evaluate secondary alignments

tobiasrausch · Aug 21, 2018 · 0b2afc7 · 0b2afc7
1 parent 9d57fb2
commit 0b2afc7
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Showing 2 changed files with 9 additions and 1 deletion.
diff --git a/src/bamstats.h b/src/bamstats.h
@@ -362,7 +362,9 @@ namespace bamstats
 	} else {
 	  ++itRg->second.rc.mappedchr[refIndex];
 	}
-	continue;
+	if (rec->core.flag & BAM_FSECONDARY) {
+	  if (!c.secondary) continue;
+	} else continue;
       }
       ++itRg->second.qc.qcount[(int32_t) rec->core.qual];
       ++itRg->second.rc.mappedchr[refIndex];

diff --git a/src/qc.h b/src/qc.h
@@ -54,6 +54,7 @@ struct ConfigQC {
   bool singleRG;
   bool isHaplotagged;
   bool isMitagged;
+  bool secondary;
   std::string rgname;
   std::string sampleName;
   std::string format;
@@ -77,6 +78,7 @@ int qc(int argc, char **argv) {
     ("bed,b", boost::program_options::value<boost::filesystem::path>(&c.regionFile), "bed file with target regions (optional)")
     ("format,f", boost::program_options::value<std::string>(&c.format)->default_value("tsv"), "output format [tsv|json]")
     ("outfile,o", boost::program_options::value<boost::filesystem::path>(&c.outfile)->default_value("qc.tsv.gz"), "gzipped output file")
+    ("secondary,s", "evaluate secondary alignments")
     ;
 
   boost::program_options::options_description rgopt("Read-group options");
@@ -111,6 +113,10 @@ int qc(int argc, char **argv) {
     return 1;
   }
 
+  // Secondary alignments
+  if (vm.count("secondary")) c.secondary = true;
+  else c.secondary = false;
+
   // Ignore read groups
   if (vm.count("ignore")) {
     c.ignoreRG = true;