From 328be9a6ab59e0178d1aa1d863ce948e0fc574b8 Mon Sep 17 00:00:00 2001
From: sajvanderzeeuw <s.a.j.van_der_zeeuw@lumc.nl>
Date: Mon, 18 Jan 2016 13:16:47 +0100
Subject: [PATCH] added fixmpileup script and removeEmptypile function
---
.../VarscanCnsSingleSample.scala | 22 ++++++++++++++++---
1 file changed, 19 insertions(+), 3 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 f838a2234..11610dd6f 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
@@ -2,6 +2,8 @@ package nl.lumc.sasc.biopet.pipelines.shiva.variantcallers
import java.io.PrintWriter
+import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
+import nl.lumc.sasc.biopet.core.extensions.PythonCommandLineFunction
import nl.lumc.sasc.biopet.extensions.gatk.CombineVariants
import nl.lumc.sasc.biopet.extensions.{ Ln, Tabix, Bgzip }
import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsMpileup
@@ -20,12 +22,12 @@ class VarscanCnsSingleSample(val root: Configurable) extends Variantcaller {
"disable_baq" -> true,
"depth" -> 1000000
),
- "mpileup2cns" -> Map("strand_filter" -> 0)
+ "varscanmpileup2cns" -> Map("strand_filter" -> 0)
)
override def fixedValues = Map(
"samtoolsmpileup" -> Map("output_mapping_quality" -> true),
- "mpileup2cns" -> Map("output_vcf" -> 1)
+ "varscanmpileup2cns" -> Map("output_vcf" -> 1)
)
def biopetScript: Unit = {
@@ -42,10 +44,24 @@ class VarscanCnsSingleSample(val root: Configurable) extends Variantcaller {
writer.println(sample)
writer.close()
+ val fixMpileup = new PythonCommandLineFunction {
+ setPythonScript("fix_mpileup.py", "/nl/lumc/sasc/biopet/pipelines/shiva/scripts/")
+ override val root: Configurable = this.root
+ override def configName = "fix_mpileup"
+ 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 | varscan | new Bgzip(this) > sampleVcf)
+ add(mpileup | fixMpileup | removeEmptyPile() | varscan | new Bgzip(this) > sampleVcf)
add(Tabix(this, sampleVcf))
sampleVcf
--
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