From 849c0757f26905a4b6a1d4c744e16ac8fa817f09 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Fri, 4 Nov 2011 10:55:09 -0400 Subject: [PATCH] Bug fix for LocusScatterFunction when no intervals are provided -- Now correctly grabs reference contigs and cuts them all up, rather than NPE as intervalString == null. --- .../sting/queue/extensions/gatk/GATKScatterFunction.scala | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/GATKScatterFunction.scala b/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/GATKScatterFunction.scala index 24c2831b6..c9adff026 100644 --- a/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/GATKScatterFunction.scala +++ b/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/GATKScatterFunction.scala @@ -56,7 +56,7 @@ trait GATKScatterFunction extends ScatterFunction { override def init() { this.originalGATK = this.originalFunction.asInstanceOf[CommandLineGATK] this.referenceSequence = this.originalGATK.reference_sequence - if (this.originalGATK.intervals.isEmpty && this.originalGATK.intervalsString.isEmpty) { + if (this.originalGATK.intervals.isEmpty && (this.originalGATK.intervalsString == null || this.originalGATK.intervalsString.isEmpty)) { this.intervals ++= GATKScatterFunction.getGATKIntervals(this.referenceSequence, List.empty[String]).contigs } else { this.intervals ++= this.originalGATK.intervals.map(_.toString)