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Commit 88adefce authored by Wai Yi Leung's avatar Wai Yi Leung
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Limit reporting of events in REF/ALT col to < SVTYPE > (saves space and post-processingpower)

parent 5164aa32
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public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Pindel.scala
+ 2
− 1
View file @ 88adefce
...@@ -31,7 +31,8 @@ class Pindel(val root: Configurable) extends SvCaller { ...@@ -31,7 +31,8 @@ class Pindel(val root: Configurable) extends SvCaller {
/** Default pipeline config */ /** Default pipeline config */
override def defaults = Map( override def defaults = Map(
"pindelvcf" -> 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() { def biopetScript() {
......
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