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Bug fix to avoid infinite loop in GATKScatterFunction

This commit is contained in:
Mark DePristo 2011-11-02 16:20:42 -04:00
parent c1da8cd5e7
commit bd977c2d92
1 changed files with 0 additions and 3 deletions
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public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/GATKScatterFunction.scala
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@ -53,9 +53,6 @@ trait GATKScatterFunction extends ScatterFunction {
/** Whether the last scatter job should also include any unmapped reads. */ /** Whether the last scatter job should also include any unmapped reads. */
protected var includeUnmapped: Boolean = _ protected var includeUnmapped: Boolean = _
/** The total number of clone jobs that will be created. */
override def scatterCount = if (intervalFilesExist) super.scatterCount min this.maxIntervals else super.scatterCount
override def init() { override def init() {
this.originalGATK = this.originalFunction.asInstanceOf[CommandLineGATK] this.originalGATK = this.originalFunction.asInstanceOf[CommandLineGATK]
this.referenceSequence = this.originalGATK.reference_sequence this.referenceSequence = this.originalGATK.reference_sequence