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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.

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kshakir 2012-10-23 12:38:39 -04:00
parent 4cd1a92358
commit 0cce1ae8b2
1 changed files with 0 additions and 1 deletions
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public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/VcfGatherFunction.scala
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@ -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)