Commit d215796c authored by bow's avatar bow Committed by Wai Yi Leung
Browse files

Fix incorrectly passed java flags for piped VarScan command

(cherry picked from commit f4d7e851)
parent b0774761
......@@ -63,20 +63,27 @@ class CustomVarScan(val root: Configurable) extends BiopetCommandLineFunction {
override def cmdLine: String = required(executable) + required("-vP") + required("""\t\t""")
}
private def varscan = new Mpileup2cns(wrapper.root) {
private val varscan = new Mpileup2cns(wrapper.root) {
strandFilter = Option(0)
outputVcf = Option(1)
}
private def compress = new Bgzip(wrapper.root) {
this.output = wrapper.output
}
private val compress = new Bgzip(wrapper.root)
private def index = new Tabix(wrapper.root) {
private val index = new Tabix(wrapper.root) {
input = compress.output
p = Option("vcf")
}
override def freezeFieldValues(): Unit = {
varscan.output = Option(new File(wrapper.output.toString.stripSuffix(".gz")))
compress.input = List(varscan.output.get)
compress.output = this.output
super.freezeFieldValues()
varscan.qSettings = this.qSettings
varscan.freezeFieldValues()
}
override def beforeGraph: Unit = {
require(output.toString.endsWith(".gz"), "Output must have a .gz file extension")
}
......@@ -85,6 +92,6 @@ class CustomVarScan(val root: Configurable) extends BiopetCommandLineFunction {
// FIXME: manual trigger of commandLine for version retrieval
mpileup.commandLine
mpileup.cmdPipe + " | " + fixMpileup.commandLine + " | " + removeEmptyPile.commandLine + " | " +
varscan.commandLine + " | " + compress.commandLine + " && " + index.commandLine
varscan.commandLine + " && " + compress.commandLine + " && " + index.commandLine
}
}
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