From e610373169354b4fa8a6174b1b8a71c883aa5790 Mon Sep 17 00:00:00 2001
From: Valentin Ruano-Rubio <valentin@broadinstitute.org>
Date: Sun, 20 Apr 2014 17:11:51 -0400
Subject: [PATCH] Fixed integration test problems from previous premature merge

---
 .../gatk/walkers/genotyper/UnifiedGenotypingEngine.java      | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotypingEngine.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotypingEngine.java
index 81eebb6fd..8686fb878 100644
--- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotypingEngine.java
+++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotypingEngine.java
@@ -61,6 +61,7 @@ import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.sting.utils.gga.GenotypingGivenAllelesUtils;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
+import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
 import org.broadinstitute.variant.variantcontext.Allele;
 import org.broadinstitute.variant.variantcontext.GenotypesContext;
 import org.broadinstitute.variant.variantcontext.VariantContext;
@@ -532,6 +533,10 @@ public class UnifiedGenotypingEngine extends GenotypingEngine<UnifiedArgumentCol
         if (configuration.genotypingOutputMode == GenotypingOutputMode.GENOTYPE_GIVEN_ALLELES)
             useSNP = useINDEL = true;
 
+        // The non-general models only support Diploid so need to go to general if not the default_ploidy == 2.
+        if (configuration.samplePloidy != GATKVariantContextUtils.DEFAULT_PLOIDY)
+            useGeneral = true;
+
         // If annotateAllSitesWithPLs requested , SNP model must be used.
         if (!useSNP && configuration.annotateAllSitesWithPLs)
             throw new UserException.BadArgumentValue("glm","Invalid genotype likelihood model specification: " +