From abef6cfcb6fb5a1ff38d1967f99ac70eeabc87af Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Sat, 8 Feb 2014 23:24:46 -0500
Subject: [PATCH] Removing parameters that were incorrectly copied over from
 RegenotypeVariants.

---
 .../sting/gatk/walkers/variantutils/GenotypeGVCFs.java      | 6 +-----
 .../walkers/variantutils/GenotypeGVCFsIntegrationTest.java  | 4 ++--
 2 files changed, 3 insertions(+), 7 deletions(-)

diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeGVCFs.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeGVCFs.java
index d2374ccb8..afd657ea3 100644
--- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeGVCFs.java
+++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeGVCFs.java
@@ -166,11 +166,7 @@ public class GenotypeGVCFs extends RodWalker<VariantContext, VariantContextWrite
         vcfWriter.writeHeader(vcfHeader);
 
         // create the genotyping engine
-        final UnifiedArgumentCollection UAC = new UnifiedArgumentCollection();
-        UAC.GLmodel = GenotypeLikelihoodsCalculationModel.Model.BOTH;
-        UAC.OutputMode = UnifiedGenotyperEngine.OUTPUT_MODE.EMIT_ALL_SITES;
-        UAC.GenotypingMode = GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES;
-        genotypingEngine = new UnifiedGenotyperEngine(getToolkit(), UAC, logger, null, null, samples, GATKVariantContextUtils.DEFAULT_PLOIDY);
+        genotypingEngine = new UnifiedGenotyperEngine(getToolkit(), new UnifiedArgumentCollection(), logger, null, null, samples, GATKVariantContextUtils.DEFAULT_PLOIDY);
 
         // create the annotation engine
         annotationEngine = new VariantAnnotatorEngine(Arrays.asList("none"), annotationsToUse, Collections.<String>emptyList(), this, getToolkit());
diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeGVCFsIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeGVCFsIntegrationTest.java
index cca2bec38..da7ec3dd4 100644
--- a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeGVCFsIntegrationTest.java
+++ b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeGVCFsIntegrationTest.java
@@ -65,7 +65,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
                         " -V:sample3 " + privateTestDir + "combine.single.sample.pipeline.3.vcf" +
                         " -L 20:10,000,000-20,000,000", b37KGReference),
                 1,
-                Arrays.asList("8fd26c30509b98372c2945405a1d7cc4"));
+                Arrays.asList("54487ea151c49d36a15eac8097a7e460"));
         executeTest("combineSingleSamplePipelineGVCF", spec);
     }
 
@@ -89,7 +89,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
                         " -V:sample3 " + privateTestDir + "combine.single.sample.pipeline.3.vcf" +
                         " -L 20:10,000,000-11,000,000 --dbsnp " + b37dbSNP132, b37KGReference),
                 1,
-                Arrays.asList("d0eb9046c24fa6a66ee20feff35457d4"));
+                Arrays.asList("9e6ef126d5e872e5b2a68c3d73471566"));
         executeTest("combineSingleSamplePipelineGVCF_addDbsnp", spec);
     }