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Pass the original GATK unsafe parameter to the VcfGatherFunction

This commit is contained in:
Joel Thibault 2012-07-02 15:37:23 -04:00
parent 1b0a775773
commit 9ee58d323a
1 changed files with 3 additions and 0 deletions
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3
public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/VcfGatherFunction.scala
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@ -52,6 +52,9 @@ class VcfGatherFunction extends CombineVariants with GatherFunction {
val sitesOnly = QFunction.findField(originalFunction.getClass, VCFWriterArgumentTypeDescriptor.SITES_ONLY_ARG_NAME) val sitesOnly = QFunction.findField(originalFunction.getClass, VCFWriterArgumentTypeDescriptor.SITES_ONLY_ARG_NAME)
this.sites_only = originalGATK.getFieldValue(sitesOnly).asInstanceOf[Boolean] 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() super.freezeFieldValues()
} }
} }