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#include "ReadAlign.h"
#include "SequenceFuns.h"
#include "ErrorWarning.h"
uint64 ReadAlign::outputSpliceGraphSAM(Transcript const &trOut, uint nTrOut, uint iTrOut, ostream *outStream)
{
uint64 outStreamPos0=(uint64)outStream->tellp();
uint16 samFLAG=0;
if (readFilter=='Y')
samFLAG |= 0x200; //not passing quality control
if (unmapType>=0) {//unmapped reads: SAM
samFLAG |= 0x4;
*outStream << readName+1 <<"\t"<< samFLAG <<"\t"<< '*' <<"\t"<< '0' <<"\t"<< '0' <<"\t"<< '*';
//mate
*outStream <<"\t"<< '*' <<"\t"<< '0' <<"\t"<< '0' ;
*outStream <<"\t"<< Read0[0] <<"\t"<< (readFileType==2 ? Qual0[0]:"*") \
<<"\tNH:i:0" <<"\tHI:i:0" <<"\tAS:i:"<<trOut.maxScore <<"\tnM:i:"<<trOut.nMM<<"\tuT:A:" <<unmapType;
if (!P.outSAMattrRG.empty()) *outStream<< "\tRG:Z:" <<P.outSAMattrRG.at(readFilesIndex);
if (P.readFilesTypeN==10 && !readNameExtra[0].empty()) {//SAM files as input - output extra attributes
*outStream << "\t" <<readNameExtra[0];
};
*outStream <<"\n";
return (uint)outStream->tellp()-outStreamPos0;
};
//mapped
if (!trOut.primaryFlag)
samFLAG |= 0x100;
if (trOut.Str==1)
samFLAG |= 0x10;
string cigar;
const static char* cigarChars="MIDNS";
for (auto &cc : trOut.cigar) {
cigar += to_string(cc[1]) + cigarChars[cc[0]];
};
char seqRev[DEF_readSeqLengthMax+1], qualRev[DEF_readSeqLengthMax+1];
char *seqOut=NULL, *qualOut=NULL;
if ( trOut.Str==0 ) {//seq strand is correct
seqOut=Read0[0];
qualOut=Qual0[0];
} else {
revComplementNucleotides(Read0[0], seqRev, Lread);
for (uint ii=0;ii<Lread; ii++)
qualRev[ii]=Qual0[0][Lread-1-ii];
seqOut=seqRev;
qualOut=qualRev;
};
seqOut[Lread]=0;//to ensure string termination
qualOut[Lread]=0;
int MAPQ=P.outSAMmapqUnique;
if (nTrOut>=5) {
MAPQ=0;
} else if (nTrOut>=3) {
MAPQ=1;
} else if (nTrOut==2) {
MAPQ=3;
};
*outStream << readName+1 <<"\t"<< ((samFLAG & P.outSAMflagAND) | P.outSAMflagOR) <<"\t"<< genOut.chrName[trOut.Chr] <<"\t"<< trOut.gStart + 1 - genOut.chrStart[trOut.Chr]
<<"\t"<< MAPQ <<"\t"<< cigar;
*outStream <<"\t"<< "*" <<"\t"<< 0 <<"\t"<< 0;
*outStream <<"\t"<< seqOut;
if (readFileType==2 && P.outSAMmode != "NoQS") {//fastq
*outStream <<"\t"<< qualOut ;
} else {
*outStream <<"\t"<< "*";
};
uint32 tagNM = trOut.nMM + trOut.lIns + trOut.lDel;
for (uint ii=0;ii<P.outSAMattrOrder.size();ii++) {
switch (P.outSAMattrOrder[ii]) {
case ATTR_NH:
*outStream <<"\tNH:i:" << nTrOut;
break;
case ATTR_HI:
*outStream <<"\tHI:i:"<<iTrOut+P.outSAMattrIHstart;
break;
case ATTR_AS:
*outStream<<"\tAS:i:"<<trOut.maxScore;
break;
case ATTR_nM:
*outStream<<"\tnM:i:"<<trOut.nMM;
break;
case ATTR_NM:
*outStream<< "\tNM:i:" <<tagNM;
break;
// case ATTR_jM:
// *outStream<<"\tjM:B:c"<< SJmotif;
// break;
// case ATTR_jI:
// *outStream<<"\tjI:B:i"<< SJintron;
// break;
// case ATTR_XS:
// if (trOut.sjMotifStrand==1) {
// *outStream<<"\tXS:A:+";
// } else if (trOut.sjMotifStrand==2) {
// *outStream<<"\tXS:A:-";
// };
// break;
// case ATTR_MD:
// *outStream<< "\tMD:Z:" <<tagMD;
// break;
case ATTR_RG:
*outStream<< "\tRG:Z:" <<P.outSAMattrRG.at(readFilesIndex);
break;
// case ATTR_MC:
// if (nMates>1) {
// *outStream<< "\tMC:Z:" <<matesCIGAR[1-imate];
// };
// break;
//do nothing - this attributes only work for BAM output
case ATTR_jM:
case ATTR_jI:
case ATTR_XS:
case ATTR_MD:
case ATTR_ch:
case ATTR_CR:
case ATTR_CY:
case ATTR_UR:
case ATTR_UY:
case ATTR_CB:
case ATTR_UB:
case ATTR_sM:
case ATTR_sS:
case ATTR_sQ:
case ATTR_rB:
case ATTR_vG:
case ATTR_vA:
case ATTR_vW:
break;
default:
ostringstream errOut;
errOut <<"EXITING because of FATAL error: unknown/unimplemented SAM atrribute (tag): "<<P.outSAMattrOrder[ii] <<"\n";
errOut <<"SOLUTION: contact Alex Dobin at dobin@cshl.edu\n";
exitWithError(errOut.str(), std::cerr, P.inOut->logMain, EXIT_CODE_PARAMETER, P);
};
};
if (P.readFilesTypeN==10 && !readNameExtra[0].empty()) {//SAM files as input - output extra attributes
*outStream << "\t" << readNameExtra.at(0);
};
*outStream << "\n"; //done with one SAM line
return (uint)outStream->tellp()-outStreamPos0;
};
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