From ceaa8fd014eb3a9b15cd1b80b74c3f2fa687de02 Mon Sep 17 00:00:00 2001
From: Wai Yi Leung <w.y.leung@lumc.nl>
Date: Mon, 19 Oct 2015 11:49:48 +0200
Subject: [PATCH] Handle RNA seq files, sam filter only takes the primary
alignment
---
.../main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala
index 59151902f..5be74f278 100644
--- a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala
+++ b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala
@@ -69,7 +69,7 @@ class Gears(val root: Configurable) extends QScript with SummaryQScript {
// sambamba view -f bam -F "unmapped or mate_is_unmapped" <alnFile> > <extracted.bam>
val samFilterUnmapped = new SambambaView(qscript)
samFilterUnmapped.input = bamfile
- samFilterUnmapped.filter = Some("unmapped or mate_is_unmapped")
+ samFilterUnmapped.filter = Some("(unmapped or mate_is_unmapped) and not (secondary_alignment)")
samFilterUnmapped.output = new File(outputDir, s"$outputName.unmapped.bam")
samFilterUnmapped.isIntermediate = false
add(samFilterUnmapped)
--
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