Merge branch 'master' of github.com:StructuralVariants/manta

src/c++/lib/applications/GenerateSVCandidates/SVScorerSplit.cpp

@@ -194,7 +194,7 @@ getSVSplitReadSupport(
     SVEvidence& evidence)
 {
     // apply the split-read scoring, only when:
-    // 1) the SV is precise, i.e. has successful somatic contigs;
+    // 1) the SV is precise, i.e. has successfully aligned contigs;
     // 2) the values of max depth are reasonable (otherwise, the read map may blow out). (filter is run externally)
 
     if (sv.isImprecise()) return;

src/c++/lib/manta/SVLocusScanner.cpp

@@ -242,6 +242,7 @@ typedef std::map<std::string, int32_t> chromMap_t;
 static
 void
 getSACandidatesFromRead(
+    const ReadScannerOptions& opt,
     const ReadScannerDerivOptions& dopt,
     const bam_record& localRead,
     const SimpleAlignment& localAlign,
@@ -257,19 +258,15 @@ getSACandidatesFromRead(
         if (NULL == saStr) return;
 
         split_string(saStr, ';', saVec);
-        if (saVec[saVec.size() - 1].empty())
+        if ( (! saVec.empty()) && saVec.back().empty())
         {
             saVec.pop_back();
         }
     }
 
-    // For now we will only handle a single split alignment
-    //  In the future we will need to sort the SA tags by order on of segments on
-    //   the actual template.
-    //  We may also have to toss conflicting segments that map to two different areas,
-    //   or at least find some way of dealing with them.
-    //std::cerr << "At: '" << saStr << "', '" << localRead << "'" << std::endl;
-    //std::cerr << "Size: " << saVec.size() << std::endl;
+    // Only handle a single split alignment right now.
+    // In the future we could sort the SA tags by order on the template, possibly
+    // also removing segments that map to two different areas,
 
     if (saVec.size() > 1) return;
 
@@ -285,6 +282,10 @@ getSACandidatesFromRead(
 
         assert((saDat.size() == 6) && "Unexpected number of SA tag values");
 
+        /// filter split reads with low MAPQ:
+        const unsigned saMapq(illumina::blt_util::parse_unsigned_str(saDat[4]));
+        if (saMapq < opt.minMapq) continue;
+
         const chromMap_t::const_iterator ci(chromToIndex.find(saDat[0]));
         assert(ci != chromToIndex.end());
 
@@ -300,13 +301,6 @@ getSACandidatesFromRead(
 
         cigar_to_apath(saDat[3].c_str(), remoteAlign.path);
 
-        /*std::cerr << "SA Values: "
-                  << ", " << saChr
-                  << ", " << saPos
-                  << ", " << saStrand
-                  << ", " << remotePath << '\n';
-        */
-
         // At this point we don't care about strand
         candidates.push_back(GetSplitSACandidate(dopt, localAlign, remoteAlign));
     }
@@ -746,7 +740,7 @@ getSingleReadSVCandidates(
 #endif
 
     /// - process split/SA reads:
-    getSACandidatesFromRead(dopt, localRead, localAlign, chromToIndex,
+    getSACandidatesFromRead(opt, dopt, localRead, localAlign, chromToIndex,
                             candidates);
 #ifdef DEBUG_SCANNER
     log_os << logtag << " post-split read candidate_size: " << candidates.size() << "\n";