int main_cat(int argc, char *argv[]) { bam_header_t *h = 0; char *outfn = 0; int c, ret; while ((c = getopt(argc, argv, "h:o:")) >= 0) { switch (c) { case 'h': { tamFile fph = sam_open(optarg); if (fph == 0) { fprintf(stderr, "[%s] ERROR: fail to read the header from '%s'.\n", __func__, argv[1]); return 1; } h = sam_header_read(fph); sam_close(fph); break; } case 'o': outfn = strdup(optarg); break; } } if (argc - optind < 2) { fprintf(stderr, "Usage: samtools cat [-h header.sam] [-o out.bam] <in1.bam> <in2.bam> [...]\n"); return 1; } ret = bam_cat(argc - optind, argv + optind, h, outfn? outfn : "-"); free(outfn); return ret; }
int bam_cat(int nfn, char * const *fn, const bam_header_t *h, const char* outbam) { BGZF *fp; FILE* fp_file; uint8_t *buf; uint8_t ebuf[BGZF_EMPTY_BLOCK_SIZE]; const int es=BGZF_EMPTY_BLOCK_SIZE; int i; fp = strcmp(outbam, "-")? bgzf_open(outbam, "w") : bgzf_fdopen(_fileno(stdout), "w"); if (fp == 0) { fprintf(stderr, "[%s] ERROR: fail to open output file '%s'.\n", __FUNCTION__, outbam); return 1; } if (h) bam_header_write(fp, h); buf = (uint8_t*) malloc(BUF_SIZE); for(i = 0; i < nfn; ++i){ BGZF *in; bam_header_t *old; int len,j; in = strcmp(fn[i], "-")? bam_open(fn[i], "r") : bam_dopen(_fileno(stdin), "r"); if (in == 0) { fprintf(stderr, "[%s] ERROR: fail to open file '%s'.\n", __FUNCTION__, fn[i]); return -1; } if (in->open_mode != 'r') return -1; old = bam_header_read(in); if (h == 0 && i == 0) bam_header_write(fp, old); if (in->block_offset < in->block_length) { bgzf_write(fp, (uint8_t*)in->uncompressed_block + in->block_offset, in->block_length - in->block_offset); bgzf_flush(fp); } j=0; #ifdef _USE_KNETFILE fp_file=fp->x.fpw; while ((len = knet_read(in->x.fpr, buf, BUF_SIZE)) > 0) { #else fp_file=fp->file; while (!feof(in->file) && (len = fread(buf, 1, BUF_SIZE, in->file)) > 0) { #endif if(len<es){ int diff=es-len; if(j==0) { fprintf(stderr, "[%s] ERROR: truncated file?: '%s'.\n", __FUNCTION__, fn[i]); return -1; } fwrite(ebuf, 1, len, fp_file); memcpy(ebuf,ebuf+len,diff); memcpy(ebuf+diff,buf,len); } else { if(j!=0) fwrite(ebuf, 1, es, fp_file); len-= es; memcpy(ebuf,buf+len,es); fwrite(buf, 1, len, fp_file); } j=1; } /* check final gzip block */ { const uint8_t gzip1=ebuf[0]; const uint8_t gzip2=ebuf[1]; const uint32_t isize=*((uint32_t*)(ebuf+es-4)); if(((gzip1!=GZIPID1) || (gzip2!=GZIPID2)) || (isize!=0)) { fprintf(stderr, "[%s] WARNING: Unexpected block structure in file '%s'.", __FUNCTION__, fn[i]); fprintf(stderr, " Possible output corruption.\n"); fwrite(ebuf, 1, es, fp_file); } } bam_header_destroy(old); bgzf_close(in); } free(buf); bgzf_close(fp); return 0; } int main_cat(int argc, char *argv[]) { bam_header_t *h = 0; char *outfn = 0; int c, ret; while ((c = getopt(argc, argv, "h:o:")) >= 0) { switch (c) { case 'h': { tamFile fph = sam_open(optarg); if (fph == 0) { fprintf(stderr, "[%s] ERROR: fail to read the header from '%s'.\n", __FUNCTION__, argv[1]); return 1; } h = sam_header_read(fph); sam_close(fph); break; } case 'o': outfn = strdup(optarg); break; } } if (argc - optind < 2) { fprintf(stderr, "Usage: samtools cat [-h header.sam] [-o out.bam] <in1.bam> <in2.bam> [...]\n"); return 1; } ret = bam_cat(argc - optind, argv + optind, h, outfn? outfn : "-"); free(outfn); return ret; }
int main(int argInN, char* argIn[]) { time(&g_statsAll.timeStart); Parameters *P = new Parameters; //all parameters P->inputParameters(argInN, argIn); *(P->inOut->logStdOut) << timeMonthDayTime(g_statsAll.timeStart) << " ..... Started STAR run\n" <<flush; //generate genome if (P->runMode=="genomeGenerate") { genomeGenerate(P); (void) sysRemoveDir (P->outFileTmp); P->inOut->logMain << "DONE: Genome generation, EXITING\n" << flush; exit(0); } else if (P->runMode!="alignReads") { P->inOut->logMain << "EXITING because of INPUT ERROR: unknown value of input parameter runMode=" <<P->runMode<<endl<<flush; exit(1); }; Genome mainGenome (P); mainGenome.genomeLoad(); if (P->genomeLoad=="LoadAndExit" || P->genomeLoad=="Remove") { return 0; }; P->twoPass.pass2=false; //this is the 1st pass SjdbClass sjdbLoci; if (P->sjdbInsert.pass1) { Parameters *P1=new Parameters; *P1=*P; sjdbInsertJunctions(P, P1, mainGenome, sjdbLoci); }; //calculate genome-related parameters Transcriptome *mainTranscriptome=NULL; /////////////////////////////////////////////////////////////////////////////////////////////////START if (P->runThreadN>1) { g_threadChunks.threadArray=new pthread_t[P->runThreadN]; pthread_mutex_init(&g_threadChunks.mutexInRead, NULL); pthread_mutex_init(&g_threadChunks.mutexOutSAM, NULL); pthread_mutex_init(&g_threadChunks.mutexOutBAM1, NULL); pthread_mutex_init(&g_threadChunks.mutexOutUnmappedFastx, NULL); pthread_mutex_init(&g_threadChunks.mutexOutFilterBySJout, NULL); pthread_mutex_init(&g_threadChunks.mutexStats, NULL); pthread_mutex_init(&g_threadChunks.mutexBAMsortBins, NULL); }; g_statsAll.progressReportHeader(P->inOut->logProgress); if (P->twoPass.yes) {//2-pass //re-define P for the pass1 Parameters *P1=new Parameters; *P1=*P; //turn off unnecessary calculations P1->outSAMtype[0]="None"; P1->outSAMbool=false; P1->outBAMunsorted=false; P1->outBAMcoord=false; P1->chimSegmentMin=0; P1->quant.yes=false; P1->quant.trSAM.yes=false; P1->quant.geCount.yes=false; P1->outFilterBySJoutStage=0; P1->outReadsUnmapped="None"; P1->outFileNamePrefix=P->twoPass.dir; P1->readMapNumber=P->twoPass.pass1readsN; // P1->inOut->logMain.open((P1->outFileNamePrefix + "Log.out").c_str()); g_statsAll.resetN(); time(&g_statsAll.timeStartMap); P->inOut->logProgress << timeMonthDayTime(g_statsAll.timeStartMap) <<"\tStarted 1st pass mapping\n" <<flush; *P->inOut->logStdOut << timeMonthDayTime(g_statsAll.timeStartMap) << " ..... Started 1st pass mapping\n" <<flush; //run mapping for Pass1 ReadAlignChunk *RAchunk1[P->runThreadN]; for (int ii=0;ii<P1->runThreadN;ii++) { RAchunk1[ii]=new ReadAlignChunk(P1, mainGenome, mainTranscriptome, ii); }; mapThreadsSpawn(P1, RAchunk1); outputSJ(RAchunk1,P1); //collapse and output junctions // for (int ii=0;ii<P1->runThreadN;ii++) { // delete [] RAchunk[ii]; // }; time_t rawtime; time (&rawtime); P->inOut->logProgress << timeMonthDayTime(rawtime) <<"\tFinished 1st pass mapping\n"; *P->inOut->logStdOut << timeMonthDayTime(rawtime) << " ..... Finished 1st pass mapping\n" <<flush; ofstream logFinal1 ( (P->twoPass.dir + "/Log.final.out").c_str()); g_statsAll.reportFinal(logFinal1,P1); P->twoPass.pass2=true;//starting the 2nd pass P->twoPass.pass1sjFile=P->twoPass.dir+"/SJ.out.tab"; sjdbInsertJunctions(P, P1, mainGenome, sjdbLoci); //reopen reads files P->closeReadsFiles(); P->openReadsFiles(); } else {//not 2-pass //nothing for now }; if ( P->quant.yes ) {//load transcriptome mainTranscriptome=new Transcriptome(P); }; //initialize Stats g_statsAll.resetN(); time(&g_statsAll.timeStartMap); *P->inOut->logStdOut << timeMonthDayTime(g_statsAll.timeStartMap) << " ..... Started mapping\n" <<flush; g_statsAll.timeLastReport=g_statsAll.timeStartMap; //open SAM/BAM files for output if (P->outSAMmode != "None") {//open SAM file and write header ostringstream samHeaderStream; for (uint ii=0;ii<P->nChrReal;ii++) { samHeaderStream << "@SQ\tSN:"<< P->chrName.at(ii) <<"\tLN:"<<P->chrLength[ii]<<"\n"; }; if (P->outSAMheaderPG.at(0)!="-") { samHeaderStream << P->outSAMheaderPG.at(0); for (uint ii=1;ii<P->outSAMheaderPG.size(); ii++) { samHeaderStream << "\t" << P->outSAMheaderPG.at(ii); }; samHeaderStream << "\n"; }; samHeaderStream << "@PG\tID:STAR\tPN:STAR\tVN:" << STAR_VERSION <<"\tCL:" << P->commandLineFull <<"\n"; if (P->outSAMheaderCommentFile!="-") { ifstream comstream (P->outSAMheaderCommentFile); while (comstream.good()) { string line1; getline(comstream,line1); if (line1.find_first_not_of(" \t\n\v\f\r")!=std::string::npos) {//skip blank lines samHeaderStream << line1 <<"\n"; }; }; }; for (uint32 ii=0;ii<P->outSAMattrRGlineSplit.size();ii++) {//@RG lines samHeaderStream << "@RG\t" << P->outSAMattrRGlineSplit.at(ii) <<"\n"; }; samHeaderStream << "@CO\t" <<"user command line: " << P->commandLine <<"\n"; if (P->outSAMheaderHD.at(0)!="-") { P->samHeaderHD = P->outSAMheaderHD.at(0); for (uint ii=1;ii<P->outSAMheaderHD.size(); ii++) { P->samHeaderHD +="\t" + P->outSAMheaderHD.at(ii); }; } else { P->samHeaderHD = "@HD\tVN:1.4"; }; P->samHeader=P->samHeaderHD+"\n"+samHeaderStream.str(); //for the sorted BAM, need to add SO:cooridnate to the header line P->samHeaderSortedCoord=P->samHeaderHD + (P->outSAMheaderHD.size()==0 ? "" : "\tSO:coordinate") + "\n" + samHeaderStream.str(); if (P->outSAMbool) {// *P->inOut->outSAM << P->samHeader; }; if (P->outBAMunsorted){ outBAMwriteHeader(P->inOut->outBAMfileUnsorted,P->samHeader,P->chrName,P->chrLength); }; // if (P->outBAMcoord){ // outBAMwriteHeader(P->inOut->outBAMfileCoord,P->samHeader,P->chrName,P->chrLength); // }; if ( P->quant.trSAM.yes ) { samHeaderStream.str(""); vector <uint> trlength; for (uint32 ii=0;ii<mainTranscriptome->trID.size();ii++) { uint32 iex1=mainTranscriptome->trExI[ii]+mainTranscriptome->trExN[ii]-1; //last exon of the transcript trlength.push_back(mainTranscriptome->exLenCum[iex1]+mainTranscriptome->exSE[2*iex1+1]-mainTranscriptome->exSE[2*iex1]+1); samHeaderStream << "@SQ\tSN:"<< mainTranscriptome->trID.at(ii) <<"\tLN:"<<trlength.back()<<"\n"; }; for (uint32 ii=0;ii<P->outSAMattrRGlineSplit.size();ii++) {//@RG lines samHeaderStream << "@RG\t" << P->outSAMattrRGlineSplit.at(ii) <<"\n"; }; outBAMwriteHeader(P->inOut->outQuantBAMfile,samHeaderStream.str(),mainTranscriptome->trID,trlength); }; }; if (P->chimSegmentMin>0) { P->inOut->outChimJunction.open((P->outFileNamePrefix + "Chimeric.out.junction").c_str()); P->inOut->outChimSAM.open((P->outFileNamePrefix + "Chimeric.out.sam").c_str()); P->inOut->outChimSAM << P->samHeader; pthread_mutex_init(&g_threadChunks.mutexOutChimSAM, NULL); pthread_mutex_init(&g_threadChunks.mutexOutChimJunction, NULL); }; // P->inOut->logMain << "mlock value="<<mlockall(MCL_CURRENT|MCL_FUTURE) <<"\n"<<flush; // prepare chunks and spawn mapping threads ReadAlignChunk *RAchunk[P->runThreadN]; for (int ii=0;ii<P->runThreadN;ii++) { RAchunk[ii]=new ReadAlignChunk(P, mainGenome, mainTranscriptome, ii); }; mapThreadsSpawn(P, RAchunk); if (P->outFilterBySJoutStage==1) {//completed stage 1, go to stage 2 P->inOut->logMain << "Completed stage 1 mapping of outFilterBySJout mapping\n"<<flush; outputSJ(RAchunk,P);//collapse novel junctions P->readFilesIndex=-1; P->outFilterBySJoutStage=2; if (P->outBAMcoord) { for (int it=0; it<P->runThreadN; it++) {//prepare the unmapped bin RAchunk[it]->chunkOutBAMcoord->coordUnmappedPrepareBySJout(); }; }; mapThreadsSpawn(P, RAchunk); }; //close some BAM files if (P->inOut->outBAMfileUnsorted!=NULL) { bgzf_flush(P->inOut->outBAMfileUnsorted); bgzf_close(P->inOut->outBAMfileUnsorted); }; if (P->inOut->outQuantBAMfile!=NULL) { bgzf_flush(P->inOut->outQuantBAMfile); bgzf_close(P->inOut->outQuantBAMfile); }; if (P->outBAMcoord && P->limitBAMsortRAM==0) {//make it equal ot the genome size P->limitBAMsortRAM=P->nGenome+mainGenome.SA.lengthByte+mainGenome.SAi.lengthByte; }; //no need for genome anymore, free the memory mainGenome.freeMemory(); if ( P->quant.geCount.yes ) {//output gene quantifications for (int ichunk=1; ichunk<P->runThreadN; ichunk++) {//sum counts from all chunks into 0th chunk RAchunk[0]->chunkTr->quants->addQuants(*(RAchunk[ichunk]->chunkTr->quants)); }; RAchunk[0]->chunkTr->quantsOutput(); }; if (P->runThreadN>1 && P->outSAMorder=="PairedKeepInputOrder") {//concatenate Aligned.* files RAchunk[0]->chunkFilesCat(P->inOut->outSAM, P->outFileTmp + "/Aligned.out.sam.chunk", g_threadChunks.chunkOutN); }; if (P->outBAMcoord) {//sort BAM if needed *P->inOut->logStdOut << timeMonthDayTime() << " ..... Started sorting BAM\n" <<flush; P->inOut->logMain << timeMonthDayTime() << " ..... Started sorting BAM\n" <<flush; uint32 nBins=P->outBAMcoordNbins; //check max size needed for sorting uint maxMem=0; for (uint32 ibin=0; ibin<nBins-1; ibin++) {//check akk bins uint binS=0; for (int it=0; it<P->runThreadN; it++) {//collect sizes from threads binS += RAchunk[it]->chunkOutBAMcoord->binTotalBytes[ibin]+24*RAchunk[it]->chunkOutBAMcoord->binTotalN[ibin]; }; if (binS>maxMem) maxMem=binS; }; P->inOut->logMain << "Max memory needed for sorting = "<<maxMem<<endl; if (maxMem>P->limitBAMsortRAM) { ostringstream errOut; errOut <<"EXITING because of fatal ERROR: not enough memory for BAM sorting: \n"; errOut <<"SOLUTION: re-run STAR with at least --limitBAMsortRAM " <<maxMem+1000000000; exitWithError(errOut.str(), std::cerr, P->inOut->logMain, EXIT_CODE_PARAMETER, *P); }; uint totalMem=0; // P->inOut->logMain << "Started sorting BAM ..." <<endl; #pragma omp parallel num_threads(P->outBAMsortingThreadNactual) #pragma omp for schedule (dynamic,1) for (uint32 ibin1=0; ibin1<nBins; ibin1++) { uint32 ibin=nBins-1-ibin1;//reverse order to start with the last bin - unmapped reads uint binN=0, binS=0; for (int it=0; it<P->runThreadN; it++) {//collect sizes from threads binN += RAchunk[it]->chunkOutBAMcoord->binTotalN[ibin]; binS += RAchunk[it]->chunkOutBAMcoord->binTotalBytes[ibin]; }; if (binS==0) continue; //empty bin if (ibin == nBins-1) {//last bin for unmapped reads BAMbinSortUnmapped(ibin,P->runThreadN,P->outBAMsortTmpDir,P->inOut->outBAMfileCoord, P); } else { uint newMem=binS+binN*24; bool boolWait=true; while (boolWait) { #pragma omp critical if (totalMem+newMem < P->limitBAMsortRAM) { boolWait=false; totalMem+=newMem; }; sleep(0.1); }; BAMbinSortByCoordinate(ibin,binN,binS,P->runThreadN,P->outBAMsortTmpDir,P->inOut->outBAMfileCoord, P); #pragma omp critical totalMem-=newMem;//"release" RAM }; }; //concatenate all BAM files, using bam_cat char **bamBinNames = new char* [nBins]; vector <string> bamBinNamesV; for (uint32 ibin=0; ibin<nBins; ibin++) { bamBinNamesV.push_back(P->outBAMsortTmpDir+"/b"+to_string((uint) ibin)); struct stat buffer; if (stat (bamBinNamesV.back().c_str(), &buffer) != 0) {//check if file exists bamBinNamesV.pop_back(); }; }; for (uint32 ibin=0; ibin<bamBinNamesV.size(); ibin++) { bamBinNames[ibin] = (char*) bamBinNamesV.at(ibin).c_str(); }; bam_cat(bamBinNamesV.size(), bamBinNames, 0, P->outBAMfileCoordName.c_str()); }; //wiggle output if (P->outWigFlags.yes) { *P->inOut->logStdOut << timeMonthDayTime() << " ..... Started wiggle output\n" <<flush; P->inOut->logMain << timeMonthDayTime() << " ..... Started wiggle output\n" <<flush; string wigOutFileNamePrefix=P->outFileNamePrefix + "Signal"; signalFromBAM(P->outBAMfileCoordName, wigOutFileNamePrefix, *P); }; //aggregate output junctions //collapse splice junctions from different threads/chunks, and output them outputSJ(RAchunk,P); g_statsAll.progressReport(P->inOut->logProgress); P->inOut->logProgress << "ALL DONE!\n"<<flush; P->inOut->logFinal.open((P->outFileNamePrefix + "Log.final.out").c_str()); g_statsAll.reportFinal(P->inOut->logFinal,P); *P->inOut->logStdOut << timeMonthDayTime(g_statsAll.timeFinish) << " ..... Finished successfully\n" <<flush; P->inOut->logMain << "ALL DONE!\n"<<flush; sysRemoveDir (P->outFileTmp); P->closeReadsFiles();//this will kill the readFilesCommand processes if necessary mainGenome.~Genome(); //need explicit call because of the 'delete P->inOut' below, which will destroy P->inOut->logStdOut delete P->inOut; //to close files delete P; return 0; };
int main_cat(int argc, char *argv[]) { bam_hdr_t *h = 0; char *outfn = 0; int c, ret; samFile *in; while ((c = getopt(argc, argv, "h:o:")) >= 0) { switch (c) { case 'h': { samFile *fph = sam_open(optarg, "r"); if (fph == 0) { fprintf(stderr, "[%s] ERROR: fail to read the header from '%s'.\n", __func__, argv[1]); return 1; } h = sam_hdr_read(fph); if (h == NULL) { fprintf(stderr, "[%s] ERROR: failed to read the header for '%s'.\n", __func__, argv[1]); return 1; } sam_close(fph); break; } case 'o': outfn = strdup(optarg); break; } } if (argc - optind < 1) { fprintf(stderr, "Usage: samtools cat [-h header.sam] [-o out.bam] <in1.bam> [...]\n"); return 1; } in = sam_open(argv[optind], "r"); if (!in) { fprintf(stderr, "[%s] ERROR: failed to open file '%s'.\n", __func__, argv[optind]); return 1; } switch (hts_get_format(in)->format) { case bam: sam_close(in); ret = bam_cat(argc - optind, argv + optind, h, outfn? outfn : "-"); break; case cram: sam_close(in); ret = cram_cat(argc - optind, argv + optind, h, outfn? outfn : "-"); break; default: sam_close(in); fprintf(stderr, "[%s] ERROR: input is not BAM or CRAM\n", __func__); return 1; } free(outfn); if (h) bam_hdr_destroy(h); return ret; }