From e49f81e35b106f4c108f90fc2406342984a5595e Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 17 May 2016 16:33:56 +0200
Subject: [PATCH] Added singletons to summary
---
.../main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala b/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala
index 5d53f2ef8..89dcb6ee6 100644
--- a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala
+++ b/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
}
--
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