Commit a35c3c9c authored by Sander van der Zeeuw's avatar Sander van der Zeeuw
Browse files

remove function removeEmptyPile()

parent 7a5e1b5c
......@@ -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
......
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