From 9e53fd688034da583dd4fad78b2cc6946ae91a3f Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Wed, 10 Aug 2011 07:28:35 -0400 Subject: [PATCH] Fixed VCFGatherFunction to not provide incorrect rod_priority_list -- simply don't provide one, since you are just 'cating' the files together and genotypes never overlap --- .../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 f8a6cb2cb..d70022147 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 @@ -44,7 +44,6 @@ class VcfGatherFunction extends CombineVariants with GatherFunction { this.intervalsString = this.originalGATK.intervalsString this.variant = this.gatherParts.zipWithIndex map { case (input, index) => new TaggedFile(input, "input"+index) } - this.rod_priority_list = (0 until this.gatherParts.size).map("input"+_).mkString(",") this.out = this.originalOutput this.assumeIdenticalSamples = true