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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.
This commit is contained in:
Mark DePristo 2011-11-04 10:55:09 -04:00
parent 9f260c0dc1
commit 849c0757f2
1 changed files with 1 additions and 1 deletions
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2
public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/GATKScatterFunction.scala
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@ -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)