int main(int argc, char* argv[]) { if (argc < 3) { cout << "usage: testRandomSequence genome.fa ntries " << endl; exit(0); } string inFile = argv[1]; int nSamples = atoi(argv[2]); if (nSamples == 0) { return 0; } FASTAReader reader; reader.Initialize(inFile); vector<FASTASequence> genome; reader.ReadAllSequences(genome); int i; cout << "title pos" << endl; for (i = 0; i < nSamples; i++) { DNALength chrIndex, chrPos; FindRandomPos(genome, chrIndex, chrPos); cout << genome[chrIndex].title << " " << chrPos << endl; } return 0; }
int main(int argc, char* argv[]) { CommandLineParser clp; string readsFileName; string alignmentsFileName; string outputFileName; float minMergeIdentity = 0.70; clp.RegisterStringOption("reads", &readsFileName, "Reads used for alignments."); clp.RegisterStringOption("alignments", &alignmentsFileName, "SAM formatted alignments."); clp.RegisterIntOption("k", &vertexSize, "Minimum match length", CommandLineParser::PositiveInteger); clp.RegisterStringOption("outfile", &outputFileName, "Alignment output."); clp.RegisterPreviousFlagsAsHidden(); clp.RegisterFlagOption("v", &verbose, ""); clp.RegisterFloatOption("minMergeIdentity", &minMergeIdentity, "Minimum identity to merge paths.", CommandLineParser::PositiveFloat); clp.ParseCommandLine(argc, argv); if (minMergeIdentity < 0 or minMergeIdentity > 1) { cout << "ERROR. minMergeIdentity must be between 0 and 1" << endl; exit(1); } vector<FASTASequence> reads; FASTAReader fastaReader; fastaReader.Initialize(readsFileName); fastaReader.ReadAllSequences(reads); // // It is necessary to go from read title to index in the list of reads. // map<string, int> readNameToIndex; BuildReadNameToIndexMap(reads, readNameToIndex); ReadWordMatchVector readWordMatches; InitializeFromReads(reads, readWordMatches); // // Get ready to read in the alignments. // SAMReader<SAMFullReferenceSequence, SAMReadGroup, SAMPosAlignment> samReader; samReader.Initialize(alignmentsFileName); AlignmentSet<SAMFullReferenceSequence, SAMReadGroup, SAMPosAlignment> alignmentSet; samReader.ReadHeader(alignmentSet); SAMAlignment samAlignment; AlignmentCandidate<> alignment; int numAlignedBases = 0; int alignmentIndex = 0; while ( samReader.GetNextAlignment( samAlignment ) ) { vector<AlignmentCandidate<> > alignments; SAMAlignmentsToCandidates(samAlignment, reads, readNameToIndex, alignments, false, true); int i; ++alignmentIndex; int a; for (a = 0; a < alignments.size();a++) { if (alignments[a].qName != alignments[a].tName) { MarkMatches(alignments[a], readNameToIndex, vertexSize, readWordMatches); } } if (alignmentIndex % 1000 == 0) { cout << alignmentIndex << endl; } } int numMatches = 0; int parentIndex = 1; int r; for (r = 0; r < readWordMatches.size(); r++) { readWordMatches[r].CreateParents(); numMatches += readWordMatches[r].pos.size(); } vector<int> parentIndices; parentIndices.resize(2*numMatches + 1); fill(parentIndices.begin(), parentIndices.end(), 0); // // Start indexing off at 1 so that 0 does not need to be treated in // a special case. // int curParentIndex = 1; cout << "There are " << numMatches << " matches." << endl; samReader.Close(); samReader.Initialize(alignmentsFileName); AlignmentSet<SAMFullReferenceSequence, SAMReadGroup, SAMPosAlignment> alignmentSet2; samReader.ReadHeader(alignmentSet2); numAlignedBases = 0; alignmentIndex = 0; while ( samReader.GetNextAlignment( samAlignment ) ) { vector<AlignmentCandidate<> > alignments; SAMAlignmentsToCandidates(samAlignment, reads, readNameToIndex, alignments, false, true); int i; ++alignmentIndex; int a; for (a = 0; a < alignments.size();a++) { if (alignments[a].qName != alignments[a].tName) { JoinVertices(alignments[a], vertexSize, readNameToIndex, readWordMatches, curParentIndex, parentIndices); } } if (alignmentIndex % 1000 == 0) { cout << alignmentIndex << endl; } } vector<int> parentCounts; parentCounts.resize(parentIndices.size()); fill(parentCounts.begin(), parentCounts.end(), 0); int p; PromoteAll(parentIndices); int i; for (r = 0; r < readWordMatches.size(); r++) { for (i = 0; i < readWordMatches[r].parents.size(); i++) { readWordMatches[r].parents[i] = parentIndices[readWordMatches[r].parents[i]]; parentCounts[readWordMatches[r].parents[i]]++; } } /* for (i = 0; i < readWordMatches.size(); i++) { readWordMatches[i].PrintPos(cout); readWordMatches[i].PrintParents(cout); } */ map<int,int> hist; int numParents = 0; for (i = 1; i < parentCounts.size() && parentIndices[i] != 0; i++) { if (parentCounts[i] != 0) { ++numParents; } if (hist.find(parentCounts[i]) == hist.end()) { hist[parentCounts[i]] = 1; } else { hist[parentCounts[i]]++; } } map<int,int>::iterator histIt; cout << " freq count" << endl; for(histIt = hist.begin(); histIt != hist.end(); ++histIt) { cout << (*histIt).second << " " << (*histIt).first << endl; } MatchVertexList vertices; vertices.resize(numParents); cout << "there are " << numParents << " parents. " << endl; }
int main(int argc, char* argv[]) { string refFileName, notNormalFileName, normalFileName; if (argc < 4) { cout << "usage: normalizeGCContent ref source dest " << endl << " flips the C/Gs in source randomly until they are the same gc content as ref." << endl; exit(1); } refFileName = argv[1]; notNormalFileName = argv[2]; normalFileName = argv[3]; FASTAReader reader; FASTAReader queryReader; FASTASequence ref; vector<FASTASequence> querySequences; int queryTotalLength; reader.Initialize(refFileName); reader.ReadAllSequencesIntoOne(ref); queryReader.Initialize(notNormalFileName); int refCounts[5], queryCounts[5]; int s; refCounts[0] = refCounts[1] =refCounts[2] = refCounts[3] = refCounts[4] = 0; queryCounts[0] = queryCounts[1] =queryCounts[2] = queryCounts[3] = queryCounts[4] = 0; queryReader.ReadAllSequences(querySequences); ofstream normOut; CrucialOpen(normalFileName, normOut); CountNucs(ref, refCounts); float refGC = (1.0*refCounts[TwoBit['c']] + refCounts[TwoBit['g']]) / (refCounts[TwoBit['a']] + refCounts[TwoBit['c']] + refCounts[TwoBit['g']] + refCounts[TwoBit['t']]); int q; for (q = 0; q < querySequences.size(); q++) { CountNucs(querySequences[q], queryCounts); } float queryGC = (1.0*queryCounts[TwoBit['c']] + queryCounts[TwoBit['g']]) / (queryCounts[TwoBit['a']] + queryCounts[TwoBit['c']] + queryCounts[TwoBit['g']] + queryCounts[TwoBit['t']]); float gcToat = 0.0; float atTogc = 0.0; if (refGC > queryGC) { atTogc = (refGC - queryGC); } else { gcToat = (queryGC - refGC); } DNALength queryGenomeLength = queryCounts[0] + queryCounts[1] + queryCounts[2] + queryCounts[3] + queryCounts[4]; DNALength unmaskedQueryLength = queryCounts[0] + queryCounts[1] + queryCounts[2] + queryCounts[3]; DNALength ngc2at = unmaskedQueryLength * gcToat; DNALength nat2gc = unmaskedQueryLength * atTogc; cout << refGC << " " << queryGC << " " << gcToat << " " << atTogc << " " << ngc2at << " " << nat2gc << endl; vector<FASTASequence> normalized; normalized.resize(querySequences.size()); vector<DNALength> cumLengths; cumLengths.resize(normalized.size()+1); cumLengths[0] = 0; for (q = 0; q < querySequences.size(); q++) { normalized[q] = querySequences[q]; cumLengths[q+1] = cumLengths[q] + querySequences[q].length; } DNALength i; for (i = 0; i < ngc2at; i+=2) { DNALength pos, chr; FindRandomNuc(normalized, queryGenomeLength, cumLengths, 'G', chr, pos); normalized[chr].seq[pos] = 'A'; FindRandomNuc(normalized, queryGenomeLength, cumLengths, 'C', chr, pos); normalized[chr].seq[pos] = 'T'; } for (i = 0; i < nat2gc; i+=2) { DNALength pos, chr; FindRandomNuc(normalized, queryGenomeLength, cumLengths, 'A', chr, pos); normalized[chr].seq[pos] = 'g'; FindRandomNuc(normalized, queryGenomeLength, cumLengths, 'T', chr, pos); normalized[chr].seq[pos] = 'c'; } for (q = 0; q < normalized.size(); q++ ){ normalized[q].PrintSeq(normOut); } }
int main(int argc, char* argv[]) { string program = "samtoh5"; string versionString = VERSION; AppendPerforceChangelist(PERFORCE_VERSION_STRING, versionString); string samFileName, cmpFileName, refFileName; bool parseSmrtTitle = false; bool useShortRefName = false; CommandLineParser clp; string readType = "standard"; int verbosity = 0; clp.SetProgramName(program); clp.SetProgramSummary("Converts in.sam file to out.cmp.h5 file."); clp.SetVersion(versionString); clp.RegisterStringOption("in.sam", &samFileName, "Input SAM file.", true); clp.RegisterStringOption("reference.fasta", &refFileName, "Reference used to generate reads.", true); clp.RegisterStringOption("out.cmp.h5", &cmpFileName, "Output cmp.h5 file.", true); clp.RegisterPreviousFlagsAsHidden(); clp.RegisterFlagOption("smrtTitle", &parseSmrtTitle, "Use this option when converting alignments " "generated from reads produced by the " "pls2fasta from bas.h5 files by parsing read " "coordinates from the SMRT read title. The title " "is in the format /name/hole/coordinates, where " "coordinates are in the format \\d+_\\d+, and " "represent the interval of the read that was " "aligned."); clp.RegisterStringOption("readType", &readType, "Set the read type: 'standard', 'strobe', 'CCS', " "or 'cDNA'"); clp.RegisterIntOption("verbosity", &verbosity, "Set desired verbosity.", CommandLineParser::PositiveInteger); clp.RegisterFlagOption("useShortRefName", &useShortRefName, "Use abbreviated reference names obtained " "from file.sam instead of using full names " "from reference.fasta."); string description = ("Because SAM has optional tags that have different " "meanings in different programs, careful usage is required in order to " "have proper output. The \"xs\" tag in bwa-sw is used to show the " "suboptimal score, but in PacBio SAM (blasr) it is defined as the start " "in the query sequence of the alignment.\nWhen \"-smrtTitle\" is " "specified, the xs tag is ignored, but when it is not specified, the " "coordinates given by the xs and xe tags are used to define the interval " "of a read that is aligned. The CIGAR string is relative to this interval."); clp.SetExamples(description); clp.ParseCommandLine(argc, argv); if (readType != "standard" and readType != "strobe" and readType != "cDNA" and readType != "CCS") { cout << "ERROR. Read type '" << readType << "' must be one of either 'standard', 'strobe', 'cDNA' or 'CCS'." << endl; exit(1); } cerr << "[INFO] " << GetTimestamp() << " [" << program << "] started." << endl; SAMReader<SAMFullReferenceSequence, SAMReadGroup, SAMPosAlignment> samReader; FASTAReader fastaReader; HDFCmpFile<AlignmentCandidate<FASTASequence, FASTASequence> > cmpFile; // // Initialize input/output files. // samReader.Initialize(samFileName); fastaReader.Initialize(refFileName); cmpFile.Create(cmpFileName); // // Configure the file log. // string command; CommandLineParser::CommandLineToString(argc, argv, command); string log = "Convert sam to cmp.h5"; cmpFile.fileLogGroup.AddEntry(command, log, program, GetTimestamp(), versionString); // // Set the readType // cmpFile.SetReadType(readType); // // Read necessary input. // vector<FASTASequence> references; fastaReader.ReadAllSequences(references); // // This should probably be handled by the alignmentSetAdapter, but // time constraints... // AlignmentSet<SAMFullReferenceSequence, SAMReadGroup, SAMPosAlignment> alignmentSet; samReader.ReadHeader(alignmentSet); // // The order of references in vector<FASTASequence> references and // AlignmentSet<, , >alignmentSet.references can be different. // Rearrange alignmentSet.references such that it is ordered in // exactly the same way as vector<FASTASequence> references. // alignmentSet.RearrangeReferences(references); // // Always recompute the MD5 values even if they exist in the input // sam file. Because MD5 is defined differently in sam and cmp.h5 files. // The SAM convention uppercases and normalizes before computing the MD5. // For cmp.h5, we compute the MD5 on the sequence 'as is'. // for(int i = 0; i < alignmentSet.references.size(); i++) { MakeMD5((const char*)&references[i].seq[0], (unsigned int)references[i].length, alignmentSet.references[i].md5); } // // Map short names for references obtained from file.sam to full names obtained from reference.fasta // map<string, string> shortRefNameToFull; map<string, string>::iterator it; assert(references.size() == alignmentSet.references.size()); if (!useShortRefName) { for (int i = 0; i < references.size(); i++) { string shortRefName = alignmentSet.references[i].GetSequenceName(); string fullRefName(references[i].title); if (shortRefNameToFull.find(shortRefName) != shortRefNameToFull.end()) { cout << "ERROR, Found more than one reference " << shortRefName << "in sam header" << endl; exit(1); } shortRefNameToFull[shortRefName] = fullRefName; alignmentSet.references[i].sequenceName = fullRefName; } } // // Start setting up the cmp.h5 file. // AlignmentSetToCmpH5Adapter<HDFCmpFile<AlignmentCandidate<FASTASequence, FASTASequence> > > alignmentSetAdapter; alignmentSetAdapter.Initialize(); alignmentSetAdapter.StoreReferenceInfo(alignmentSet.references, cmpFile); // // Store the alignments. // SAMAlignment samAlignment; int alignIndex = 0; while (samReader.GetNextAlignment(samAlignment)) { if (samAlignment.rName == "*") { continue; } if (!useShortRefName) { //convert shortRefName to fullRefName it = shortRefNameToFull.find(samAlignment.rName); if (it == shortRefNameToFull.end()) { cout << "ERROR, Could not find " << samAlignment.rName << " in the reference repository." << endl; exit(1); } samAlignment.rName = (*it).second; } vector<AlignmentCandidate<> > convertedAlignments; if (verbosity > 0) { cout << "Storing alignment for " << samAlignment.qName << endl; } SAMAlignmentsToCandidates(samAlignment, references, alignmentSetAdapter.refNameToIndex, convertedAlignments, parseSmrtTitle, false); alignmentSetAdapter.StoreAlignmentCandidateList(convertedAlignments, cmpFile, alignIndex); int a; for (a = 0; a < convertedAlignments.size(); a++) { convertedAlignments[a].FreeSubsequences(); } ++alignIndex; /* if (alignIndex == 100) { return 0; }*/ } cerr << "[INFO] " << GetTimestamp() << " [" << program << "] ended." << endl; return 0; }
int main(int argc, char* argv[]) { string gencodeGffFileName, genomeFileName, genesOutFileName; string geneType = "protein_coding"; bool randomSplicing = false; int numRandomSplicing = 1; float pSkip = 0.5; if (argc < 4) { cout << "Usage: extractGenes gencodeGTFFile genomeFile genesOutFileName [-geneType type (protein_coding)] [-randomSplicing] [-numRandomSplicing n] [-pSkip prob (0-1, default:0.5)]" << endl; exit(1); } gencodeGffFileName = argv[1]; genomeFileName = argv[2]; genesOutFileName = argv[3]; int argi = 4; string coordinatesFileName; while (argi < argc) { if (strcmp(argv[argi], "-geneType") == 0) { geneType = argv[++argi]; } else if (strcmp(argv[argi], "-randomSplicing") == 0) { randomSplicing = true; } else if (strcmp(argv[argi], "-numRandomSplicing") == 0) { numRandomSplicing = atoi(argv[++argi]); } else if (strcmp(argv[argi], "-pSkip") == 0) { pSkip = atof(argv[++argi]); } else { cout << "ERROR, bad option " << argv[argi] << endl; exit(1); } ++argi; } coordinatesFileName = genesOutFileName; coordinatesFileName.append(".pos"); FASTAReader reader; reader.Initialize(genomeFileName); ofstream outFile, coordsFile; CrucialOpen(genesOutFileName, outFile, std::ios::out); string coordsFileName = genesOutFileName + ".coords"; CrucialOpen(coordsFileName, coordsFile, std::ios::out); vector<FASTASequence> referenceSequences; reader.ReadAllSequences(referenceSequences); int i; map<string, int> titleToIndex; for (i = 0; i < referenceSequences.size(); i++) { titleToIndex[referenceSequences[i].title] = i; } GencodeGFFFile gencodeFile; gencodeFile.ReadAll(gencodeGffFileName); vector<GencodeGFFGene> genes; IndexGencodeGenes(gencodeFile, genes, geneType); for (i = 0; i < genes.size(); i++) { genes[i].OrderExonsByStart(); } int e; for (i = 0; i < genes.size(); i++) { FASTASequence geneSequence; geneSequence.CopyTitle(genes[i].geneName); if (titleToIndex.find(genes[i].chromosome) == titleToIndex.end()) { continue; } int chrIndex = titleToIndex[genes[i].chromosome]; string sequence = ""; // // Do nothing with 0 length exons. // if (genes[i].exons.size() == 0) { continue; } vector<FASTASequence> geneSequences; vector<GeneCoordinates> geneCoordinates; genes[i].GenerateGeneSequences(referenceSequences[chrIndex], geneSequences, geneCoordinates, randomSplicing); int gi; for (gi = 0; gi < geneSequences.size(); gi++) { if (genes[i].GetStrand() == '+') { geneSequences[gi].PrintSeq(outFile); } else { FASTASequence rc; geneSequences[gi].MakeRC(rc); rc.PrintSeq(outFile); rc.Free(); } coordsFile << geneSequences[gi].title << " " << geneCoordinates[gi].chromosome << " " << geneCoordinates[gi].exonCoordinates.size() << " " << geneCoordinates[gi].strand; int i; for (i = 0; i < geneCoordinates[gi].exonCoordinates.size(); i++) { coordsFile << " " << geneCoordinates[gi].exonCoordinates[i].start << " " << geneCoordinates[gi].exonCoordinates[i].end << " "; } coordsFile << endl; geneSequences[gi].Free(); } // // No need to free the seq, since it is controlled by the string. // } coordsFile.close(); }
int main(int argc, char* argv[]) { string inFileName, readsFileName; DNALength readLength; float coverage = 0; bool noRandInit = false; int numReads = -1; CommandLineParser clp; int qualityValue = 20; bool printFastq = false; int stratify = 0; string titleType = "pacbio"; string fastqType = "illumina"; // or "sanger" clp.RegisterStringOption("inFile", &inFileName, "Reference sequence", 0); clp.RegisterPreviousFlagsAsHidden(); clp.RegisterIntOption("readLength", (int*) &readLength, "The length of reads to simulate. The length is fixed.", CommandLineParser::PositiveInteger, "Length of every read.", 0); clp.RegisterFloatOption("coverage", &coverage, "Total coverage (from which the number of reads is calculated", CommandLineParser::PositiveFloat, 0); clp.RegisterFlagOption("nonRandInit", &noRandInit, "Skip initializing the random number generator with time."); clp.RegisterIntOption("nReads", &numReads, "Total number of reads (from which coverage is calculated)", CommandLineParser::PositiveInteger, 0); clp.RegisterStringOption("readsFile", &readsFileName, "Reads output file", 0); clp.RegisterFlagOption("fastq", &printFastq, "Fake fastq output with constant quality value (20)"); clp.RegisterIntOption("quality", &qualityValue, "Value to use for fastq quality", CommandLineParser::PositiveInteger); clp.RegisterIntOption("stratify", &stratify, "Sample a read every 'stratify' bases, rather than randomly.", CommandLineParser::PositiveInteger); clp.RegisterStringOption("titleType", &titleType, "Set the name of the title: 'pacbio'|'illumina'"); clp.RegisterStringOption("fastqType", &fastqType, "Set the type of fastq: 'illumina'|'sanger'"); vector<string> leftovers; clp.ParseCommandLine(argc, argv, leftovers); if (!noRandInit) { InitializeRandomGeneratorWithTime(); } FASTAReader inReader; inReader.Init(inFileName); vector<FASTASequence> reference; inReader.ReadAllSequences(reference); ofstream readsFile; if (readsFileName == "") { cout << "ERROR. You must specify a reads file." << endl; exit(0); } CrucialOpen(readsFileName, readsFile, std::ios::out); ofstream sangerFastqFile; if (fastqType == "sanger") { string sangerFastqFileName = readsFileName + ".fastq"; CrucialOpen(sangerFastqFileName, sangerFastqFile, std::ios::out); } DNALength refLength = 0; int i; for (i = 0; i < reference.size(); i++) { refLength += reference[i].length; } if (numReads == -1 and coverage == 0 and stratify == 0) { cout << "Error, you must specify either coverage, nReads, or stratify." << endl; exit(1); } else if (numReads == -1) { numReads = (refLength / readLength) * coverage; } if (stratify) { if (!readLength) { cout << "ERROR. If you are using stratification, a read length must be specified." << endl; exit(1); } } DNASequence sampleSeq; sampleSeq.length = readLength; int maxRetry = 10000000; int retryNumber = 0; DNALength seqIndex, seqPos; if (stratify) { seqIndex = 0; seqPos = 0; } DNALength origReadLength = readLength; for (i = 0; stratify or i < numReads; i++) { if (stratify == 0) { FindRandomPos(reference, seqIndex, seqPos, readLength ); } else { // // find the next start pos, or bail if done // if (seqPos >= reference[seqIndex].length) { if (seqIndex == reference.size() - 1) { break; } else { seqIndex = seqIndex + 1; seqPos = 0; continue; } } readLength = min(reference[seqIndex].length - seqPos, origReadLength); } sampleSeq.seq = &reference[seqIndex].seq[seqPos]; int j; int gappedRead = 0; string title; stringstream titleStrm; if (titleType == "pacbio") { titleStrm << i << "|"<< reference[seqIndex].GetName() << "|" << seqPos << "|" << seqPos + readLength; } else if (titleType == "illumina") { titleStrm << "SE_" << i << "_0@" << seqPos << "-"<<seqPos+readLength <<"/1"; } else { cout << "ERROR. Bad title type " << titleType << endl; exit(0); } title = titleStrm.str(); sampleSeq.length = readLength; if (!printFastq) { readsFile << ">" << title << endl; sampleSeq.PrintSeq(readsFile); } else { FASTQSequence fastqSampleSeq; fastqSampleSeq.CopyTitle(title); fastqSampleSeq.seq = sampleSeq.seq; fastqSampleSeq.length = sampleSeq.length; fastqSampleSeq.qual.data = new unsigned char[sampleSeq.length]; fill(fastqSampleSeq.qual.data, fastqSampleSeq.qual.data + sampleSeq.length, qualityValue); if (fastqType == "illumina") { fastqSampleSeq.PrintFastq(readsFile, fastqSampleSeq.length+1); } else { fastqSampleSeq.PrintSeq(readsFile); fastqSampleSeq.PrintQual(sangerFastqFile); } delete[] fastqSampleSeq.qual.data; delete[] fastqSampleSeq.title; } if (stratify) { seqPos += readLength; } } return 0; }
int main(int argc, char* argv[]) { if (argc < 4) { PrintUsage(); exit(0); } string rgFileName, vertexSeqFileName, scaffoldDirName; rgFileName = argv[1]; vertexSeqFileName = argv[2]; scaffoldDirName = argv[3]; string repeatFileName = ""; bool printRepeatsSeparately = false; int argi = 4; bool printSeparate=false; while (argi < argc) { if (strcmp(argv[argi], "-separate") == 0) { printSeparate=true; } else if (strcmp(argv[argi], "-repeats") == 0) { printRepeatsSeparately = true; repeatFileName = argv[++argi]; } else { cout << "bad option: " << argv[argi] << endl; PrintUsage(); exit(1); } ++argi; } FASTAReader vertexSequenceReader; vertexSequenceReader.Init(vertexSeqFileName); // // Input necessary data // vector<FASTASequence> vertexSequences; vertexSequenceReader.ReadAllSequences(vertexSequences); RepeatGraph<string> rg; rg.ReadGraph(rgFileName); vector<FASTASequence> vertexRCSequences; VectorIndex vertexIndex; vertexRCSequences.resize(vertexSequences.size()); for (vertexIndex = 0; vertexIndex < vertexSequences.size(); vertexIndex++ ){ vertexSequences[vertexIndex].MakeRC(vertexRCSequences[vertexIndex]); } VectorIndex outEdgeIndex; int scaffoldIndex = 0; ofstream scaffoldOut; if (printSeparate==false) { // scaffold dir name is really a file name here. CrucialOpen(scaffoldDirName, scaffoldOut, std::ios::out); } for (vertexIndex = 0; vertexIndex < rg.vertices.size(); vertexIndex++ ){ rg.vertices[vertexIndex].traversed = false; } // // Set up flow for calling multiplicity. // /* Test all this out later. AssignMinimumFlowToEdges(rg, 2); AssignVertexFlowBalance(rg); BalanceKirchhoffFlow(rg); UInt edgeIndex; for (edgeIndex = 0; edgeIndex < rg.edges.size(); edgeIndex++) { if (rg.edges[edgeIndex].flow > 1) { cout << edgeIndex << " " << rg.edges[edgeIndex].flow << endl; } } */ int numPrintedVertices = 0; for (vertexIndex = 0; vertexIndex < rg.vertices.size(); vertexIndex++ ){ // // Look to see if this vertex is a branching vertex. // if ((rg.vertices[vertexIndex].inEdges.size() != 1 or rg.vertices[vertexIndex].outEdges.size() != 1) and rg.vertices[vertexIndex].traversed == false) { // // This is a branching vertex. Print all paths from this vertex, but not the vertex // itself if it appears repetitive. // VectorIndex outEdgeIndex; bool printedThisVertex = false; for (outEdgeIndex = 0; outEdgeIndex < rg.vertices[vertexIndex].outEdges.size(); outEdgeIndex++ ){ // // This is a branching vertex. // VectorIndex pathIndex; stringstream scaffoldFileNameStrm; cout << " printing scaffold: " << scaffoldIndex << endl; if (printSeparate) { scaffoldFileNameStrm << scaffoldDirName << "/" << scaffoldIndex << ".fasta"; string scaffoldFileName = scaffoldFileNameStrm.str(); CrucialOpen(scaffoldFileName, scaffoldOut, std::ios::out); } ++scaffoldIndex; // // Store the nonbranching path in a list so that it may be quickly processed. // bool pathIsPrinted = false; vector<VectorIndex> path; if (rg.vertices[vertexIndex].InDegree() == 0 and rg.vertices[vertexIndex].OutDegree() == 1) { path.push_back(vertexIndex); } VectorIndex pathVertex = rg.edges[rg.vertices[vertexIndex].outEdges[outEdgeIndex]].dest; while(rg.vertices[pathVertex].inEdges.size() == 1 and rg.vertices[pathVertex].outEdges.size() == 1) { if (rg.vertices[pathVertex].traversed == true) { pathIsPrinted = true; break; } path.push_back(pathVertex); // Mark the forward and reverse complement as traversed. pathVertex = rg.edges[rg.vertices[pathVertex].outEdges[0]].dest; // } // // Look to see if this is the end of a simple path, if so, add it to the scaffold. // pathVertex = rg.edges[rg.vertices[vertexIndex].outEdges[outEdgeIndex]].dest; if (rg.vertices[pathVertex].OutDegree() == 0 and rg.vertices[pathVertex].InDegree() == 1) { path.push_back(pathVertex); } // // Determine the sequences in the scaffold and the total scaffold length. // if (pathIsPrinted == false) { VectorIndex p; DNALength scaffoldLength = 0; for (p = 0; p < path.size(); p++ ){ scaffoldLength += vertexSequences[path[p]/2].length; rg.vertices[path[p]].traversed = true; // rg.vertices[2*(path[p]/2)+ !(path[p]%2)].traversed = true; ++numPrintedVertices; } cout << "path is of size " << path.size() << " length " << scaffoldLength << endl; if (!printSeparate) { scaffoldOut << ">" << scaffoldIndex << " " << path.size() << " " << scaffoldLength << endl; } for (p = 0; p < path.size(); p++) { if (printSeparate) { scaffoldOut << ">" << p << " " << path[p]/2 << " " << vertexSequences[path[p]/2].length << endl; } if (path[p]%2 == 0) { ((DNASequence)vertexSequences[path[p]/2]).PrintSeq(scaffoldOut); } else { ((DNASequence)vertexRCSequences[path[p]/2]).PrintSeq(scaffoldOut); } rg.vertices[path[p]].traversed = true; rg.vertices[2*(path[p]/2) + !(path[p]%2)].traversed = true; } if (printSeparate) { scaffoldOut.close(); scaffoldOut.clear(); } } } } } ofstream* outPtr; ofstream repeatOut; if (printRepeatsSeparately) { CrucialOpen(repeatFileName, repeatOut, std::ios::out); outPtr = &repeatOut; } else { outPtr = &scaffoldOut; } for (vertexIndex = 0; vertexIndex < rg.vertices.size(); vertexIndex++ ){ if (rg.vertices[vertexIndex].traversed == false) { // // Print this vertex sequence only. It is repetitive, or isolated. // *outPtr << ">" << scaffoldIndex << endl; ++scaffoldIndex; if (vertexIndex%2 == 0) { ((DNASequence)vertexSequences[vertexIndex/2]).PrintSeq(*outPtr); } else { ((DNASequence)vertexRCSequences[vertexIndex/2]).PrintSeq(*outPtr); } rg.vertices[vertexIndex].traversed = true; rg.vertices[2*(vertexIndex/2)+ !(vertexIndex%2)].traversed = true; } } cout << "printed: " << numPrintedVertices << " of " << rg.vertices.size() << endl; }
int main(int argc, char* argv[]) { string program = "samtom4"; string versionString = VERSION; AppendPerforceChangelist(PERFORCE_VERSION_STRING, versionString); string samFileName, refFileName, outFileName; bool printHeader = false; bool parseSmrtTitle = false; bool useShortRefName = false; CommandLineParser clp; clp.SetProgramName(program); clp.SetVersion(versionString); clp.SetProgramSummary("Converts a SAM file generated by blasr to M4 format."); clp.RegisterStringOption("in.sam", &samFileName, "Input SAM file, which is produced by blasr."); clp.RegisterStringOption("reference.fasta", &refFileName, "Reference used to generate file.sam."); clp.RegisterStringOption("out.m4", &outFileName, "Output in blasr M4 format."); clp.RegisterPreviousFlagsAsHidden(); clp.RegisterFlagOption("header", &printHeader, "Print M4 header."); clp.RegisterFlagOption("useShortRefName", &useShortRefName, "Use abbreviated reference names obtained " "from file.sam instead of using full names " "from reference.fasta."); //clp.SetExamples(program + " file.sam reference.fasta out.m4"); clp.ParseCommandLine(argc, argv); ostream * outFilePtr = &cout; ofstream outFileStrm; if (outFileName != "") { CrucialOpen(outFileName, outFileStrm, std::ios::out); outFilePtr = &outFileStrm; } SAMReader<SAMFullReferenceSequence, SAMReadGroup, SAMAlignment> samReader; FASTAReader fastaReader; // // Initialize samReader and fastaReader. // samReader.Initialize(samFileName); fastaReader.Initialize(refFileName); // // Configure the file log. // string command; CommandLineParser::CommandLineToString(argc, argv, command); // // Read necessary input. // vector<FASTASequence> references; fastaReader.ReadAllSequences(references); AlignmentSet<SAMFullReferenceSequence, SAMReadGroup, SAMAlignment> alignmentSet; samReader.ReadHeader(alignmentSet); // // The order of references in vector<FASTASequence> references and // AlignmentSet<, , >alignmentSet.references can be different. // Rearrange alignmentSet.references such that it is ordered in // exactly the same way as vector<FASTASequence> references. // alignmentSet.RearrangeReferences(references); // // Map short names for references obtained from file.sam to // full names obtained from reference.fasta // map<string, string> shortRefNameToFull; map<string, string>::iterator it; assert(references.size() == alignmentSet.references.size()); if (!useShortRefName) { for (size_t i = 0; i < references.size(); i++) { string shortRefName = alignmentSet.references[i].GetSequenceName(); string fullRefName(references[i].title); if (shortRefNameToFull.find(shortRefName) != shortRefNameToFull.end()) { cout << "ERROR, Found more than one reference " << shortRefName << "in sam header" << endl; exit(1); } shortRefNameToFull[shortRefName] = fullRefName; alignmentSet.references[i].sequenceName = fullRefName; } } // Map reference name obtained from SAM file to indices map<string, int> refNameToIndex; for (size_t i = 0; i < references.size(); i++) { string refName = alignmentSet.references[i].GetSequenceName(); refNameToIndex[refName] = i; } // // Store the alignments. // SAMAlignment samAlignment; size_t alignIndex = 0; // // For 150K, each chip produces about 300M sequences // (not including quality values and etc.). // Let's assume that the sam file and reference data can // fit in the memory. // Need to scale for larger sequal data in the future. // if (printHeader) IntervalOutput::PrintHeader(*outFilePtr); // The socre matrix does not matter because we will use the // aligner's score from SAM file anyway. DistanceMatrixScoreFunction<DNASequence, DNASequence> distScoreFn; while (samReader.GetNextAlignment(samAlignment)) { if (samAlignment.rName == "*") { continue; } if (!useShortRefName) { //convert shortRefName to fullRefName it = shortRefNameToFull.find(samAlignment.rName); if (it == shortRefNameToFull.end()) { cout << "ERROR, Could not find " << samAlignment.rName << " in the reference repository." << endl; exit(1); } samAlignment.rName = (*it).second; } // The padding character 'P' is not supported if (samAlignment.cigar.find('P') != string::npos) { cout << "WARNING. Could not process sam record with 'P' in its cigar string." << endl; continue; } vector<AlignmentCandidate<> > convertedAlignments; // // Keep reference as forward. // So if IsReverseComplement(sam.flag)==true, then qStrand is reverse // and tStrand is forward. // bool keepRefAsForward = false; SAMAlignmentsToCandidates(samAlignment, references, refNameToIndex, convertedAlignments, parseSmrtTitle, keepRefAsForward); if (convertedAlignments.size() > 1) { cout << "WARNING. Ignore an alignment which has multiple segments." << endl; continue; } //all alignments are unique single-ended alignments. for (int i = 0; i < 1; i++) { AlignmentCandidate<> & alignment = convertedAlignments[i]; ComputeAlignmentStats(alignment, alignment.qAlignedSeq.seq, alignment.tAlignedSeq.seq, distScoreFn); // Use aligner's score from SAM file anyway. alignment.score = samAlignment.as; alignment.mapQV = samAlignment.mapQV; // Since SAM only has the aligned sequence, many info of the // original query (e.g. the full length) is missing. // Overwrite alignment.qLength (which is length of the query // in the SAM alignment) with xq (which is the length of the // original query sequence saved by blasr) right before printing // the output so that one can reconstruct a blasr m4 record from // a blasr sam alignment. if (samAlignment.xq!=0) alignment.qLength = samAlignment.xq; IntervalOutput::PrintFromSAM(alignment, *outFilePtr); alignment.FreeSubsequences(); } ++alignIndex; } if (outFileName != "") { outFileStrm.close(); } return 0; }
int main(int argc, char* argv[]) { string rgInName, rgOutName; int minPathLength; string vertexSequenceFileName; if (argc < 5) { cout << "usage: trimShortEnds in.rg vertexSequences minPathLength out.rg" << endl; exit(1); } rgInName = argv[1]; vertexSequenceFileName = argv[2]; minPathLength = atoi(argv[3]); rgOutName = argv[4]; ofstream rgOut; CrucialOpen(rgOutName, rgOut, std::ios::out); FASTAReader vertexSequenceReader; vertexSequenceReader.Init(vertexSequenceFileName); RepeatGraph<string> rg; vector<FASTASequence> vertexSequences; rg.ReadGraph(rgInName); vertexSequenceReader.ReadAllSequences(vertexSequences); VectorIndex vertexIndex; VectorIndex outEdgeIndex; VectorIndex edgeIndex; if (rg.edges.size() == 0) { cout << "LIKELY INVALID GRAPH. There are no edges." << endl; return 0; } // // At first, any edge that exists is connected to a vertex. This // will change as low coverage edges are deleted and replaced by // high coverage edges from the end of the array. // for (edgeIndex = 0; edgeIndex < rg.edges.size(); edgeIndex++) { rg.edges[edgeIndex].connected = true; } set<std::pair<VectorIndex, VectorIndex> > srcDestToRemove; for (vertexIndex = 0; vertexIndex < rg.vertices.size(); vertexIndex++) { if (rg.vertices[vertexIndex].inEdges.size() == 0 and rg.vertices[vertexIndex].outEdges.size() == 1) { // // This is a source. Traverse this until a branching vertex or the end is found. // vector<VectorIndex> path; path.push_back(vertexIndex); int pathLength = 0; VectorIndex pathVertex; VectorIndex pathEdge; pathEdge = rg.vertices[vertexIndex].outEdges[0]; pathVertex = rg.edges[pathEdge].dest; while (rg.vertices[pathVertex].inEdges.size() == 1 and rg.vertices[pathVertex].outEdges.size() == 1) { path.push_back(pathVertex); pathEdge = rg.vertices[pathVertex].outEdges[0]; pathVertex = rg.edges[pathEdge].dest; pathLength += vertexSequences[pathVertex/2].length; } pathLength += vertexSequences[pathVertex/2].length; path.push_back(pathVertex); if (pathLength < minPathLength and path.size() < 3) { // // Remove this path, it is too short. // Also remove the complement. // cout << "trimming path of " << path.size() << " is of sequence length " << pathLength << endl; VectorIndex pathIndex; for (pathIndex = 0; pathIndex < path.size() - 1; pathIndex++) { srcDestToRemove.insert(pair<VectorIndex, VectorIndex>(path[pathIndex], path[pathIndex+1])); srcDestToRemove.insert(pair<VectorIndex, VectorIndex>(2*(path[pathIndex+1]/2) + !(path[pathIndex+1]%2), 2*(path[pathIndex]/2) + !(path[pathIndex]%2))); } } } } MarkEdgePairsForRemoval(srcDestToRemove, rg.vertices, rg.edges); RemoveUnconnectedEdges(rg.vertices, rg.edges); rg.WriteGraph(rgOut); return 0; }
int main(int argc, char* argv[]) { FASTAReader reader; FASTASequence read; int maxLength = 100; if (argc < 3) { cout << "usage: pairAlignAllContigs inFile maxLength equivalencies [-minIdent i]" << endl; exit(0); } string readsFileName, equivalenciesFileName; readsFileName = argv[1]; maxLength = atoi(argv[2]); equivalenciesFileName = argv[3]; int argi = 4; float minIdentity = 80; while (argi < argc) { if (strcmp(argv[argi], "-minIdent") == 0) { minIdentity = atoi(argv[++argi]); } ++argi; } vector<FASTASequence> reads, readsRC;; reader.Init(readsFileName); reader.ReadAllSequences(reads); readsRC.resize(reads.size()); int r; for (r =0; r < reads.size();r++) { reads[r].MakeRC(readsRC[r]); } ofstream equivOut; CrucialOpen(equivalenciesFileName, equivOut); Matrix<int> alignScores; Matrix<float> alignIdentities; alignScores.Resize(reads.size(), reads.size()); alignIdentities.Resize(reads.size(), reads.size()); vector<int> scoreMat; vector<Arrow> pathMat; int i, j; int alignScore; FASTASequence readi, readj; FASTASequence rcReadi, rcReadj; for (i = 0; i < reads.size(); i++) { float maxFrontIdent, maxEndIdent; int maxFrontIdentIndex, maxEndIdentIndex; maxFrontIdent = 0; maxEndIdent = 0; maxFrontIdentIndex = 0; maxEndIdentIndex = 0; int maxFrontIdentLength = 0; int maxEndIdentLength = 0; int maxFrontLength = 0; int maxEndLength = 0; int nmaxFrontLengthIndex = 0; int maxEndLengthIndex = 0; float maxFrontLengthIdent = 0; float maxEndLengthIdent = 0; int maxFrontLengthIndex = 0; equivOut << reads[i].GetName(); for (j = 0; j < reads.size(); j++ ){ // // Store the two ends of the alignment. // alignScore = 0; int rcAlignScore; Alignment alignment; Alignment rcAlignment; Alignment *optAlignment; if (i != j) { if (reads[i].length < maxLength and reads[j].length < maxLength) { alignScore = SWAlign(reads[i], reads[j], SMRTDistanceMatrix, 3, scoreMat, pathMat, alignment, Global); } if (reads[i].length < maxLength and reads[j].length < maxLength) { rcAlignScore = SWAlign(reads[i], readsRC[j], SMRTDistanceMatrix, 3, scoreMat, pathMat, rcAlignment, Global); } ComputeAlignmentStats(alignment, reads[i].seq, reads[j].seq, SMRTDistanceMatrix, 3,3 ); ComputeAlignmentStats(rcAlignment, reads[i].seq, readsRC[j].seq, SMRTDistanceMatrix, 3,3 ); if (alignment.pctSimilarity > minIdentity or rcAlignment.pctSimilarity > minIdentity) { equivOut << " " << reads[j].GetName(); } } } equivOut << endl; } return 0; }
int main(int argc, char* argv[]) { #ifdef USE_GOOGLE_PROFILER char *profileFileName = getenv("CPUPROFILE"); if (profileFileName != NULL) { ProfilerStart(profileFileName); } else { ProfilerStart("google_profile.txt"); } #endif // Register inputs and outputs. string samFileName, refFileName, outFileName; CommandLineParser clp; clp.RegisterStringOption("file.sam", &samFileName, "Input SAM file."); clp.RegisterStringOption("reference.fasta", &refFileName, "Reference used to generate reads."); clp.RegisterStringOption("out.sam", &outFileName, "Output SAM file."); clp.RegisterPreviousFlagsAsHidden(); // Register filter criteria options. int minAlnLength = 50; float minPctSimilarity = 70, minPctAccuracy = 70; string hitPolicyStr = "randombest"; bool useScoreCutoff = false; int scoreCutoff = INF_INT; int scoreSignInt = -1; RegisterFilterOptions(clp, minAlnLength, minPctSimilarity, minPctAccuracy, hitPolicyStr, useScoreCutoff, scoreSignInt, scoreCutoff); int seed = 1; clp.RegisterIntOption("seed", &seed, "(1) Seed for random number generator.\n" "If seed is 0, then use current time as seed.", CommandLineParser::Integer); string holeNumberStr; Ranges holeNumberRanges; clp.RegisterStringOption("holeNumbers", &holeNumberStr, "A string of comma-delimited hole number ranges to output hits, " "such as '1,2,10-12'. " "This requires hit titles to be in SMRT read title format."); bool parseSmrtTitle = false; clp.RegisterFlagOption("smrtTitle", &parseSmrtTitle, "Use this option when filtering alignments generated by " "programs other than blasr, e.g. bwa-sw or gmap. " " Parse read coordinates from the SMRT read title. " "The title is in the format /name/hole/coordinates, where" " coordinates are in the format \\d+_\\d+, and represent " "the interval of the read that was aligned."); /* This experimental option can be useful for metagenomics, in which case * there are hundreds of sequences in the target, of which many titles are * long and may contain white spaces (e.g., ' ', '\t'). * In order to save disc space and avoid the (possibly) none unique mapping * between full and short reference names, one may call blasr with * -titleTable option to represent all target sequences in the output * by their indices in the title table.*/ string titleTableName = ""; clp.RegisterStringOption("titleTable", &titleTableName, "Use this experimental option when filtering alignments generated by " "blasr with -titleTable titleTableName, in which case " "reference titles in SAM are represented by their " "indices (e.g., 0, 1, 2, ...) in the title table."); string adapterGffFileName = ""; clp.RegisterStringOption("filterAdapterOnly", &adapterGffFileName, "Use this option to remove reads which can only map to adapters " "specified in the GFF file."); bool verbose = false; clp.RegisterFlagOption("v", &verbose, "Be verbose."); clp.SetExamples( "Because SAM has optional tags that have different meanings" " in different programs, careful usage is required in order " "to have proper output. The \"xs\" tag in bwa-sw is used to " "show the suboptimal score, but in PacBio SAM (blasr) it is " "defined as the start in the query sequence of the alignment.\n" "When \"-smrtTitle\" is specified, the xs tag is ignored, but " "when it is not specified, the coordinates given by the xs and " "xe tags are used to define the interval of a read that is " "aligned. The CIGAR string is relative to this interval."); clp.ParseCommandLine(argc, argv); // Set random number seed. if (seed == 0) { srand(time(NULL)); } else { srand(seed); } scoreSign = (scoreSignInt == -1)?ScoreSign::NEGATIVE:ScoreSign::POSITIVE; Score s(static_cast<float>(scoreCutoff), scoreSign); FilterCriteria filterCriteria(minAlnLength, minPctSimilarity, minPctAccuracy, true, s); filterCriteria.Verbose(verbose); HitPolicy hitPolicy(hitPolicyStr, scoreSign); string errMsg; if (not filterCriteria.MakeSane(errMsg)) { cout << errMsg << endl; exit(1); } // Parse hole number ranges. if (holeNumberStr.size() != 0) { if (not holeNumberRanges.setRanges(holeNumberStr)) { cout << "Could not parse hole number ranges: " << holeNumberStr << "." << endl; exit(1); } } // Open output file. ostream * outFilePtr = &cout; ofstream outFileStrm; if (outFileName != "") { CrucialOpen(outFileName, outFileStrm, std::ios::out); outFilePtr = &outFileStrm; } GFFFile adapterGffFile; if (adapterGffFileName != "") adapterGffFile.ReadAll(adapterGffFileName); SAMReader<SAMFullReferenceSequence, SAMReadGroup, SAMAlignment> samReader; FASTAReader fastaReader; // // Initialize samReader and fastaReader. // samReader.Initialize(samFileName); fastaReader.Initialize(refFileName); // // Configure the file log. // string command; CommandLineParser::CommandLineToString(argc, argv, command); string log = "Filter sam hits."; string program = "samFilter"; string versionString = VERSION; AppendPerforceChangelist(PERFORCE_VERSION_STRING, versionString); // // Read necessary input. // vector<FASTASequence> references; fastaReader.ReadAllSequences(references); // If the SAM file is generated by blasr with -titleTable, // then references in the SAM are represented by // their corresponding indices in the title table. // In that case, we need to convert reference titles in fasta file // to their corresponding indices in the title table, such that // references in both SAM and fasta files are represented // by title table indices and therefore can match. if (titleTableName != "") { ConvertTitlesToTitleTableIndices(references, titleTableName); } AlignmentSet<SAMFullReferenceSequence, SAMReadGroup, SAMAlignment> alignmentSet; vector<string> allHeaders = samReader.ReadHeader(alignmentSet); // Process SAM Header. string commandLineString; clp.CommandLineToString(argc, argv, commandLineString); allHeaders.push_back("@PG\tID:SAMFILTER\tVN:" + versionString + \ "\tCL:" + program + " " + commandLineString); for (int i = 0; i < allHeaders.size(); i++) { outFileStrm << allHeaders[i] << endl; } // // The order of references in vector<FASTASequence> references and // AlignmentSet<, , >alignmentSet.references can be different. // Rearrange alignmentSet.references such that they are ordered in // exactly the same way as vector<FASTASequence> references. // alignmentSet.RearrangeReferences(references); // Map reference name obtained from SAM file to indices map<string, int> refNameToIndex; for (int i = 0; i < references.size(); i++) { string refName = alignmentSet.references[i].GetSequenceName(); refNameToIndex[refName] = i; } // // Store the alignments. // SAMAlignment samAlignment; int alignIndex = 0; // // For 150K, each chip produces about 300M sequences // (not including quality values and etc.). // Let's assume that the sam file and reference data can // fit in the memory. // Need to scale for larger sequal data in the future. // vector<SAMAlignment> allSAMAlignments; while (samReader.GetNextAlignment(samAlignment)) { if (samAlignment.rName == "*") { continue; } if (parseSmrtTitle and holeNumberStr.size() != 0) { string movieName; int thisHoleNumber; if (not ParsePBIReadName(samAlignment.qName, movieName, thisHoleNumber)) { cout << "ERROR, could not parse SMRT title: " << samAlignment.qName << "." << endl; exit(1); } if (not holeNumberRanges.contains(UInt(thisHoleNumber))) { if (verbose) cout << thisHoleNumber << " is not in range." << endl; continue; } } if (samAlignment.cigar.find('P') != string::npos) { cout << "WARNING. Could not process SAM record with 'P' in " << "its cigar string." << endl; continue; } vector<AlignmentCandidate<> > convertedAlignments; SAMAlignmentsToCandidates(samAlignment, references, refNameToIndex, convertedAlignments, parseSmrtTitle, false); if (convertedAlignments.size() > 1) { cout << "WARNING. Ignore multiple segments." << endl; continue; } for (int i = 0; i < 1; i++) { AlignmentCandidate<> & alignment = convertedAlignments[i]; //score func does not matter DistanceMatrixScoreFunction<DNASequence, DNASequence> distFunc; ComputeAlignmentStats(alignment, alignment.qAlignedSeq.seq, alignment.tAlignedSeq.seq, distFunc); // Check whether this alignment can only map to adapters in // the adapter GFF file. if (adapterGffFileName != "" and CheckAdapterOnly(adapterGffFile, alignment, refNameToIndex)) { if (verbose) cout << alignment.qName << " filter adapter only." << endl; continue; } // Assign score to samAlignment. samAlignment.score = samAlignment.as; if (not filterCriteria.Satisfy(static_cast<AlignmentCandidate<> *>(&alignment))) { continue; } allSAMAlignments.push_back( samAlignment ); alignment.FreeSubsequences(); } ++alignIndex; } // Sort all SAM alignments by qName, score and target position. sort(allSAMAlignments.begin(), allSAMAlignments.end(), byQNameScoreTStart); unsigned int groupBegin = 0; unsigned int groupEnd = -1; vector<SAMAlignment> filteredSAMAlignments; while(groupBegin < allSAMAlignments.size()) { // Get the next group of SAM alignments which have the same qName // from allSAMAlignments[groupBegin ... groupEnd) GetNextSAMAlignmentGroup(allSAMAlignments, groupBegin, groupEnd); vector<unsigned int> hitIndices = ApplyHitPolicy( hitPolicy, allSAMAlignments, groupBegin, groupEnd); for(unsigned int i = 0; i < hitIndices.size(); i++) { filteredSAMAlignments.push_back(allSAMAlignments[hitIndices[i]]); } groupBegin = groupEnd; } // Sort all SAM alignments by reference name and query name sort(filteredSAMAlignments.begin(), filteredSAMAlignments.end(), byRNameQName); for(unsigned int i = 0; i < filteredSAMAlignments.size(); i++) { filteredSAMAlignments[i].PrintSAMAlignment(outFileStrm); } if (outFileName != "") { outFileStrm.close(); } #ifdef USE_GOOGLE_PROFILER ProfilerStop(); #endif return 0; }