Commit 4df69c64 authored by bow's avatar bow
Browse files

Merge branch 'feature-singletons_flagstat' into 'develop'

Added singletons to summary



See merge request !404
parents e11ff161 e37fd3ac
...@@ -211,7 +211,8 @@ object BiopetFlagstat extends ToolCommand { ...@@ -211,7 +211,8 @@ object BiopetFlagstat extends ToolCommand {
def summary: String = { def summary: String = {
val map = (for (t <- 0 until names.size) yield { val map = (for (t <- 0 until names.size) yield {
names(t) -> totalCounts(t) 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 ConfigUtils.mapToJson(map).spaces4
} }
......
...@@ -11,6 +11,7 @@ ...@@ -11,6 +11,7 @@
"MateNegativeStrand" : 1, "MateNegativeStrand" : 1,
"FirstOfPair" : 1, "FirstOfPair" : 1,
"ReadPaired" : 1, "ReadPaired" : 1,
"Singletons" : 0,
"SecondaryOrSupplementary" : 0, "SecondaryOrSupplementary" : 0,
"SecondOfPair" : 0 "SecondOfPair" : 0
} }
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