From bd977c2d92ddc9e5670e4431e72c320937cdcb12 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Wed, 2 Nov 2011 16:20:42 -0400 Subject: [PATCH] Bug fix to avoid infinite loop in GATKScatterFunction --- .../sting/queue/extensions/gatk/GATKScatterFunction.scala | 3 --- 1 file changed, 3 deletions(-) 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 c89e63668..24c2831b6 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 @@ -53,9 +53,6 @@ trait GATKScatterFunction extends ScatterFunction { /** Whether the last scatter job should also include any unmapped reads. */ 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() { this.originalGATK = this.originalFunction.asInstanceOf[CommandLineGATK] this.referenceSequence = this.originalGATK.reference_sequence