Pass the original GATK unsafe parameter to the VcfGatherFunction
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@ -52,6 +52,9 @@ class VcfGatherFunction extends CombineVariants with GatherFunction {
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val sitesOnly = QFunction.findField(originalFunction.getClass, VCFWriterArgumentTypeDescriptor.SITES_ONLY_ARG_NAME)
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this.sites_only = originalGATK.getFieldValue(sitesOnly).asInstanceOf[Boolean]
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// ensure that the gather function receives the same unsafe parameter as the scattered function
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this.unsafe = this.originalGATK.unsafe
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super.freezeFieldValues()
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}
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}
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