From a35c3c9c75a62e0146dabc18ffbade1a3e1be809 Mon Sep 17 00:00:00 2001
From: sajvanderzeeuw <s.a.j.van_der_zeeuw@lumc.nl>
Date: Mon, 18 Jan 2016 14:09:11 +0100
Subject: [PATCH] remove function removeEmptyPile()
---
.../shiva/variantcallers/VarscanCnsSingleSample.scala | 11 ++---------
1 file changed, 2 insertions(+), 9 deletions(-)
diff --git a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/VarscanCnsSingleSample.scala b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/VarscanCnsSingleSample.scala
index 11610dd6f..5cde45d4c 100644
--- a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/VarscanCnsSingleSample.scala
+++ b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/VarscanCnsSingleSample.scala
@@ -39,7 +39,7 @@ class VarscanCnsSingleSample(val root: Configurable) extends Variantcaller {
val sampleFile = new File(outputDir, s"$sample.name.txt")
sampleFile.getParentFile.mkdirs()
- sampleFile.deleteOnExit()
+ //sampleFile.deleteOnExit()
val writer = new PrintWriter(sampleFile)
writer.println(sample)
writer.close()
@@ -51,17 +51,10 @@ class VarscanCnsSingleSample(val root: Configurable) extends Variantcaller {
def cmdLine = getPythonCommand
}
- def removeEmptyPile() = new BiopetCommandLineFunction {
- override val root: Configurable = this.root
- override def configName = "remove_empty_pile"
- executable = config("exe", default = "grep", freeVar = false)
- override def cmdLine: String = required(executable) + required("-vP") + required("""\t\t""")
- }
-
val varscan = new VarscanMpileup2cns(this)
varscan.vcfSampleList = Some(sampleVcf)
- add(mpileup | fixMpileup | removeEmptyPile() | varscan | new Bgzip(this) > sampleVcf)
+ add(mpileup | fixMpileup | varscan | new Bgzip(this) > sampleVcf)
add(Tabix(this, sampleVcf))
sampleVcf
--
GitLab