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Don't use the default deletion value from UG if not asking to have it set

This commit is contained in:
Eric Banks 2011-08-29 13:48:10 -04:00
parent bb7a37e8f2
commit c2f0db969b
1 changed files with 4 additions and 1 deletions
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5
public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidateWalker.java
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@ -303,7 +303,10 @@ public class GenotypeAndValidateWalker extends RodWalker<GenotypeAndValidateWalk
uac.alleles = alleles;
if (!bamIsTruth) uac.GenotypingMode = GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES;
if (mbq >= 0) uac.MIN_BASE_QUALTY_SCORE = mbq;
if (deletions >= 0) uac.MAX_DELETION_FRACTION = deletions;
if (deletions >= 0)
uac.MAX_DELETION_FRACTION = deletions;
else
uac.MAX_DELETION_FRACTION = 1.0;
if (emitConf >= 0) uac.STANDARD_CONFIDENCE_FOR_EMITTING = emitConf;
if (callConf >= 0) uac.STANDARD_CONFIDENCE_FOR_CALLING = callConf;