From 0cce1ae8b2fc568182befeefe3d00cdc92c434c2 Mon Sep 17 00:00:00 2001 From: kshakir Date: Tue, 23 Oct 2012 12:38:39 -0400 Subject: [PATCH] When gathering VCFs, using CombineVariants from the current classpath, and not the GATK used to run the command. This was a concern for external modules that bundled the engine but not CombineVariants. --- .../sting/queue/extensions/gatk/VcfGatherFunction.scala | 1 - 1 file changed, 1 deletion(-) diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/VcfGatherFunction.scala b/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/VcfGatherFunction.scala index fb22554f0..3fb5101d0 100644 --- a/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/VcfGatherFunction.scala +++ b/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/VcfGatherFunction.scala @@ -39,7 +39,6 @@ class VcfGatherFunction extends CombineVariants with GatherFunction with RetryMe private lazy val originalGATK = this.originalFunction.asInstanceOf[CommandLineGATK] override def freezeFieldValues() { - this.jarFile = this.originalGATK.jarFile this.variant = this.gatherParts.zipWithIndex map { case (input, index) => new TaggedFile(input, "input"+index) } this.out = this.originalOutput GATKIntervals.copyIntervalArguments(this.originalGATK, this)