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#include "ReadAlignChunk.h"
#include <pthread.h>
#include "ErrorWarning.h"
ReadAlignChunk::ReadAlignChunk(Parameters& Pin, Genome &genomeIn, Transcriptome *TrIn, int iChunk) : P(Pin), mapGen(genomeIn) {//initialize chunk
iThread=iChunk;
if ( P.quant.yes ) {//allocate transcriptome structures
chunkTr=new Transcriptome(*TrIn);
chunkTr->quantsAllocate();
} else {
chunkTr=NULL;
};
RA = new ReadAlign(P, mapGen, chunkTr, iChunk);//new local copy of RA for each chunk
RA->iRead=0;
chunkIn=new char* [P.readNends];
readInStream=new istringstream* [P.readNends];
for (uint ii=0;ii<P.readNends;ii++) {
chunkIn[ii]=new char[P.chunkInSizeBytesArray];//reserve more space to finish loading one read
memset(chunkIn[ii],'\n',P.chunkInSizeBytesArray);
readInStream[ii] = new istringstream;
readInStream[ii]->rdbuf()->pubsetbuf(chunkIn[ii],P.chunkInSizeBytesArray);
RA->readInStream[ii]=readInStream[ii];
};
if (P.outSAMbool) {
chunkOutBAM=new char [P.chunkOutBAMsizeBytes];
RA->outBAMarray=chunkOutBAM;
chunkOutBAMstream=new ostringstream;
chunkOutBAMstream->rdbuf()->pubsetbuf(chunkOutBAM,P.chunkOutBAMsizeBytes);
RA->outSAMstream=chunkOutBAMstream;
RA->outSAMstream->seekp(0,ios::beg);
chunkOutBAMtotal=0;
};
if (P.outBAMunsorted) {
chunkOutBAMunsorted = new BAMoutput (P.inOut->outBAMfileUnsorted, P);
RA->outBAMunsorted = chunkOutBAMunsorted;
} else {
chunkOutBAMunsorted=NULL;
RA->outBAMunsorted=NULL;
};
if (P.outBAMcoord) {
chunkOutBAMcoord = new BAMoutput (iChunk, P.outBAMsortTmpDir, P);
RA->outBAMcoord = chunkOutBAMcoord;
} else {
chunkOutBAMcoord=NULL;
RA->outBAMcoord=NULL;
};
if ( P.quant.trSAM.bamYes ) {
chunkOutBAMquant = new BAMoutput (P.inOut->outQuantBAMfile,P);
RA->outBAMquant = chunkOutBAMquant;
} else {
chunkOutBAMquant=NULL;
RA->outBAMquant=NULL;
};
chunkOutSJ=new OutSJ (P.limitOutSJcollapsed, P, mapGen);
chunkOutSJ1=new OutSJ (P.limitOutSJcollapsed, P, mapGen);
RA->chunkOutSJ=chunkOutSJ;
RA->chunkOutSJ1=chunkOutSJ1;
if (P.pCh.segmentMin>0) {
if (P.pCh.out.samOld) {
chunkFstreamOpen(P.outFileTmp + "/Chimeric.out.sam.thread", iChunk, RA->chunkOutChimSAM);
};
if (P.pCh.out.junctions) {
chunkFstreamOpen(P.outFileTmp + "/Chimeric.out.junction.thread", iChunk, *RA->chunkOutChimJunction);
};
};
if (P.outReadsUnmapped=="Fastx" ) {
for (uint32 imate=0; imate < P.readNends; imate++)
chunkFstreamOpen(P.outFileTmp + "/Unmapped.out.mate"+ to_string(imate) +".thread",iChunk, RA->chunkOutUnmappedReadsStream[imate]);
};
if (P.outFilterType=="BySJout") {
chunkFstreamOpen(P.outFileTmp + "/FilterBySJoutFiles.mate1.thread",iChunk, RA->chunkOutFilterBySJoutFiles[0]);
if (P.readNends==2) chunkFstreamOpen(P.outFileTmp + "/FilterBySJoutFiles.mate2.thread",iChunk, RA->chunkOutFilterBySJoutFiles[1]); //here we do not output barcode read
};
if (P.wasp.yes) {
RA->waspRA= new ReadAlign(Pin,genomeIn,TrIn,iChunk);
};
if (P.peOverlap.yes) {
RA->peMergeRA= new ReadAlign(Pin,genomeIn,TrIn,iChunk);
delete RA->peMergeRA->chunkOutChimJunction;
RA->peMergeRA->chunkOutChimJunction=RA->chunkOutChimJunction;//point to the same out-stream
RA->peMergeRA->chimDet->ostreamChimJunction=RA->peMergeRA->chunkOutChimJunction;
RA->peMergeRA->outBAMunsorted=RA->outBAMunsorted;
RA->peMergeRA->outBAMcoord=RA->outBAMcoord;
};
};
///////////////
void ReadAlignChunk::chunkFstreamOpen(string filePrefix, int iChunk, fstream &fstreamOut) {//open fstreams for chunks
ostringstream fNameStream1;
fNameStream1 << filePrefix << iChunk;
string fName1=fNameStream1.str();
P.inOut->logMain << "Opening the file: " << fName1 << " ... " <<flush;
remove(fName1.c_str()); //remove the file
fstreamOut.open(fName1.c_str(),ios::out); //create empty file
fstreamOut.close();
fstreamOut.open(fName1.c_str(), ios::in | ios::out); //re-open the file in in/out mode
if (fstreamOut.fail()) {
P.inOut->logMain << "failed!\n";
ostringstream errOut;
errOut << "EXITING because of FATAL ERROR: could not create output file "<< fName1 << "\n";
errOut << "Solution: check that you have permission to write this file\n";
exitWithError(errOut.str(),std::cerr, P.inOut->logMain, EXIT_CODE_INPUT_FILES, P);
};
P.inOut->logMain << "ok" <<endl;
};
void ReadAlignChunk::chunkFstreamCat (fstream &chunkOut, ofstream &allOut, bool mutexFlag, pthread_mutex_t &mutexVal){
chunkOut.flush();
chunkOut.seekg(0,ios::beg);
if (mutexFlag) pthread_mutex_lock(&mutexVal);
allOut << chunkOut.rdbuf();
allOut.clear();
allOut.flush();
allOut.clear();
if (mutexFlag) pthread_mutex_unlock(&mutexVal);
chunkOut.clear();
chunkOut.seekp(0,ios::beg); //set put pointer at the beginning
};
void ReadAlignChunk::chunkFilesCat(ostream *allOut, string filePrefix, uint &iC) {//concatenates a file into main output
while (true) {
ostringstream name1("");
name1 << filePrefix <<iC;
ifstream fileChunkIn(name1.str().c_str());
if (fileChunkIn.good()) {
*allOut << fileChunkIn.rdbuf();
allOut->flush();
allOut->clear();
fileChunkIn.close();
fileChunkIn.clear();
remove(name1.str().c_str());
iC++;
} else {
fileChunkIn.close();
break;
};
};
};
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