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Merge pull request #612 from broadinstitute/vrr_integration_test_error_quickfix 

Fixed integration test problems from previous premature merge
This commit is contained in:
Valentin Ruano Rubio 2014-04-20 18:40:22 -04:00
parent f03e5ffeb1 e610373169
commit d38835822e
1 changed files with 5 additions and 0 deletions
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5
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotypingEngine.java
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@ -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: " +