static void runCSL(const CSLOptions& opt) { SVLocusSet set; set.load(opt.graphFilename.c_str()); set.finalize(); set.checkState(true,true); }
static void runCSL(const CSLOptions& opt) { log_os << "INFO: loading graph: " << opt.graphFilename << "\n"; SVLocusSet set; set.load(opt.graphFilename.c_str()); log_os << "INFO: cleaning/finalizing graph: " << opt.graphFilename << "\n"; set.finalize(); log_os << "INFO: checking cleaned graph: " << opt.graphFilename << "\n"; set.checkState(true,true); log_os << "INFO: finished checking graph: " << opt.graphFilename << "\n"; }
static void runSSL(const SSLOptions& opt) { SVLocusSet set; set.load(opt.graphFilename.c_str()); std::ostream& os(std::cout); if (opt.isGlobalStats) { set.dumpStats(os); } else { set.dumpLocusStats(os); } }
static void runDSL(const DSLOptions& opt) { SVLocusSet set; set.load(opt.graphFilename.c_str()); const SVLocusSet& cset(set); std::ostream& os(std::cout); // add this handy map of chromosome id to chromosome label at the start of all output types: os << cset.header << "\n"; if (! opt.region.empty()) { int32_t tid,beginPos,endPos; parse_bam_region(set.header, opt.region, tid, beginPos, endPos); // parse the region set.dumpRegion(os,GenomeInterval(tid,beginPos,endPos)); } else if (opt.isLocusIndex) { const SVLocus& locus(cset.getLocus(opt.locusIndex)); if (opt.locusFilename.empty()) { os << locus; } else { std::ofstream ofs(opt.locusFilename.c_str(), std::ios::binary); boost::archive::binary_oarchive oa(ofs); oa << locus; } } else { cset.dump(os); } }