delly v0.7.9

Author: tobiasrausch

Makefile

@@ -13,7 +13,7 @@ bindir ?= $(exec_prefix)/bin
 
 # Flags
 CXX=g++
-CXXFLAGS += -isystem ${EBROOTHTSLIB} -pedantic -W -Wall -Wno-unknown-pragmas -D__STDC_LIMIT_MACROS -fno-strict-aliasing
+CXXFLAGS += -isystem ${EBROOTHTSLIB} -pedantic -W -Wall -Wno-unknown-pragmas -D__STDC_LIMIT_MACROS -fno-strict-aliasing -fpermissive
 LDFLAGS += -L${EBROOTHTSLIB} -L${EBROOTHTSLIB}/lib -lboost_iostreams -lboost_filesystem -lboost_system -lboost_program_options -lboost_date_time 
 
 # Flags for parallel computation

src/coverage.h

@@ -622,7 +622,7 @@ annotateCoverage(TConfig& c, TSampleLibrary& sampleLib, TCovRecord& ict, TCovera
 
 	  // Get the library information
 	  int32_t libIdx = 0;
-	  if (!c.ignoreRG) libIdx = _findLib(rec, sampleLib[file_c]);
+	  if ((c.readgroups) && (sampleLib[file_c].size() > 1)) libIdx = _findLib(rec, sampleLib[file_c]);
 	  if (sampleLib[file_c][libIdx].median == 0) continue; // Single-end library or non-valid library
 
 	  // Normal spanning pair

src/delly.h

@@ -81,7 +81,7 @@ struct Config {
   int32_t indelsize;
   uint32_t graphPruning;
   float flankQuality;
-  bool ignoreRG;
+  bool readgroups;
   bool indels;
   bool hasExcludeFile;
   bool hasVcfFile;
@@ -208,7 +208,7 @@ _annotateCoverage(TConfig& c, bam_hdr_t* hdr, TSampleLib& sampleLib, TSVs& svs,
   for(uint32_t file_c = 0; file_c < c.files.size(); ++file_c) {
     countMap[file_c].resize(svs.size());
     for (uint32_t id = 0; id < svs.size(); ++id) {
-      if ((c.indels) && (svSize[id] <= c.indelsize)) {
+      if (svSize[id] <= c.indelsize) {
 	countMap[file_c][id].rc = readCountMap[file_c][id].first;
 	countMap[file_c][id].leftRC = readCountMap[file_c][id + lastId].first;
 	countMap[file_c][id].rightRC = readCountMap[file_c][id + 2*lastId].first;
@@ -596,8 +596,8 @@ int delly(int argc, char **argv) {
   else c.indels = false;
 
   // Read-group aware calling
-  if (vm.count("readgroup")) c.ignoreRG = false;
-  else c.ignoreRG = true;
+  if (vm.count("readgroup")) c.readgroups = true;
+  else c.readgroups = false;
 
   // Run main program
   c.aliscore = DnaScore<int>(5, -4, -10, -1);

src/shortpe.h

@@ -804,7 +804,7 @@ namespace torali
 
 	      // Library
 	      int32_t libIdx = 0;
-	      if (!c.ignoreRG) libIdx = _findLib(rec, sampleLib[file_c]);
+	      if ((c.readgroups) && (sampleLib[file_c].size() > 1)) libIdx = _findLib(rec, sampleLib[file_c]);
 	      if (sampleLib[file_c][libIdx].median == 0) continue; // Single-end library
 
 	      // Check library-specific insert size for deletions

src/util.h

@@ -383,7 +383,7 @@ namespace torali
 
       // Get read groups
       bool rgPresent = false;
-      if (!c.ignoreRG) {
+      if (c.readgroups) {
 	std::string header(hdr[file_c]->text);
 	std::string delimiters("\n");
 	typedef std::vector<std::string> TStrParts;
@@ -429,7 +429,7 @@ namespace torali
 	      ++alignmentCount;
 
 	      std::string rG = "DefaultLib";
-	      if (!c.ignoreRG) {
+	      if (c.readgroups) {
 		uint8_t *rgptr = bam_aux_get(rec, "RG");
 		if (rgptr) {
 		  char* rg = (char*) (rgptr + 1);

src/version.h

@@ -28,7 +28,7 @@ namespace torali
 {
 
 
-  std::string dellyVersionNumber = "0.7.8";
+  std::string dellyVersionNumber = "0.7.9";
 
   inline 
     void printTitle(std::string const& title)