNmax));
parArray.push_back(new ParameterInfoScalar <uint> (-1, -1, "alignTranscriptsPerWindowNmax", &alignTranscriptsPerWindowNmax));
parArray.push_back(new ParameterInfoScalar <string> (-1, -1, "alignEndsType", &alignEndsType.in));
parArray.push_back(new ParameterInfoScalar <string> (-1, -1, "alignSoftClipAtReferenceEnds", &alignSoftClipAtReferenceEnds.in));
parArray.push_back(new ParameterInfoVector <string> (-1, -1, "alignEndsProtrude", &alignEndsProtrude.in));
parArray.push_back(new ParameterInfoScalar <string> (-1, -1, "alignInsertionFlush", &alignInsertionFlush.in));
//peOverlap
parArray.push_back(new ParameterInfoScalar <uint> (-1, -1, "peOverlapNbasesMin", &peOverlap.NbasesMin));
parArray.push_back(new ParameterInfoScalar <double> (-1, -1, "peOverlapMMp", &peOverlap.MMp));
//chimeric
parArray.push_back(new ParameterInfoScalar <uint> (-1, -1, "chimSegmentMin", &pCh.segmentMin));
parArray.push_back(new ParameterInfoScalar <int> (-1, -1, "chimScoreMin", &pCh.scoreMin));
parArray.push_back(new ParameterInfoScalar <int> (-1, -1, "chimScoreDropMax", &pCh.scoreDropMax));
parArray.push_back(new ParameterInfoScalar <int> (-1, -1, "chimScoreSeparation", &pCh.scoreSeparation));
parArray.push_back(new ParameterInfoScalar <int> (-1, -1, "chimScoreJunctionNonGTAG", &pCh.scoreJunctionNonGTAG));
parArray.push_back(new ParameterInfoScalar <uint> (-1, -1, "chimMainSegmentMultNmax", &pCh.mainSegmentMultNmax));
parArray.push_back(new ParameterInfoScalar <uint> (-1, -1, "chimJunctionOverhangMin", &pCh.junctionOverhangMin));
parArray.push_back(new ParameterInfoVector <string> (-1, -1, "chimOutType", &pCh.out.type));
parArray.push_back(new ParameterInfoVector <string> (-1, -1, "chimFilter", &pCh.filter.stringIn));
parArray.push_back(new ParameterInfoScalar <uint> (-1, -1, "chimSegmentReadGapMax", &pCh.segmentReadGapMax));
parArray.push_back(new ParameterInfoScalar <uint> (-1, -1, "chimMultimapNmax", &pCh.multimapNmax));
parArray.push_back(new ParameterInfoScalar <uint> (-1, -1, "chimMultimapScoreRange", &pCh.multimapScoreRange));
parArray.push_back(new ParameterInfoScalar <uint> (-1, -1, "chimNonchimScoreDropMin", &pCh.nonchimScoreDropMin));
parArray.push_back(new ParameterInfoVector <int> (-1, -1, "chimOutJunctionFormat", &pCh.outJunctionFormat));
//sjdb
parArray.push_back(new ParameterInfoVector <string> (-1, -1, "sjdbFileChrStartEnd", &pGe.sjdbFileChrStartEnd));
parArray.push_back(new ParameterInfoScalar <string> (-1, -1, "sjdbGTFfile", &pGe.sjdbGTFfile));
parArray.push_back(new ParameterInfoScalar <string> (-1, -1, "sjdbGTFchrPrefix", &pGe.sjdbGTFchrPrefix));
parArray.push_back(new ParameterInfoScalar <string> (-1, -1, "sjdbGTFfeatureExon", &pGe.sjdbGTFfeatureExon));
parArray.push_back(new ParameterInfoScalar <string> (-1, -1, "sjdbGTFtagExonParentTranscript", &pGe.sjdbGTFtagExonParentTranscript));
parArray.push_back(new ParameterInfoScalar <string> (-1, -1, "sjdbGTFtagExonParentGene", &pGe.sjdbGTFtagExonParentGene));
parArray.push_back(new ParameterInfoVector <string> (-1, -1, "sjdbGTFtagExonParentGeneName", &pGe.sjdbGTFtagExonParentGeneName));
parArray.push_back(new ParameterInfoVector <string> (-1, -1, "sjdbGTFtagExonParentGeneType", &pGe.sjdbGTFtagExonParentGeneType));
parArray.push_back(new ParameterInfoScalar <uint> (-1, -1, "sjdbOverhang", &pGe.sjdbOverhang));
pGe.sjdbOverhang_par=parArray.size()-1;
parArray.push_back(new ParameterInfoScalar <int> (-1, -1, "sjdbScore", &pGe.sjdbScore));
parArray.push_back(new ParameterInfoScalar <string> (-1, -1, "sjdbInsertSave", &pGe.sjdbInsertSave));
//variation
parArray.push_back(new ParameterInfoScalar <string> (-1, -1, "varVCFfile", &var.vcfFile));
//WASP
parArray.push_back(new ParameterInfoScalar <string> (-1, -1, "waspOutputMode", &wasp.outputMode));
//quant
parArray.push_back(new ParameterInfoVector <string> (-1, -1, "quantMode", &quant.mode));
parArray.push_back(new ParameterInfoScalar <int> (-1, -1, "quantTranscriptomeBAMcompression", &quant.trSAM.bamCompression));
parArray.push_back(new ParameterInfoScalar <string> (-1, -1, "quantTranscriptomeBan", &quant.trSAM.ban));
//2-pass
parArray.push_back(new ParameterInfoScalar <uint> (-1, -1, "twopass1readsN", &twoPass.pass1readsN));
twoPass.pass1readsN_par=parArray.size()-1;
parArray.push_back(new ParameterInfoScalar <string> (-1, -1, "twopassMode", &twoPass.mode));
//solo
parArray.push_back(new ParameterInfoScalar <string> (-1, -1, "soloType", &pSolo.typeStr));
parArray.push_back(new ParameterInfoScalar <uint32> (-1, -1, "soloCBstart", &pSolo.cbS));
parArray.push_back(new ParameterInfoScalar <uint32> (-1, -1, "soloUMIstart", &pSolo.umiS));
parArray.push_back(new ParameterInfoScalar <uint32> (-1, -1, "soloCBlen", &pSolo.cbL));
parArray.push_back(new ParameterInfoScalar <uint32> (-1, -1, "soloUMIlen", &pSolo.umiL));
parArray.push_back(new ParameterInfoScalar <uint32> (-1, -1, "soloBarcodeReadLength", &pSolo.bL));
parArray.push_back(new ParameterInfoScalar <string> (-1, -1, "soloCBwhitelist", &pSolo.soloCBwhitelist));
parArray.push_back(new ParameterInfoScalar <string> (-1, -1, "soloStrand", &pSolo.strandStr));
parArray.push_back(new ParameterInfoVector <string> (-1, -1, "soloOutFileNames", &pSolo.outFileNames));
parArray.push_back(new ParameterInfoVector <string> (-1, -1, "soloFeatures", &pSolo.featureIn));
parArray.push_back(new ParameterInfoVector <string> (-1, -1, "soloUMIdedup", &pSolo.umiDedup));
parameterInputName.push_back("Default");
parameterInputName.push_back("Command-Line-Initial");
parameterInputName.push_back("Command-Line");
parameterInputName.push_back("genomeParameters.txt");
};
Parameters::~Parameters() {
// TODO cleanup sjNovel*? clip3pAdapterSeqNum?
for (auto *p : parArray) {
if (p != nullptr) {
delete p;
}
}
if (inOut != nullptr) {
delete inOut;
}
}
void Parameters::inputParameters (int argInN, char* argIn[]) {//input parameters: default, from files, from command line
///////// Default parameters
#include "parametersDefault.xxd"
string parString( (const char*) parametersDefault,parametersDefault_len);
stringstream parStream (parString);
scanAllLines(parStream, 0, -1);
for (uint ii=0; ii<parArray.size(); ii++) {
if (parArray[ii]->inputLevel<0) {
ostringstream errOut;
errOut <<"BUG: DEFAULT parameter value not defined: "<<parArray[ii]->nameString;
exitWithError(errOut.str(), std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
};
};
///////// Initial parameters from Command Line
commandLine="";
string commandLineFile="";
if (argInN>1) {//scan parameters from command line
commandLine += string(argIn[0]);
for (int iarg=1; iarg<argInN; iarg++) {
string oneArg=string(argIn[iarg]);
if (oneArg=="--version") {//print version and exit
std::cout << STAR_VERSION <<std::endl;
exit(0);
};
size_t found = oneArg.find("=");
if (found!=string::npos && oneArg.substr(0,2)=="--") {// --parameter=value
string key = oneArg.substr(2, found - 2);
string val = oneArg.substr(found + 1);
if (val.find_first_of(" \t")!=std::string::npos) {//there is white space in the argument, put "" around
val ='\"' + val + '\"';
};
commandLineFile += '\n' + key + ' ' + val;
}
else if (oneArg.substr(0,2)=="--") {//parameter name, cut --
commandLineFile +='\n' + oneArg.substr(2);
} else {//parameter value
if (oneArg.find_first_of(" \t")!=std::string::npos) {//there is white space in the argument, put "" around
oneArg ='\"' + oneArg +'\"';
};
commandLineFile +=' ' + oneArg;
};
commandLine += ' ' + oneArg;
};
istringstream parStreamCommandLine(commandLineFile);
scanAllLines(parStreamCommandLine, 1, 2); //read only initial Command Line parameters
};
// need to be careful since runMode and pGe.gDir are not Command-Line-Initial
// if (runMode=="genomeGenerate" && outFileNamePrefix=="./") {// for genome generation, output into pGe.gDir
// outFileNamePrefix=pGe.gDir;
// };
inOut->logMain.open((outFileNamePrefix + "Log.out").c_str());
if (inOut->logMain.fail()) {
ostringstream errOut;
errOut <<"EXITING because of FATAL ERROR: could not create output file: "<<outFileNamePrefix + "Log.out"<<"\n";
errOut <<"Check if the path " << outFileNamePrefix << " exists and you have permissions to write there\n";
exitWithError(errOut.str(),std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
};
inOut->logMain << "STAR version=" << STAR_VERSION << "\n";
inOut->logMain << "STAR compilation time,server,dir=" << COMPILATION_TIME_PLACE << "\n";
#ifdef COMPILE_FOR_LONG_READS
inOut->logMain << "Compiled for LONG reads" << "\n";
#endif
//define what goes to cout
if (outStd=="Log") {
inOut->logStdOut=& std::cout;
} else if (outStd=="SAM" || outStd=="BAM_Unsorted" || outStd=="BAM_SortedByCoordinate" || outStd=="BAM_Quant") {
inOut->logStdOutFile.open((outFileNamePrefix + "Log.std.out").c_str());
inOut->logStdOut= & inOut->logStdOutFile;
} else {
ostringstream errOut;
errOut <<"EXITING because of FATAL PARAMETER error: outStd="<<outStd <<" is not a valid value of the parameter\n";
errOut <<"SOLUTION: provide a valid value fot outStd: Log / SAM / BAM_Unsorted / BAM_SortedByCoordinate";
exitWithError(errOut.str(),std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
};
/*
inOut->logMain << "##### DEFAULT parameters:\n" <<flush;
for (uint ii=0; ii<parArray.size(); ii++) {
if (parArray[ii]->inputLevel==0) {
inOut->logMain << setw(PAR_NAME_PRINT_WIDTH) << parArray[ii]->nameString <<" "<< *(parArray[ii]) << endl;
};
};
*/
inOut->logMain <<"##### Command Line:\n"<<commandLine <<endl ;
inOut->logMain << "##### Initial USER parameters from Command Line:\n";
for (uint ii=0; ii<parArray.size(); ii++) {
if (parArray[ii]->inputLevel==1) {
inOut->logMain << setw(PAR_NAME_PRINT_WIDTH) << parArray[ii]->nameString <<" "<< *(parArray[ii]) << endl;
};
};
///////// Parameters files
if (parametersFiles.at(0) != "-") {//read parameters from a user-defined file
for (uint ii=0; ii<parametersFiles.size(); ii++) {
parameterInputName.push_back(parametersFiles.at(ii));
ifstream parFile(parametersFiles.at(ii).c_str());
if (parFile.good()) {
inOut->logMain << "##### USER parameters from user-defined parameters file " <<parametersFiles.at(ii)<< ":\n" <<flush;
scanAllLines(parFile, parameterInputName.size()-1, -1);
parFile.close();
} else {
ostringstream errOut;
errOut <<"EXITING because of fatal input ERROR: could not open user-defined parameters file " <<parametersFiles.at(ii)<< "\n" <<flush;
exitWithError(errOut.str(), std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
};
};
};
///////// Command Line Final
if (argInN>1) {//scan all parameters from command line and override previuos values
inOut->logMain << "###### All USER parameters from Command Line:\n" <<flush;
istringstream parStreamCommandLine(commandLineFile);
scanAllLines(parStreamCommandLine, 2, -1);
};
inOut->logMain << "##### Finished reading parameters from all sources\n\n" << flush;
inOut->logMain << "##### Final user re-defined parameters-----------------:\n" << flush;
ostringstream clFull;
clFull << argIn[0];
for (uint ii=0; ii<parArray.size(); ii++) {
if (parArray[ii]->inputLevel>0) {
inOut->logMain << setw(PAR_NAME_PRINT_WIDTH) << parArray[ii]->nameString <<" "<< *(parArray[ii]) << endl;
if (strcmp(parArray[ii]->nameString, "parametersFiles")) {
clFull << " --" << parArray[ii]->nameString << " " << *(parArray[ii]);
};
};
};
commandLineFull=clFull.str();
inOut->logMain << "\n-------------------------------\n##### Final effective command line:\n" << clFull.str() << "\n";
/*
// parOut.close();
inOut->logMain << "\n##### Final parameters after user input--------------------------------:\n" << flush;
// parOut.open("Parameters.all.out");
for (uint ii=0; ii<parArray.size(); ii++) {
inOut->logMain << setw(PAR_NAME_PRINT_WIDTH) << parArray[ii]->nameString <<" "<< *(parArray[ii]) << endl;
};
// parOut.close();
*/
inOut->logMain << "----------------------------------------\n\n" << flush;
///////////////////////////////////////// Old variables
//splitting
Qsplit=0;
maxNsplit=10;
minLsplit=seedSplitMin;
minLmap=5;
////////////////////////////////////////////////////// Calculate and check parameters
iReadAll=0;
if (runDirPermIn=="User_RWX")
{
runDirPerm=S_IRWXU;
} else if (runDirPermIn=="All_RWX")
{
runDirPerm= S_IRWXU | S_IRWXG | S_IRWXO;
} else
{
ostringstream errOut;
errOut << "EXITING because of FATAL INPUT ERROR: unrecognized option in --runDirPerm=" << runDirPerm << "\n";
errOut << "SOLUTION: use one of the allowed values of --runDirPerm : 'User_RWX' or 'All_RWX' \n";
exitWithError(errOut.str(),std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
};
/*
if (outTmpDir=="-") {
outFileTmp=outFileNamePrefix +"_STARtmp/";
sysRemoveDir (outFileTmp);
} else {
outFileTmp=outTmpDir + "/";
};
*/
/*
if (mkdir (outFileTmp.c_str(),runDirPerm)!=0) {
ostringstream errOut;
errOut <<"EXITING because of fatal ERROR: could not make temporary directory: "<< outFileTmp<<"\n";
errOut <<"SOLUTION: (i) please check the path and writing permissions \n (ii) if you specified --outTmpDir, and this directory exists - please remove it before running STAR\n"<<flush;
exitWithError(errOut.str(), std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
};
*/
//g_threadChunks.threadBool=(runThreadN>1);
//wigOut parameters
if (outWigType.at(0)=="None") {
outWigFlags.yes=false;
} else if (outWigType.at(0)=="bedGraph") {
outWigFlags.yes=true;
outWigFlags.format=0;
} else if (outWigType.at(0)=="wiggle") {
outWigFlags.yes=true;
outWigFlags.format=1;
} else {
ostringstream errOut;
errOut << "EXITING because of FATAL INPUT ERROR: unrecognized option in --outWigType=" << outWigType.at(0) << "\n";
errOut << "SOLUTION: use one of the allowed values of --outWigType : 'None' or 'bedGraph' \n";
exitWithError(errOut.str(),std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
};
if (outWigStrand.at(0)=="Stranded") {
outWigFlags.strand=true;
} else if (outWigStrand.at(0)=="Unstranded") {
outWigFlags.strand=false;
} else {
ostringstream errOut;
errOut << "EXITING because of FATAL INPUT ERROR: unrecognized option in --outWigStrand=" << outWigStrand.at(0) << "\n";
errOut << "SOLUTION: use one of the allowed values of --outWigStrand : 'Stranded' or 'Unstranded' \n";
exitWithError(errOut.str(),std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
};
if (outWigType.size()==1) {//simple bedGraph
outWigFlags.type=0;
} else {
if (outWigType.at(1)=="read1_5p") {
outWigFlags.type=1;
} else if (outWigType.at(1)=="read2") {
outWigFlags.type=2;
} else {
ostringstream errOut;
errOut << "EXITING because of FATAL INPUT ERROR: unrecognized second option in --outWigType=" << outWigType.at(1) << "\n";
errOut << "SOLUTION: use one of the allowed values of --outWigType : 'read1_5p' \n";
exitWithError(errOut.str(),std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
};
};
//wigOut parameters
if (outWigNorm.at(0)=="None") {
outWigFlags.norm=0;
} else if (outWigNorm.at(0)=="RPM") {
outWigFlags.norm=1;
} else {
ostringstream errOut;
errOut << "EXITING because of fatal parameter ERROR: unrecognized option in --outWigNorm=" << outWigNorm.at(0) << "\n";
errOut << "SOLUTION: use one of the allowed values of --outWigNorm : 'None' or 'RPM' \n";
exitWithError(errOut.str(),std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
};
//remove duplicates parameters
if (removeDuplicates.mode=="UniqueIdentical")
{
removeDuplicates.yes=true;
removeDuplicates.markMulti=true;
} else if (removeDuplicates.mode=="UniqueIdenticalNotMulti")
{
removeDuplicates.yes=true;
removeDuplicates.markMulti=false;
};
if (runMode=="alignReads") {
inOut->logProgress.open((outFileNamePrefix + "Log.progress.out").c_str());
}
outSAMbool=false;
outBAMunsorted=false;
outBAMcoord=false;
if (runMode=="alignReads" && outSAMmode != "None") {//open SAM file and write header
if (outSAMtype.at(0)=="BAM") {
if (outSAMtype.size()<2) {
ostringstream errOut;
errOut <<"EXITING because of fatal PARAMETER error: missing BAM option\n";
errOut <<"SOLUTION: re-run STAR with one of the allowed values of --outSAMtype BAM Unsorted OR SortedByCoordinate OR both\n";
exitWithError(errOut.str(), std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
};
for (uint32 ii=1; ii<outSAMtype.size(); ii++) {
if (outSAMtype.at(ii)=="Unsorted") {
outBAMunsorted=true;
} else if (outSAMtype.at(ii)=="SortedByCoordinate") {
outBAMcoord=true;
} else {
ostringstream errOut;
errOut <<"EXITING because of fatal input ERROR: unknown value for the word " <<ii+1<<" of outSAMtype: "<< outSAMtype.at(ii) <<"\n";
errOut <<"SOLUTION: re-run STAR with one of the allowed values of --outSAMtype BAM Unsorted or SortedByCoordinate or both\n";
exitWithError(errOut.str(), std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
};
};
//TODO check for conflicts
if (outBAMunsorted) {
if (outStd=="BAM_Unsorted") {
outBAMfileUnsortedName="-";
} else {
outBAMfileUnsortedName=outFileNamePrefix + "Aligned.out.bam";
};
throw std::runtime_error("Unimplemented!");
//inOut->outBAMfileUnsorted = bgzf_open(outBAMfileUnsortedName.c_str(),("w"+to_string((long long) outBAMcompression)).c_str());
};
if (outBAMcoord) {
if (outStd=="BAM_SortedByCoordinate") {
outBAMfileCoordName="-";
} else {
outBAMfileCoordName=outFileNamePrefix + "Aligned.sortedByCoord.out.bam";
};
throw std::runtime_error("Unimplemented!");
//inOut->outBAMfileCoord = bgzf_open(outBAMfileCoordName.c_str(),("w"+to_string((long long) outBAMcompression)).c_str());
if (outBAMsortingThreadN==0) {
outBAMsortingThreadNactual=min(6, runThreadN);
} else {
outBAMsortingThreadNactual=outBAMsortingThreadN;
};
outBAMcoordNbins=max((uint32)outBAMsortingThreadNactual*3,outBAMsortingBinsN);
outBAMsortingBinStart= new uint64 [outBAMcoordNbins];
outBAMsortingBinStart[0]=1;//this initial value means that the bin sizes have not been determined yet
outBAMsortTmpDir=outFileTmp+"/BAMsort/";
mkdir(outBAMsortTmpDir.c_str(),runDirPerm);
};
} else if (outSAMtype.at(0)=="SAM") {
if (outSAMtype.size()>1)
{
ostringstream errOut;
errOut <<"EXITING because of fatal PARAMETER error: --outSAMtype SAM can cannot be combined with "<<outSAMtype.at(1)<<" or any other options\n";
errOut <<"SOLUTION: re-run STAR with with '--outSAMtype SAM' only, or with --outSAMtype BAM Unsorted|SortedByCoordinate\n";
exitWithError(errOut.str(), std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
};
outSAMbool=true;
if (outStd=="SAM") {
inOut->outSAM = & std::cout;
} else {
inOut->outSAMfile.open((outFileNamePrefix + "Aligned.out.sam").c_str());
inOut->outSAM = & inOut->outSAMfile;
};
} else if (outSAMtype.at(0)=="None") {
//nothing to do, all flags are already false
} else {
ostringstream errOut;
errOut <<"EXITING because of fatal input ERROR: unknown value for the first word of outSAMtype: "<< outSAMtype.at(0) <<"\n";
errOut <<"SOLUTION: re-run STAR with one of the allowed values of outSAMtype: BAM or SAM \n"<<flush;
exitWithError(errOut.str(), std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
};
};
if (!outBAMcoord && outWigFlags.yes && runMode=="alignReads") {
ostringstream errOut;
errOut <<"SOLUTION: re-run STAR with with --outSAMtype BAM SortedByCoordinate, or, id you also need unsroted BAM, with --outSAMtype BAM SortedByCoordinate Unsorted\n";
exitWithError(errOut.str(), std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
};
//versions
for (uint ii=0;ii<1;ii++) {
if (parArray[ii]->inputLevel>0) {
ostringstream errOut;
errOut <<"EXITING because of fatal input ERROR: the version parameter "<< parArray[ii]->nameString << " cannot be re-defined by the user\n";
errOut <<"SOLUTION: please remove this parameter from the command line or input files and re-start STAR\n"<<flush;
exitWithError(errOut.str(), std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
};
};
//run
if (runThreadN<=0) {
ostringstream errOut;
errOut <<"EXITING: fatal input ERROR: runThreadN must be >0, user-defined runThreadN="<<runThreadN<<"\n";
exitWithError(errOut.str(), std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
};
//
if (outFilterType=="BySJout" && outSAMorder=="PairedKeepInputOrder") {
ostringstream errOut;
errOut <<"EXITING: fatal input ERROR: --outFilterType=BySJout is not presently compatible with --outSAMorder=PairedKeepInputOrder\n";
errOut <<"SOLUTION: re-run STAR without setting one of those parameters.\n";
exitWithError(errOut.str(), std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
};
if (!outSAMbool && outSAMorder=="PairedKeepInputOrder") {
ostringstream errOut;
errOut <<"EXITING: fatal input ERROR: --outSAMorder=PairedKeepInputOrder is presently only compatible with SAM output, i.e. default --outSMAtype SAM\n";
errOut <<"SOLUTION: re-run STAR without --outSAMorder=PairedKeepInputOrder, or with --outSAMorder=PairedKeepInputOrder --outSMAtype SAM .\n";
exitWithError(errOut.str(), std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
};
//SJ filtering
for (int ii=0;ii<4;ii++) {
if (outSJfilterOverhangMin.at(ii)<0) outSJfilterOverhangMin.at(ii)=numeric_limits<int32>::max();
if (outSJfilterCountUniqueMin.at(ii)<0) outSJfilterCountUniqueMin.at(ii)=numeric_limits<int32>::max();
if (outSJfilterCountTotalMin.at(ii)<0) outSJfilterCountTotalMin.at(ii)=numeric_limits<int32>::max();
if (outSJfilterDistToOtherSJmin.at(ii)<0) outSJfilterDistToOtherSJmin.at(ii)=numeric_limits<int32>::max();
if (alignSJstitchMismatchNmax.at(ii)<0) alignSJstitchMismatchNmax.at(ii)=numeric_limits<int32>::max();
};
if (limitGenomeGenerateRAM==0) {//must be >0
inOut->logMain <<"EXITING because of FATAL PARAMETER ERROR: limitGenomeGenerateRAM=0\n";
inOut->logMain <<"SOLUTION: please specify a >0 value for limitGenomeGenerateRAM\n"<<flush;
exit(1);
} else if (limitGenomeGenerateRAM>1000000000000) {//
inOut->logMain <<"WARNING: specified limitGenomeGenerateRAM="<<limitGenomeGenerateRAM<<" bytes appears to be too large, if you do not have enough memory the code will crash!\n"<<flush;
};
{//read groups
if (outSAMattrRGline.at(0)!="-") {
string linefull;
for (uint ii=0;ii<outSAMattrRGline.size(); ii++) {//concatenate into one line
if (ii==0 || outSAMattrRGline.at(ii)==",") {//start new entry
if (ii>0) ++ii;//skip comma
outSAMattrRGlineSplit.push_back(outSAMattrRGline.at(ii)); //star new RG line with the first field which must be ID:xxx
if (outSAMattrRGlineSplit.back().substr(0,3)!="ID:") {
ostringstream errOut;
errOut <<"EXITING because of FATAL INPUT ERROR: the first word of a line from --outSAMattrRGline="<<outSAMattrRGlineSplit.back()<<" does not start with ID:xxx read group identifier\n";
errOut <<"SOLUTION: re-run STAR with all lines in --outSAMattrRGline starting with ID:xxx\n";
exitWithError(errOut.str(), std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
};
outSAMattrRG.push_back(outSAMattrRGlineSplit.back().substr(3)); //this adds the ID field
} else {//keep adding fields to this RG line, until the next comma
outSAMattrRGlineSplit.back()+="\t" + outSAMattrRGline.at(ii);
};
};
};
};
outSAMfilter.KeepOnlyAddedReferences=false;
outSAMfilter.KeepAllAddedReferences=false;
outSAMfilter.yes=true;
if (outSAMfilter.mode.at(0)=="KeepOnlyAddedReferences")
{
outSAMfilter.KeepOnlyAddedReferences=true;
} else if (outSAMfilter.mode.at(0)=="KeepAllAddedReferences")
{
outSAMfilter.KeepAllAddedReferences=true;
} else if (outSAMfilter.mode.at(0)=="None")
{
outSAMfilter.yes=false;
} else
{
ostringstream errOut;
errOut <<"EXITING because of FATAL INPUT ERROR: unknown/unimplemented value for --outSAMfilter: "<<outSAMfilter.mode.at(0) <<"\n";
errOut <<"SOLUTION: specify one of the allowed values: KeepOnlyAddedReferences or None\n";
exitWithError(errOut.str(), std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
};
if ( (outSAMfilter.KeepOnlyAddedReferences || outSAMfilter.KeepAllAddedReferences) && pGe.gFastaFiles.at(0)=="-" ) {
ostringstream errOut;
errOut <<"EXITING because of FATAL INPUT ERROR: --outSAMfilter KeepOnlyAddedReferences OR KeepAllAddedReferences options can only be used if references are added on-the-fly with --genomeFastaFiles" <<"\n";
errOut <<"SOLUTION: use default --outSAMfilter None, OR add references with --genomeFataFiles\n";
exitWithError(errOut.str(), std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
};
if (outMultimapperOrder.mode=="Old_2.4")
{
outMultimapperOrder.random=false;
} else if (outMultimapperOrder.mode=="Random")
{
outMultimapperOrder.random=true;
} else
{
ostringstream errOut;
errOut <<"EXITING because of FATAL INPUT ERROR: unknown/unimplemented value for --outMultimapperOrder: "<<outMultimapperOrder.mode <<"\n";
errOut <<"SOLUTION: specify one of the allowed values: Old_2.4 or SortedByCoordinate or Random\n";
exitWithError(errOut.str(), std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
};
//read parameters
if (readFilesType.at(0)=="Fastx") {
readFilesTypeN=1;
} else if (readFilesType.at(0)=="SAM"){
readFilesTypeN=10;
} else {
ostringstream errOut;
errOut <<"EXITING because of FATAL INPUT ERROR: unknown/unimplemented value for --readFilesType: "<<readFilesType.at(0) <<"\n";
errOut <<"SOLUTION: specify one of the allowed values: Fastx or SAM\n";
exitWithError(errOut.str(), std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
};
if (readFilesTypeN==1) {
readNmates=readFilesIn.size(); //for now the number of mates is defined by the number of input files
} else if (readFilesTypeN==10) {//find the number of mates from the SAM file
if (readFilesType.size()==2 && readFilesType.at(1)=="SE") {
readNmates=1;
} else if (readFilesType.size()==2 && readFilesType.at(1)=="PE") {
readNmates=2;
} else {
ostringstream errOut;
errOut <<"EXITING because of FATAL INPUT ERROR: --readFilesType SAM requires specifying SE or PE reads"<<"\n";
errOut <<"SOLUTION: specify --readFilesType SAM SE for single-end reads or --readFilesType SAM PE for paired-end reads\n";
exitWithError(errOut.str(), std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
};
};
readNmatesIn=readNmates;
//two-pass
if (parArray.at(twoPass.pass1readsN_par)->inputLevel>0 && twoPass.mode=="None")
{
ostringstream errOut;
errOut << "EXITING because of fatal PARAMETERS error: --twopass1readsN is defined, but --twoPassMode is not defined\n";
errOut << "SOLUTION: to activate the 2-pass mode, use --twopassMode Basic";
exitWithError(errOut.str(),std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
};
twoPass.yes=false;
twoPass.pass2=false;
if (twoPass.mode!="None") {//2-pass parameters
if (runMode!="alignReads")
{
ostringstream errOut;
errOut << "EXITING because of fatal PARAMETERS error: 2-pass mapping option can only be used with --runMode alignReads\n";
errOut << "SOLUTION: remove --twopassMode option";
exitWithError(errOut.str(),std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
};
if (twoPass.mode!="Basic")
{
ostringstream errOut;
errOut << "EXITING because of fatal PARAMETERS error: unrecognized value of --twopassMode="<<twoPass.mode<<"\n";
errOut << "SOLUTION: for the 2-pass mode, use allowed values --twopassMode: Basic";
exitWithError(errOut.str(),std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
};
if (twoPass.pass1readsN==0)
{
ostringstream errOut;
errOut << "EXITING because of fatal PARAMETERS error: --twopass1readsN = 0 in the 2-pass mode\n";
errOut << "SOLUTION: for the 2-pass mode, specify --twopass1readsN > 0. Use a very large number or -1 to map all reads in the 1st pass.\n";
exitWithError(errOut.str(),std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
};
if (pGe.gLoad!="NoSharedMemory") {
ostringstream errOut;
errOut << "EXITING because of fatal PARAMETERS error: 2-pass method is not compatible with --genomeLoad "<<pGe.gLoad<<"\n";
errOut << "SOLUTION: re-run STAR with --genomeLoad NoSharedMemory ; this is the only option compatible with --twopassMode Basic .\n";
exitWithError(errOut.str(),std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
};
/*
twoPass.yes=true;
twoPass.dir=outFileNamePrefix+"_STARpass1/";
sysRemoveDir (twoPass.dir);
if (mkdir (twoPass.dir.c_str(),runDirPerm)!=0) {
ostringstream errOut;
errOut <<"EXITING because of fatal ERROR: could not make pass1 directory: "<< twoPass.dir<<"\n";
errOut <<"SOLUTION: please check the path and writing permissions \n";
exitWithError(errOut.str(), std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
};
*/
};
// openReadFiles depends on twoPass for reading SAM header
if (runMode=="alignReads" && pGe.gLoad!="Remove" && pGe.gLoad!="LoadAndExit") {//open reads files to check if they are present
//openReadsFiles();
readNmates = 2;
//check sizes of the mate files, if not the same, assume mates are not the same length
if (readNmates==1) {
readMatesEqualLengths=true;
} else if (readNmates > 2){
ostringstream errOut;
errOut <<"EXITING: because of fatal input ERROR: number of read mates files > 2: " <<readNmates << "\n";
errOut <<"SOLUTION:specify only one or two files in the --readFilesIn option. If file names contain spaces, use quotes: \"file name\"\n";
exitWithError(errOut.str(), std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
} else if (readMatesLengthsIn=="Equal") {
readMatesEqualLengths=true;
} else if (readMatesLengthsIn=="NotEqual") {
readMatesEqualLengths=false;
} else {
ostringstream errOut;
errOut <<"EXITING because of FATAL input ERROR: the value of the parameter readMatesLengthsIn=" << readMatesLengthsIn <<" is not among the allowed values: Equal or NotEqual\n";
errOut <<"SOLUTION: specify one of the allowed values: Equal or NotEqual\n";
exitWithError(errOut.str(), std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
};
if ( runMode=="alignReads" && outReadsUnmapped=="Fastx" ) {//open unmapped reads file
for (uint imate=0;imate<readNmates;imate++) {
ostringstream ff;
ff << outFileNamePrefix << "Unmapped.out.mate" << imate+1;
inOut->outUnmappedReadsStream[imate].open(ff.str().c_str());
};
};
if (outFilterType=="Normal") {
outFilterBySJoutStage=0;
} else if (outFilterType=="BySJout") {
outFilterBySJoutStage=1;
} else {
ostringstream errOut;
errOut <<"EXITING because of FATAL input ERROR: unknown value of parameter outFilterType: " << outFilterType <<"\n";
errOut <<"SOLUTION: specify one of the allowed values: Normal | BySJout\n";
exitWithError(errOut.str(), std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
};
};
if (outSAMmapqUnique<0 || outSAMmapqUnique>255) {
ostringstream errOut;
errOut <<"EXITING because of FATAL input ERROR: out of range value for outSAMmapqUnique=" << outSAMmapqUnique <<"\n";
errOut <<"SOLUTION: specify outSAMmapqUnique within the range of 0 to 255\n";
exitWithError(errOut.str(), std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
};
// in/out buffers
#define BUFFER_InSizeFraction 0.5
if (limitIObufferSize<limitOutSJcollapsed*Junction::dataSize+1000000)
{
ostringstream errOut;
errOut <<"EXITING because of FATAL INPUT ERROR: --limitIObufferSize="<<limitIObufferSize <<" is too small for ";
errOut << "--limitOutSJcollapsed*"<<Junction::dataSize<<"="<< limitOutSJcollapsed<<"*"<<Junction::dataSize<<"="<<limitOutSJcollapsed*Junction::dataSize<<"\n";
errOut <<"SOLUTION: re-run STAR with larger --limitIObufferSize or smaller --limitOutSJcollapsed\n";
exitWithError(errOut.str(), std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
};
chunkInSizeBytesArray=(uint) ((int64_t)((limitIObufferSize-limitOutSJcollapsed*Junction::dataSize)*BUFFER_InSizeFraction)/2);
chunkOutBAMsizeBytes= (uint) ((int64_t)((1.0/BUFFER_InSizeFraction-1.0)*chunkInSizeBytesArray*2.0));
chunkInSizeBytes=chunkInSizeBytesArray-2*(DEF_readSeqLengthMax+1)-2*DEF_readNameLengthMax;//to prevent overflow
//basic trimming
if (clip5pNbases.size()==1 && readNmates==2) clip5pNbases.push_back(clip5pNbases[0]);
if (clip3pNbases.size()==1 && readNmates==2) clip3pNbases.push_back(clip3pNbases[0]);
if (clip3pAfterAdapterNbases.size()==1 && readNmates==2) clip3pAfterAdapterNbases.push_back(clip3pAfterAdapterNbases[0]);
//adapter clipping
if (clip3pAdapterSeq.size()==1 && readNmates==2) clip3pAdapterSeq.push_back(clip3pAdapterSeq[0]);
if (clip3pAdapterMMp.size()==1 && readNmates==2) clip3pAdapterMMp.push_back(clip3pAdapterMMp[0]);
for (uint imate=0;imate<readNmates;imate++) {
if (clip3pAdapterSeq.at(imate).at(0)=='-') {// no clipping
clip3pAdapterSeq.at(imate).assign("");
} else {//clipping
clip3pAdapterSeqNum[imate]=new char [clip3pAdapterSeq.at(imate).length()];
convertNucleotidesToNumbers(clip3pAdapterSeq.at(imate).data(),clip3pAdapterSeqNum[imate],clip3pAdapterSeq.at(imate).length());
//inOut->fastaOutSeqs.open("Seqs.out.fasta");
};
};
//variation
var.yes=false;
if (var.vcfFile!="-")
{
var.yes=true;
};
//WASP
wasp.yes=false;
wasp.SAMtag=false;
if (wasp.outputMode=="SAMtag") {
wasp.yes=true;
wasp.SAMtag=true;
} else if (wasp.outputMode=="None") {
//nothing to do
} else {
ostringstream errOut;
errOut <<"EXITING because of FATAL INPUT ERROR: unknown/unimplemented --waspOutputMode option: "<<wasp.outputMode <<"\n";
errOut <<"SOLUTION: re-run STAR with allowed --waspOutputMode options: None or SAMtag\n";
exitWithError(errOut.str(), std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
};
if (wasp.yes && !var.yes) {
ostringstream errOut;
errOut <<"EXITING because of FATAL INPUT ERROR: --waspOutputMode option requires VCF file: "<<wasp.outputMode <<"\n";
errOut <<"SOLUTION: re-run STAR with --waspOutputMode ... and --varVCFfile /path/to/file.vcf\n";
exitWithError(errOut.str(), std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
};
if (wasp.yes && outSAMtype.at(0)!="BAM") {
ostringstream errOut;
errOut <<"EXITING because of FATAL INPUT ERROR: --waspOutputMode requires output to BAM file\n";
errOut <<"SOLUTION: re-run STAR with --waspOutputMode ... and --outSAMtype BAM ... \n";
exitWithError(errOut.str(), std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
};
//quantification parameters
quant.yes=false;
quant.geneFull.yes=false;
quant.geCount.yes=false;
quant.trSAM.yes=false;
quant.trSAM.bamYes=false;
quant.trSAM.indel=false;
quant.trSAM.softClip=false;
quant.trSAM.singleEnd=false;
if (quant.mode.at(0) != "-") {
quant.yes=true;
for (uint32 ii=0; ii<quant.mode.size(); ii++) {
if (quant.mode.at(ii)=="TranscriptomeSAM") {
quant.trSAM.yes=true;
if (quant.trSAM.bamCompression>-2)
quant.trSAM.bamYes=true;
if (quant.trSAM.bamYes) {
if (outStd=="BAM_Quant") {
outFileNamePrefix="-";
} else {
outQuantBAMfileName=outFileNamePrefix + "Aligned.toTranscriptome.out.bam";
};
throw std::runtime_error("Unimplemented!");
//inOut->outQuantBAMfile=bgzf_open(outQuantBAMfileName.c_str(),("w"+to_string((long long) quant.trSAM.bamCompression)).c_str());
};
if (quant.trSAM.ban=="IndelSoftclipSingleend") {
quant.trSAM.indel=false;
quant.trSAM.softClip=false;
quant.trSAM.singleEnd=false;
} else if (quant.trSAM.ban=="Singleend") {
quant.trSAM.indel=true;
quant.trSAM.softClip=true;
quant.trSAM.singleEnd=false;
};
} else if (quant.mode.at(ii)=="GeneCounts") {
quant.geCount.yes=true;
quant.geCount.outFile=outFileNamePrefix + "ReadsPerGene.out.tab";
} else {
ostringstream errOut;
errOut << "EXITING because of fatal INPUT error: unrecognized option in --quantMode=" << quant.mode.at(ii) << "\n";
errOut << "SOLUTION: use one of the allowed values of --quantMode : TranscriptomeSAM or GeneCounts or - .\n";
exitWithError(errOut.str(),std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
};
};
};
outSAMstrandField.type=0; //none
if (outSAMstrandField.in=="None") {