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Fix for error in HaplotypeCaller. HC has a UG argument collection for the UG engine but some of those arguments aren't appropriate to set.

This commit is contained in:
Ryan Poplin 2012-08-02 11:41:06 -04:00
parent fabca66d09
commit cb8bc18aeb
1 changed files with 1 additions and 0 deletions
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protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
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@ -239,6 +239,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
Set<String> samples = SampleUtils.getSAMFileSamples(getToolkit().getSAMFileHeader());
samplesList.addAll( samples );
// initialize the UnifiedGenotyper Engine which is used to call into the exact model
UAC.GLmodel = GenotypeLikelihoodsCalculationModel.Model.SNP; // the GLmodel isn't used by the HaplotypeCaller but it is dangerous to let the user change this argument
UG_engine = new UnifiedGenotyperEngine(getToolkit(), UAC.clone(), logger, null, null, samples, VariantContextUtils.DEFAULT_PLOIDY);
UAC.OutputMode = UnifiedGenotyperEngine.OUTPUT_MODE.EMIT_VARIANTS_ONLY; // low values used for isActive determination only, default/user-specified values used for actual calling
UAC.GenotypingMode = GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.DISCOVERY; // low values used for isActive determination only, default/user-specified values used for actual calling