From dd1631783429269db8270623efaecc09eea43d53 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 5 Apr 2016 12:57:54 +0200
Subject: [PATCH] Let SortVcf also use Reference trait
---
.../nl/lumc/sasc/biopet/extensions/picard/SortVcf.scala | 8 +++++++-
1 file changed, 7 insertions(+), 1 deletion(-)
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SortVcf.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SortVcf.scala
index cdc730428..623708024 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SortVcf.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SortVcf.scala
@@ -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)
--
GitLab