v1.3.2

README.md

@@ -155,6 +155,10 @@ Structural variants are still reported with respect to GRCh38 coordinates but th
 
 `bcftools view -i '(QUAL>=300) && ( ((SVTYPE=="INS") && (INFO/SVLEN>50)) || (SVTYPE="BND") || ((INFO/END - POS)>50) )' delly.bcf`
 
+Please note that for inter-chromosomal translocations, delly uses `INFO/CHR2` for the second chromosome. You can convert an inter-chromosomal translocation to the two-record breakend format using:
+
+`python scripts/delly2bnd.py -v delly.bcf -r hg38.fa -o delly.bnd.bcf`
+
 
 Read-depth profiles and copy-number variant calling
 ---------------------------------------------------

src/asmode.h

@@ -36,7 +36,6 @@ namespace torali {
 
   struct AsmConfig {
     bool hasVcfFile;
-    bool skipGenotyping;
     uint16_t minMapQual;
     uint32_t minClip;
     uint32_t minCliqueSize;

src/assemble.h

@@ -855,7 +855,7 @@ namespace torali
 			    tmpCons = svs[svid].consensus;
 			    svs[svid].consensus = svs[svid].consensus.substr(offsetTmpCons, svSize);
 			  }
-			  if ((c.skipGenotyping) || (alignConsensus(c, hdr, seq, NULL, svs[svid], true))) msaSuccess = true;
+			  if (alignConsensus(c, hdr, seq, NULL, svs[svid], true)) msaSuccess = true;
 			  if (!tmpCons.empty()) {
 			    svs[svid].consensus = tmpCons;
 			    svs[svid].consBp += offsetTmpCons;
@@ -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 ((c.skipGenotyping) || (alignConsensus(c, hdr, seq, NULL, svs[svid], false))) msaSuccess = true;
+			    if (alignConsensus(c, hdr, seq, NULL, svs[svid], false)) msaSuccess = true;
 			  }
 			}
 			//std::cerr << msaSuccess << std::endl;
@@ -921,7 +921,7 @@ namespace torali
 		    tmpCons = svs[svid].consensus;
 		    svs[svid].consensus = svs[svid].consensus.substr(offsetTmpCons, svSize);
 		  }
-		  if ((c.skipGenotyping) || (alignConsensus(c, hdr, seq, sndSeq, svs[svid], true))) msaSuccess = true;
+		  if (alignConsensus(c, hdr, seq, sndSeq, svs[svid], true)) msaSuccess = true;
 		  if (!tmpCons.empty()) {
 		    svs[svid].consensus = tmpCons;
 		    svs[svid].consBp += offsetTmpCons;
@@ -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 ((c.skipGenotyping) || (alignConsensus(c, hdr, seq, NULL, svs[svid], false))) msaSuccess = true;
+		    if (alignConsensus(c, hdr, seq, NULL, svs[svid], false)) msaSuccess = true;
 		  }
 		}
 		//std::cerr << msaSuccess << std::endl;

src/delly.h

@@ -65,7 +65,6 @@ namespace torali
     bool hasExcludeFile;
     bool hasVcfFile;
     bool hasDumpFile;
-    bool skipGenotyping;
     std::set<int32_t> svtset;
     DnaScore<int> aliscore;
     boost::filesystem::path outfile;

src/modvcf.h

@@ -419,7 +419,7 @@ vcfOutput(TConfig const& c, std::vector<TStructuralVariantRecord>& svs, TJunctio
     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) && (!c.skipGenotyping)) {
+      if (!c.hasVcfFile) {
 	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();
@@ -449,7 +449,6 @@ vcfOutput(TConfig const& c, std::vector<TStructuralVariantRecord>& svs, TJunctio
       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);

src/tegua.h

@@ -39,7 +39,6 @@ namespace torali {
     bool hasExcludeFile;
     bool hasVcfFile;
     bool hasAltFile;
-    bool skipGenotyping;
     uint16_t minMapQual;
     uint16_t minGenoQual;
     uint32_t minClip;
@@ -170,7 +169,7 @@ namespace torali {
    }
 
    // SV Genotyping
-   if (!c.skipGenotyping) genotypeLR(c, svs, jctMap, rcMap);
+   genotypeLR(c, svs, jctMap, rcMap);
 
    // VCF Output
    vcfOutput(c, svs, jctMap, rcMap, spanMap);
@@ -236,7 +235,6 @@ 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;
@@ -384,10 +382,6 @@ 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) << "] ";

src/version.h

@@ -5,7 +5,7 @@ namespace torali
 {
 
 
-  std::string dellyVersionNumber = "1.3.1";
+  std::string dellyVersionNumber = "1.3.2";
 
   inline 
     void printTitle(std::string const& title)