Merge branch 'feature-singletons_flagstat' into 'develop'

Added singletons to summary



See merge request !404

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala

@@ -211,7 +211,8 @@ object BiopetFlagstat extends ToolCommand {
     def summary: String = {
       val map = (for (t <- 0 until names.size) yield {
         names(t) -> totalCounts(t)
-      }).toMap
+      }).toMap ++ Map("Singletons" -> crossCounts(names.find(_._2 == "Mapped").map(_._1).getOrElse(-1))(names.find(_._2 == "MateUnmapped").map(_._1).getOrElse(-1))
+      )
 
       ConfigUtils.mapToJson(map).spaces4
     }

biopet-tools/src/test/resources/flagstat_summary.txt

@@ -11,6 +11,7 @@
     "MateNegativeStrand" : 1,
     "FirstOfPair" : 1,
     "ReadPaired" : 1,
+    "Singletons" : 0,
     "SecondaryOrSupplementary" : 0,
     "SecondOfPair" : 0
 }
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