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skipGT
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@tobiasrausch
tobiasrausch committed Nov 25, 2024
1 parent 0ca9b39 commit 8696a1a
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Showing 5 changed files with 18 additions and 8 deletions.
1 change: 1 addition & 0 deletions src/asmode.h
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Expand Up @@ -36,6 +36,7 @@ namespace torali {

struct AsmConfig {
bool hasVcfFile;
bool skipGenotyping;
uint16_t minMapQual;
uint32_t minClip;
uint32_t minCliqueSize;
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8 changes: 4 additions & 4 deletions src/assemble.h
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Expand Up @@ -855,7 +855,7 @@ namespace torali
tmpCons = svs[svid].consensus;
svs[svid].consensus = svs[svid].consensus.substr(offsetTmpCons, svSize);
}
if (alignConsensus(c, hdr, seq, NULL, svs[svid], true)) msaSuccess = true;
if ((c.skipGenotyping) || (alignConsensus(c, hdr, seq, NULL, svs[svid], true))) msaSuccess = true;
if (!tmpCons.empty()) {
svs[svid].consensus = tmpCons;
svs[svid].consBp += offsetTmpCons;
Expand All @@ -865,7 +865,7 @@ namespace torali
std::string suffix = boost::to_upper_copy(std::string(seq + svs[svid].svStart, seq + std::min(seqlen, svs[svid].svStart + c.minConsWindow)));
msaWfa(c, seqStore[svid], svs[svid].consensus, prefix, suffix);
if ((int32_t) svs[svid].consensus.size() < svs[svid].insLen + 4 * c.minConsWindow) {
if (alignConsensus(c, hdr, seq, NULL, svs[svid], false)) msaSuccess = true;
if ((c.skipGenotyping) || (alignConsensus(c, hdr, seq, NULL, svs[svid], false))) msaSuccess = true;
}
}
//std::cerr << msaSuccess << std::endl;
Expand Down Expand Up @@ -921,7 +921,7 @@ namespace torali
tmpCons = svs[svid].consensus;
svs[svid].consensus = svs[svid].consensus.substr(offsetTmpCons, svSize);
}
if (alignConsensus(c, hdr, seq, sndSeq, svs[svid], true)) msaSuccess = true;
if ((c.skipGenotyping) || (alignConsensus(c, hdr, seq, sndSeq, svs[svid], true))) msaSuccess = true;
if (!tmpCons.empty()) {
svs[svid].consensus = tmpCons;
svs[svid].consBp += offsetTmpCons;
Expand All @@ -931,7 +931,7 @@ namespace torali
std::string suffix = boost::to_upper_copy(std::string(seq + svs[svid].svStart, seq + std::min(seqlen, svs[svid].svStart + c.minConsWindow)));
msaWfa(c, seqStore[svid], svs[svid].consensus, prefix, suffix);
if ((int32_t) svs[svid].consensus.size() < svs[svid].insLen + 4 * c.minConsWindow) {
if (alignConsensus(c, hdr, seq, NULL, svs[svid], false)) msaSuccess = true;
if ((c.skipGenotyping) || (alignConsensus(c, hdr, seq, NULL, svs[svid], false))) msaSuccess = true;
}
}
//std::cerr << msaSuccess << std::endl;
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1 change: 1 addition & 0 deletions src/delly.h
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Expand Up @@ -65,6 +65,7 @@ namespace torali
bool hasExcludeFile;
bool hasVcfFile;
bool hasDumpFile;
bool skipGenotyping;
std::set<int32_t> svtset;
DnaScore<int> aliscore;
boost::filesystem::path outfile;
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8 changes: 5 additions & 3 deletions src/modvcf.h
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Expand Up @@ -319,7 +319,7 @@ vcfParse(TConfig const& c, bam_hdr_t* hd, std::vector<TStructuralVariantRecord>&

template<typename TConfig, typename TStructuralVariantRecord, typename TJunctionCountMap, typename TReadCountMap, typename TCountMap>
inline void
vcfOutput(TConfig const& c, std::vector<TStructuralVariantRecord> const& svs, TJunctionCountMap const& jctCountMap, TReadCountMap const& readCountMap, TCountMap const& spanCountMap)
vcfOutput(TConfig const& c, std::vector<TStructuralVariantRecord>& svs, TJunctionCountMap const& jctCountMap, TReadCountMap const& readCountMap, TCountMap const& spanCountMap)
{
// BoLog class
BoLog<double> bl;
Expand Down Expand Up @@ -416,10 +416,10 @@ vcfOutput(TConfig const& c, std::vector<TStructuralVariantRecord> const& svs, TJ
now = boost::posix_time::second_clock::local_time();
std::cerr << '[' << boost::posix_time::to_simple_string(now) << "] " << "Genotyping" << std::endl;
bcf1_t *rec = bcf_init();
for(typename TSVs::const_iterator svIter = svs.begin(); svIter!=svs.end(); ++svIter) {
for(typename TSVs::iterator svIter = svs.begin(); svIter!=svs.end(); ++svIter) {
if ((svIter->srSupport == 0) && (svIter->peSupport == 0)) continue;
// In discovery mode, skip SVs that have less than 2 reads support after genotyping
if (!c.hasVcfFile) {
if ((!c.hasVcfFile) && (!c.skipGenotyping)) {
uint32_t totalGtSup = 0;
for(unsigned int file_c = 0; file_c < c.files.size(); ++file_c) {
totalGtSup += spanCountMap[file_c][svIter->id].alt.size() + jctCountMap[file_c][svIter->id].alt.size();
Expand Down Expand Up @@ -449,6 +449,7 @@ vcfOutput(TConfig const& c, std::vector<TStructuralVariantRecord> const& svs, TJ
padNumber.insert(padNumber.begin(), 8 - padNumber.length(), '0');
id += padNumber;
bcf_update_id(hdr, rec, id.c_str());
if (c.skipGenotyping) svIter->alleles = _addAlleles("N", std::string(bamhd->target_name[svIter->chr2]), *svIter, svIter->svt);
std::string alleles = _replaceIUPAC(svIter->alleles);
bcf_update_alleles_str(hdr, rec, alleles.c_str());
bcf_update_filter(hdr, rec, &tmpi, 1);
Expand All @@ -461,6 +462,7 @@ vcfOutput(TConfig const& c, std::vector<TStructuralVariantRecord> const& svs, TJ
dellyVersion += dellyVersionNumber;
bcf_update_info_string(hdr,rec, "SVMETHOD", dellyVersion.c_str());
if (svIter->svt < DELLY_SVT_TRANS) {
if (svEndPos <= svStartPos) svEndPos = svStartPos + 1;
tmpi = svEndPos;
bcf_update_info_int32(hdr, rec, "END", &tmpi, 1);
} else {
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8 changes: 7 additions & 1 deletion src/tegua.h
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Expand Up @@ -39,6 +39,7 @@ namespace torali {
bool hasExcludeFile;
bool hasVcfFile;
bool hasAltFile;
bool skipGenotyping;
uint16_t minMapQual;
uint16_t minGenoQual;
uint32_t minClip;
Expand Down Expand Up @@ -169,7 +170,7 @@ namespace torali {
}

// SV Genotyping
genotypeLR(c, svs, jctMap, rcMap);
if (!c.skipGenotyping) genotypeLR(c, svs, jctMap, rcMap);

// VCF Output
vcfOutput(c, svs, jctMap, rcMap, spanMap);
Expand Down Expand Up @@ -235,6 +236,7 @@ namespace torali {
("pruning,j", boost::program_options::value<uint32_t>(&c.graphPruning)->default_value(1000), "graph pruning cutoff")
("extension,e", boost::program_options::value<float>(&c.indelExtension)->default_value(0.5), "enforce indel extension")
("scoring,s", boost::program_options::value<std::string>(&scoring)->default_value("3,-2,-3,-1"), "alignment scoring")
("skipGT,k", "skip consensus realignment and genotyping (useful for complex SVs)")
;

boost::program_options::positional_options_description pos_args;
Expand Down Expand Up @@ -382,6 +384,10 @@ namespace torali {
}
}

// Consensus alignment?
if (vm.count("skipGT")) c.skipGenotyping = true;
else c.skipGenotyping = false;

// Show cmd
boost::posix_time::ptime now = boost::posix_time::second_clock::local_time();
std::cerr << '[' << boost::posix_time::to_simple_string(now) << "] ";
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