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Fixed integration test problems from previous premature merge

This commit is contained in:
Valentin Ruano-Rubio 2014-04-20 17:11:51 -04:00
parent f03e5ffeb1
commit e610373169
1 changed files with 5 additions and 0 deletions
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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.gga.GenotypingGivenAllelesUtils;
import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; 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.Allele;
import org.broadinstitute.variant.variantcontext.GenotypesContext; import org.broadinstitute.variant.variantcontext.GenotypesContext;
import org.broadinstitute.variant.variantcontext.VariantContext; import org.broadinstitute.variant.variantcontext.VariantContext;
@ -532,6 +533,10 @@ public class UnifiedGenotypingEngine extends GenotypingEngine<UnifiedArgumentCol
if (configuration.genotypingOutputMode == GenotypingOutputMode.GENOTYPE_GIVEN_ALLELES) if (configuration.genotypingOutputMode == GenotypingOutputMode.GENOTYPE_GIVEN_ALLELES)
useSNP = useINDEL = true; 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 annotateAllSitesWithPLs requested , SNP model must be used.
if (!useSNP && configuration.annotateAllSitesWithPLs) if (!useSNP && configuration.annotateAllSitesWithPLs)
throw new UserException.BadArgumentValue("glm","Invalid genotype likelihood model specification: " + throw new UserException.BadArgumentValue("glm","Invalid genotype likelihood model specification: " +