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Fix GenotypeAndValidate to handle SNPs and indels as reported on the forum. Recent changes to the UnifiedArgumentCollection made this stop working. Adding in JIRA to create integration tests for this tool.

This commit is contained in:
Eric Banks 2012-10-25 10:06:13 -04:00
parent c53c55da12
commit 6dc7d872ec
1 changed files with 3 additions and 2 deletions
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5
public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidate.java
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@ -333,8 +333,9 @@ public class GenotypeAndValidate extends RodWalker<GenotypeAndValidate.CountedDa
snpEngine = new UnifiedGenotyperEngine(getToolkit(), uac);
// Adding the INDEL calling arguments for UG
uac.GLmodel = GenotypeLikelihoodsCalculationModel.Model.INDEL;
indelEngine = new UnifiedGenotyperEngine(getToolkit(), uac);
UnifiedArgumentCollection uac_indel = new UnifiedArgumentCollection(uac);
uac_indel.GLmodel = GenotypeLikelihoodsCalculationModel.Model.INDEL;
indelEngine = new UnifiedGenotyperEngine(getToolkit(), uac_indel);
// make sure we have callConf set to the threshold set by the UAC so we can use it later.
callConf = uac.STANDARD_CONFIDENCE_FOR_CALLING;