Commit 33e49a22 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

fix BIOPET-415

parent 85708a4a
...@@ -33,10 +33,15 @@ class SortVcf(val root: Configurable) extends Picard with Reference { ...@@ -33,10 +33,15 @@ class SortVcf(val root: Configurable) extends Picard with Reference {
@Input(doc = "Sequence dictionary to use", required = true) @Input(doc = "Sequence dictionary to use", required = true)
var sequenceDictionary: File = _ var sequenceDictionary: File = _
@Output
private var outputIndex: File = _
override val dictRequired = true override val dictRequired = true
override def beforeGraph(): Unit = { override def beforeGraph(): Unit = {
super.beforeGraph() super.beforeGraph()
if (output.getName.endsWith(".vcf.gz")) outputIndex = new File(output.getAbsolutePath + ".tbi")
if (output.getName.endsWith(".vcf")) outputIndex = new File(output.getAbsolutePath + ".idx")
if (sequenceDictionary == null) sequenceDictionary = referenceDictFile if (sequenceDictionary == null) sequenceDictionary = referenceDictFile
} }
......
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