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Bug fix for Genotype given alleles: if we are in INDEL mode ignore SNPs and MNPs instead of emitting an empty site with alleles but no annotations

This commit is contained in:
Guillermo del Angel 2011-07-12 13:43:46 -04:00
parent 8a78414432
commit cfe43e3971
1 changed files with 14 additions and 4 deletions
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14
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
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@ -634,11 +634,21 @@ public class UnifiedGenotyperEngine {
if (vcInput == null) if (vcInput == null)
return null; return null;
if (vcInput.isSNP() && ( UAC.GLmodel == GenotypeLikelihoodsCalculationModel.Model.BOTH || UAC.GLmodel == GenotypeLikelihoodsCalculationModel.Model.SNP)) // todo - no support to genotype MNP's yet
if (vcInput.isMNP())
return null;
if (vcInput.isSNP()) {
if (( UAC.GLmodel == GenotypeLikelihoodsCalculationModel.Model.BOTH || UAC.GLmodel == GenotypeLikelihoodsCalculationModel.Model.SNP))
return GenotypeLikelihoodsCalculationModel.Model.SNP; return GenotypeLikelihoodsCalculationModel.Model.SNP;
else
// ignore SNP's if user chose INDEL mode
return null;
}
else if ((vcInput.isIndel() || vcInput.isMixed()) && (UAC.GLmodel == GenotypeLikelihoodsCalculationModel.Model.BOTH || UAC.GLmodel == GenotypeLikelihoodsCalculationModel.Model.INDEL)) else if ((vcInput.isIndel() || vcInput.isMixed()) && (UAC.GLmodel == GenotypeLikelihoodsCalculationModel.Model.BOTH || UAC.GLmodel == GenotypeLikelihoodsCalculationModel.Model.INDEL))
return GenotypeLikelihoodsCalculationModel.Model.INDEL; return GenotypeLikelihoodsCalculationModel.Model.INDEL;
} else { }
else {
// todo - this assumes SNP's take priority when BOTH is selected, should do a smarter way once extended events are removed // todo - this assumes SNP's take priority when BOTH is selected, should do a smarter way once extended events are removed
if( UAC.GLmodel == GenotypeLikelihoodsCalculationModel.Model.BOTH || UAC.GLmodel == GenotypeLikelihoodsCalculationModel.Model.SNP) if( UAC.GLmodel == GenotypeLikelihoodsCalculationModel.Model.BOTH || UAC.GLmodel == GenotypeLikelihoodsCalculationModel.Model.SNP)
return GenotypeLikelihoodsCalculationModel.Model.SNP; return GenotypeLikelihoodsCalculationModel.Model.SNP;