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#include "ParametersChimeric.h"
#include "Parameters.h"
#include "ErrorWarning.h"
#include "GlobalVariables.h"
void ParametersChimeric::initialize(Parameters *pPin)
{
out.bam=false;
out.junctions=false;
out.samOld=false;
out.bamHardClip=true;//default
if (segmentMin==0)
return;
pP=pPin;
pthread_mutex_init(&g_threadChunks.mutexOutChimSAM, NULL);
pthread_mutex_init(&g_threadChunks.mutexOutChimJunction, NULL);
for (const auto& type1 : out.type) {
if (type1=="WithinBAM") {
out.bam=true;
} else if (type1=="SeparateSAMold") {
out.samOld=true;
} else if (type1=="Junctions") {
out.junctions=true;
} else if (type1=="HardClip") {
out.bamHardClip=true;
} else if (type1=="SoftClip") {
out.bamHardClip=false;
} else {
ostringstream errOut;
errOut <<"EXITING because of FATAL INPUT ERROR: unknown/unimplemented value for --chimOutType: "<<type1 <<"\n";
errOut <<"SOLUTION: re-run STAR with --chimOutType Junctions , SeparateSAMold , WithinBAM , HardClip \n";
exitWithError(errOut.str(), std::cerr, pP->inOut->logMain, EXIT_CODE_PARAMETER, *pP);
};
};
if (out.samOld) {
pP->inOut->outChimSAM.open((pP->outFileNamePrefix + "Chimeric.out.sam").c_str());
pP->inOut->outChimSAM << pP->samHeader;
};
if (out.junctions) {
pP->inOut->outChimJunction.open((pP->outFileNamePrefix + "Chimeric.out.junction").c_str());
if (multimapNmax>0)
// column headers for Chimeric.out.junction file
pP->inOut->outChimJunction <<
"chr_donorA" <<"\t"<<
"brkpt_donorA" <<"\t"<<
"strand_donorA" <<"\t"<<
"chr_acceptorB" <<"\t"<<
"brkpt_acceptorB" <<"\t"<<
"strand_acceptorB" <<"\t"<<
"junction_type" <<"\t"<<
"repeat_left_lenA" <<"\t"<<
"repeat_right_lenB" <<"\t"<<
"read_name" <<"\t"<<
"start_alnA" <<"\t"<<
"cigar_alnA" <<"\t"<<
"start_alnB" <<"\t"<<
"cigar_alnB" <<"\t"<<
"num_chim_aln" <<"\t"<<
"max_poss_aln_score" <<"\t"<<
"non_chim_aln_score" <<"\t"<<
"this_chim_aln_score" <<"\t"<<
"bestall_chim_aln_score" <<"\t"<<
"PEmerged_bool" <<"\t"<<
"readgrp" <<"\n";
};
if (out.bam && !pP->outBAMunsorted && !pP->outBAMcoord) {
ostringstream errOut;
errOut <<"EXITING because of fatal PARAMETERS error: --chimOutType WithinBAM requires BAM output\n";
errOut <<"SOLUTION: re-run with --outSAMtype BAM Unsorted/SortedByCoordinate\n";
exitWithError(errOut.str(), std::cerr, pP->inOut->logMain, EXIT_CODE_PARAMETER, *pP);
};
if (multimapNmax>0 && out.samOld) {
ostringstream errOut;
errOut <<"EXITING because of fatal PARAMETERS error: --chimMultimapNmax > 0 (new chimeric detection) presently only works with --chimOutType Junctions/WithinBAM\n";
errOut <<"SOLUTION: re-run with --chimOutType Junctions/WithinBAM\n";
exitWithError(errOut.str(), std::cerr, pP->inOut->logMain, EXIT_CODE_PARAMETER, *pP);
};
if (pP->peOverlap.NbasesMin > 0) {
if (multimapNmax == 0 && (out.junctions || out.samOld)) {
ostringstream errOut;
errOut <<"EXITING because of fatal PARAMETERS error: --chimMultimapNmax 0 (default old chimeric detection) and --peOverlapNbasesMin > 0 (merging ovelrapping mates) presently only works with --chimOutType WithinBAM\n";
errOut <<"SOLUTION: re-run with --chimOutType WithinBAM\n";
exitWithError(errOut.str(), std::cerr, pP->inOut->logMain, EXIT_CODE_PARAMETER, *pP);
};
};
if (out.bam && !pP->outSAMattrPresent.NM) {
pP->outSAMattrOrder.push_back(ATTR_NM);
pP->inOut->logMain << "WARNING --chimOutType=WithinBAM, therefore STAR will output NM attribute" <<endl;
};
filter.genomicN=false;
for (uint ii=0; ii<filter.stringIn.size(); ii++) {
if (filter.stringIn.at(ii)=="banGenomicN") {
filter.genomicN=true;
} else if (filter.stringIn.at(ii)=="None") {
//nothing to do
}
else{
ostringstream errOut;
errOut << "EXITING because of fatal PARAMETERS error: unrecognized value of --chimFilter="<<filter.stringIn.at(ii)<<"\n";
errOut << "SOLUTION: use allowed values: banGenomicN || None";
exitWithError(errOut.str(),std::cerr, pP->inOut->logMain, EXIT_CODE_PARAMETER, *pP);
};
};
};
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