Commit 7825fcdf authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added args to queue extension

parent f4b0b185
...@@ -34,6 +34,11 @@ class VcfStats(val root: Configurable) extends BiopetJavaCommandLineFunction wit ...@@ -34,6 +34,11 @@ class VcfStats(val root: Configurable) extends BiopetJavaCommandLineFunction wit
protected var outputDir: File = _ protected var outputDir: File = _
var infoTags: List[String] = Nil
var genotypeTags: List[String] = Nil
var allInfoTags = false
var allGenotypeTags = false
/** Set output dir and a output file */ /** Set output dir and a output file */
def setOutputDir(dir: File): Unit = { def setOutputDir(dir: File): Unit = {
outputDir = dir outputDir = dir
...@@ -45,7 +50,11 @@ class VcfStats(val root: Configurable) extends BiopetJavaCommandLineFunction wit ...@@ -45,7 +50,11 @@ class VcfStats(val root: Configurable) extends BiopetJavaCommandLineFunction wit
/** Creates command to execute extension */ /** Creates command to execute extension */
override def commandLine = super.commandLine + override def commandLine = super.commandLine +
required("-I", input) + required("-I", input) +
required("-o", outputDir) required("-o", outputDir) +
repeat("--infoTag", infoTags) +
repeat("--genotypeTag", genotypeTags) +
conditional(allInfoTags, "--allInfoTags") +
conditional(allGenotypeTags, "--allGenotypeTags")
/** Returns general stats to the summary */ /** Returns general stats to the summary */
def summaryStats: Map[String, Any] = { def summaryStats: Map[String, Any] = {
...@@ -204,7 +213,7 @@ object VcfStats extends ToolCommand { ...@@ -204,7 +213,7 @@ object VcfStats extends ToolCommand {
val defaultGenotypeFields = List("DP", "GQ", "AD", "AD-ref", "AD-alt", "AD-used", "AD-not_used", "general") val defaultGenotypeFields = List("DP", "GQ", "AD", "AD-ref", "AD-alt", "AD-used", "AD-not_used", "general")
val defaultInfoFields = List("QUAL", "general") val defaultInfoFields = List("QUAL", "general", "AC", "AF", "AN", "DP")
/** /**
* @param args the command line arguments * @param args the command line arguments
......
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