From 9d8c963fccf1086182973e3aff95bb19cc32c00b Mon Sep 17 00:00:00 2001
From: kshakir <kshakir@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 25 May 2011 17:24:56 +0000
Subject: [PATCH] Switched arguments from short name to long name.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5873 348d0f76-0448-11de-a6fe-93d51630548a
---
 scala/qscript/playground/HybridSelectionPipeline.scala | 2 +-
 scala/qscript/playground/WholeGenomePipeline.scala     | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/scala/qscript/playground/HybridSelectionPipeline.scala b/scala/qscript/playground/HybridSelectionPipeline.scala
index 64d50bbf2..649d7139f 100755
--- a/scala/qscript/playground/HybridSelectionPipeline.scala
+++ b/scala/qscript/playground/HybridSelectionPipeline.scala
@@ -134,7 +134,7 @@ class HybridSelectionPipeline extends QScript {
     combineSNPsIndels.rodBind :+= RodBind("indels", "VCF", filterIndels.out)
     combineSNPsIndels.rodBind :+= RodBind("snps", "VCF", filterSNPs.out)
     combineSNPsIndels.rod_priority_list = "indels,snps"
-    combineSNPsIndels.filteredRecordsMergeType = org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED
+    combineSNPsIndels.filteredrecordsmergetype = org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED
     combineSNPsIndels.assumeIdenticalSamples = true
     combineSNPsIndels.out = projectBase + ".unannotated.vcf"
     combineSNPsIndels.jobOutputFile = combineSNPsIndels.out + ".out"
diff --git a/scala/qscript/playground/WholeGenomePipeline.scala b/scala/qscript/playground/WholeGenomePipeline.scala
index a2b4a4945..49619b458 100644
--- a/scala/qscript/playground/WholeGenomePipeline.scala
+++ b/scala/qscript/playground/WholeGenomePipeline.scala
@@ -158,7 +158,7 @@ class WholeGenomePipeline extends QScript {
     val combineChunks = new CombineVariants with CommandLineGATKArgs
     combineChunks.rodBind = chunkVcfs.zipWithIndex.map { case (vcf, index) => RodBind("input"+index, "VCF", vcf) }
     combineChunks.rod_priority_list = chunkVcfs.zipWithIndex.map { case (vcf, index) => "input"+index }.mkString(",")
-    combineChunks.filteredRecordsMergeType = org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED
+    combineChunks.filteredrecordsmergetype = org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED
     combineChunks.assumeIdenticalSamples = true
     combineChunks.out = projectBase + ".unfiltered.vcf"
     combineChunks.jobOutputFile = combineChunks.out + ".out"