consensus

Author: tobiasrausch

src/merge.h

@@ -450,12 +450,12 @@ void _outputSelectedIntervals(MergeConfig& c, TGenomeIntervals const& iSelected,
 	    float srAlignQuality = 0;
 	    if (bcf_get_info_float(hdr[idx], rec[idx], "SRQ", &srq, &nsrq) > 0) srAlignQuality = *srq;
 
-	    std::string consensus;
+	    std::string consStr;
 	    float ceVal = 0;
 	    int32_t consBpVal = 0;
 	    if (precise) {
 	      if (bcf_get_info_float(hdr[idx], rec[idx], "CE", &ce, &nce) > 0) ceVal = *ce;
-	      if (bcf_get_info_string(hdr[idx], rec[idx], "CONSENSUS", &cons, &ncons) > 0) consensus = boost::to_upper_copy(std::string(cons));
+	      if (bcf_get_info_string(hdr[idx], rec[idx], "CONSENSUS", &cons, &ncons) > 0) consStr = boost::to_upper_copy(std::string(cons));
 	      if (bcf_get_info_int32(hdr[idx], rec[idx], "CONSBP", &consbp, &nconsbp) > 0) consBpVal = *consbp;
 	    }
 
@@ -508,8 +508,8 @@ void _outputSelectedIntervals(MergeConfig& c, TGenomeIntervals const& iSelected,
 	      bcf_update_info_int32(hdr_out, rout, "HOMLEN", &homlenVal, 1);
 	      bcf_update_info_int32(hdr_out, rout, "SR", &srSupport, 1);
 	      bcf_update_info_float(hdr_out, rout, "SRQ", &srAlignQuality, 1);
-	      if (consensus.size()) {
-		bcf_update_info_string(hdr_out, rout, "CONSENSUS", consensus.c_str());
+	      if (consStr.size()) {
+		bcf_update_info_string(hdr_out, rout, "CONSENSUS", consStr.c_str());
 		bcf_update_info_float(hdr_out, rout, "CE", &ceVal, 1);
 		bcf_update_info_int32(hdr_out, rout, "CONSBP", &consBpVal, 1);
 	      }

src/modvcf.h

@@ -12,11 +12,11 @@ namespace torali
 {
 
 
-void _remove_info_tag(bcf_hdr_t* hdr, bcf1_t* rec, std::string const& tag) {
+void _remove_info_tag(bcf_hdr_t const* hdr, bcf1_t* rec, std::string const& tag) {
   bcf_update_info(hdr, rec, tag.c_str(), NULL, 0, BCF_HT_INT);  // Type does not matter for n = 0
 }
 
-void _remove_format_tag(bcf_hdr_t* hdr, bcf1_t* rec, std::string const& tag) {
+void _remove_format_tag(bcf_hdr_t const* hdr, bcf1_t* rec, std::string const& tag) {
   bcf_update_format(hdr, rec, tag.c_str(), NULL, 0, BCF_HT_INT);  // Type does not matter for n = 0
 }
 

src/split.h

@@ -729,7 +729,7 @@ namespace torali
 
   template<typename TConfig>
   inline bool
-  alignConsensus(TConfig const& c, bam_hdr_t* hdr, char const* seq, char const* sndSeq, StructuralVariantRecord& sv, bool const realign) {
+  alignConsensus(TConfig const& c, bam_hdr_t const* hdr, char const* seq, char const* sndSeq, StructuralVariantRecord& sv, bool const realign) {
     if ( (int32_t) sv.consensus.size() < (2 * c.minimumFlankSize + sv.insLen)) return false;
 
     // Get reference slice