From 9ee58d323aeebe4a331ffd24b61fad8f59036a6a Mon Sep 17 00:00:00 2001 From: Joel Thibault Date: Mon, 2 Jul 2012 15:37:23 -0400 Subject: [PATCH] Pass the original GATK unsafe parameter to the VcfGatherFunction --- .../sting/queue/extensions/gatk/VcfGatherFunction.scala | 3 +++ 1 file changed, 3 insertions(+) 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 7862dec41..739e6cc91 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 @@ -52,6 +52,9 @@ class VcfGatherFunction extends CombineVariants with GatherFunction { val sitesOnly = QFunction.findField(originalFunction.getClass, VCFWriterArgumentTypeDescriptor.SITES_ONLY_ARG_NAME) this.sites_only = originalGATK.getFieldValue(sitesOnly).asInstanceOf[Boolean] + // ensure that the gather function receives the same unsafe parameter as the scattered function + this.unsafe = this.originalGATK.unsafe + super.freezeFieldValues() } }