Fix strand-specific separation in Gentrap

This fixes a bug caused by incorrect creation of plus and minus strand BAM files.
It was caused by incorrectly specifying the SAM flags, causing the plus and minus
strand BAM files to still contain mixed strand reads.

public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala

@@ -552,7 +552,7 @@ class Gentrap(val root: Configurable) extends QScript
             job.input = alnFile
             job.b = true
             job.h = true
-            job.f = List("0x40")
+            job.f = List("0x80")
             job.F = List("0x10")
             job.output = createFile(".r2.bam")
             job.isIntermediate = true
@@ -594,7 +594,7 @@ class Gentrap(val root: Configurable) extends QScript
             job.input = alnFile
             job.b = true
             job.h = true
-            job.f = List("0x80")
+            job.f = List("0x40")
             job.F = List("0x10")
             job.output = createFile(".r1.bam")
             job.isIntermediate = true