GenomicRegion::GenomicRegion(const std::string& tchr, const std::string& tpos1, const std::string& tpos2, const SeqLib::BamHeader& hdr) { strand = '*'; // convert the pos strings // throws invalid_argument if conversion can't be performed // or throws an out_of_range if it is too big for result #ifdef HAVE_C11 pos1 = std::stoi(tpos1); pos2 = std::stoi(tpos2); #else pos1 = std::atoi(tpos1.c_str()); pos2 = std::atoi(tpos2.c_str()); #endif // if no header, assume that it is "standard" if (hdr.isEmpty()) { if (tchr == "X" || tchr == "chrX") chr = 22; else if (tchr == "Y" || tchr == "chrY") chr = 23; else #ifdef HAVE_C11 chr = std::stoi(SeqLib::scrubString(tchr, "chr")) - 1; #else chr = std::atoi(SeqLib::scrubString(tchr, "chr").c_str()); #endif return; } else { chr = hdr.Name2ID(tchr); //bam_name2id(hdr.get(), tchr.c_str()); } }
int main(int argc, char** argv) { int c; FastaReference reference; bool has_ref = false; bool suppress_output = false; bool debug = false; bool isuncompressed = true; int maxiterations = 50; if (argc < 2) { printUsage(argv); exit(1); } while (true) { static struct option long_options[] = { {"help", no_argument, 0, 'h'}, {"debug", no_argument, 0, 'd'}, {"fasta-reference", required_argument, 0, 'f'}, {"max-iterations", required_argument, 0, 'm'}, {"suppress-output", no_argument, 0, 's'}, {"compressed", no_argument, 0, 'c'}, {0, 0, 0, 0} }; int option_index = 0; c = getopt_long (argc, argv, "hdcsf:m:", long_options, &option_index); /* Detect the end of the options. */ if (c == -1) break; switch (c) { case 'f': reference.open(optarg); // will exit on open failure has_ref = true; break; case 'm': maxiterations = atoi(optarg); break; case 'd': debug = true; break; case 's': suppress_output = true; break; case 'c': isuncompressed = false; break; case 'h': printUsage(argv); exit(0); break; case '?': printUsage(argv); exit(1); break; default: abort(); break; } } if (!has_ref) { cerr << "no FASTA reference provided, cannot realign" << endl; exit(1); } BAMSINGLEREADER reader; if (!reader.Open(STDIN)) { cerr << "could not open stdin for reading" << endl; exit(1); } #ifdef HAVE_BAMTOOLS BamWriter writer; if (isuncompressed) { writer.SetCompressionMode(BamWriter::Uncompressed); } if (!suppress_output && !writer.Open("stdout", reader.GetHeaderText(), reader.GetReferenceData())) { cerr << "could not open stdout for writing" << endl; exit(1); } #else SeqLib::BamWriter writer(isuncompressed ? SeqLib::SAM : SeqLib::BAM); SeqLib::BamHeader hdr = reader.Header(); if (hdr.isEmpty()) { cerr << "could not open header for input" << endl; exit(1); } writer.SetHeader(hdr); if (!suppress_output && !writer.Open("-")) { cerr << "could not open stdout for writing" << endl; exit(1); } #endif // store the names of all the reference sequences in the BAM file map<int, string> referenceIDToName; REFVEC referenceSequences = reader.GETREFDATA; int i = 0; for (REFVEC::iterator r = referenceSequences.begin(); r != referenceSequences.end(); ++r) { referenceIDToName[i] = r->REFNAME; ++i; } BAMALIGN alignment; while (GETNEXT(reader, alignment)) { DEBUG("--------------------------- read --------------------------" << endl); DEBUG("| " << referenceIDToName[alignment.REFID] << ":" << alignment.POSITION << endl); DEBUG("| " << alignment.QNAME << ":" << alignment.ENDPOSITION << endl); DEBUG("| " << alignment.QNAME << ":" << (alignment.ISMAPPED ? " mapped" : " unmapped") << endl); DEBUG("| " << alignment.QNAME << ":" << " cigar data size: " << alignment.GETCIGAR.size() << endl); DEBUG("--------------------------- realigned --------------------------" << endl); // skip unmapped alignments, as they cannot be left-realigned without CIGAR data if (alignment.ISMAPPED) { int endpos = alignment.ENDPOSITION; int length = endpos - alignment.POSITION + 1; if (alignment.POSITION >= 0 && length > 0) { if (!stablyLeftAlign(alignment, reference.getSubSequence( referenceIDToName[alignment.REFID], alignment.POSITION, length), maxiterations, debug)) { cerr << "unstable realignment of " << alignment.QNAME << " at " << referenceIDToName[alignment.REFID] << ":" << alignment.POSITION << endl << alignment.QUERYBASES << endl; } } } DEBUG("----------------------------------------------------------------" << endl); DEBUG(endl); if (!suppress_output) WRITEALIGNMENT(writer, alignment); } reader.Close(); if (!suppress_output) writer.Close(); return 0; }