f7c44ad01916666a8f18717f2362ea57df2341fe,java/src/org/broadinstitute/sting/gatk/walkers/genotyper/PointEstimateGenotypeCalculationModel.java,PointEstimateGenotypeCalculationModel,calculateGenotype,#RefMetaDataTracker#char#AlignmentContext#DiploidGenotypePriors#,29
Before Change
// we can now create the genotype call object
GenotypeCall call = GenotypeWriterFactory.createSupportedGenotypeCall(OUTPUT_FORMAT, ref, context.getLocation());
call.setVariation(null);
if ( call instanceof ReadBacked ) {
((ReadBacked)call).setPileup(discoveryGL.first);
After Change
locusdata.setGenotypeCalls(Arrays.asList((Genotype)call));
}
call.setVariation(locusdata);
return new Pair<VariationCall, List<Genotype>>(locusdata, Arrays.asList((Genotype)call));
}