From 88adefce7ca0b424d8e0f84992dd4dd311e6017d Mon Sep 17 00:00:00 2001
From: Wai Yi Leung <w.y.leung@lumc.nl>
Date: Fri, 29 Jan 2016 15:24:15 +0100
Subject: [PATCH] Limit reporting of events in REF/ALT col to < SVTYPE > (saves
space and post-processingpower)
---
.../nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Pindel.scala | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Pindel.scala b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Pindel.scala
index 44393b3fb..d732e3d10 100644
--- a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Pindel.scala
+++ b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Pindel.scala
@@ -31,7 +31,8 @@ class Pindel(val root: Configurable) extends SvCaller {
/** Default pipeline config */
override def defaults = Map(
"pindelvcf" -> Map(
- "rdate" -> new SimpleDateFormat("yyyyMMdd").format(Calendar.getInstance().getTime())
+ "rdate" -> new SimpleDateFormat("yyyyMMdd").format(Calendar.getInstance().getTime()),
+ "compact_output_limit" -> 10
))
def biopetScript() {
--
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