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Don't ever return null for the list of GL models

This commit is contained in:
Eric Banks 2012-03-30 00:22:40 -04:00
parent 44ac49aa34
commit f4d4969f23
1 changed files with 1 additions and 1 deletions
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public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
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@ -571,7 +571,7 @@ public class UnifiedGenotyperEngine {
if ( UAC.GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES ) {
final VariantContext vcInput = UnifiedGenotyperEngine.getVCFromAllelesRod(tracker, refContext, rawContext.getLocation(), false, logger, UAC.alleles);
if ( vcInput == null )
return null;
return models;
if ( vcInput.isSNP() ) {
// ignore SNPs if the user chose INDEL mode only