Commit dd163178 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Let SortVcf also use Reference trait

parent 2af46d82
......@@ -17,11 +17,12 @@ package nl.lumc.sasc.biopet.extensions.picard
import java.io.File
import nl.lumc.sasc.biopet.core.Reference
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{Input, Output}
/** Extension for picard SortVcf */
class SortVcf(val root: Configurable) extends Picard {
class SortVcf(val root: Configurable) extends Picard with Reference {
javaMainClass = new picard.vcf.SortVcf().getClass.getName
@Input(doc = "Input VCF(s) to be sorted. Multiple inputs must have the same sample names (in order)", required = true)
......@@ -33,6 +34,11 @@ class SortVcf(val root: Configurable) extends Picard {
@Input(doc = "Sequence dictionary to use", required = true)
var sequenceDictionary: File = _
override def beforeGraph(): Unit = {
super.beforeGraph()
if (sequenceDictionary == null) sequenceDictionary = referenceDict
}
/** Returns command to execute */
override def cmdLine = super.cmdLine +
(if (inputAsStdin) required("INPUT=", new File("/dev/stdin"), spaceSeparated = false)
......
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment