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Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable

This commit is contained in:
Mark DePristo 2011-08-29 17:04:21 -04:00
parent 5defaf5fac 71680e3fd6
commit 1e5001b447
2 changed files with 11 additions and 6 deletions
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15
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;
@ -347,12 +350,14 @@ public class GenotypeAndValidateWalker extends RodWalker<GenotypeAndValidateWalk
}
VariantCallContext call;
if ( vcComp.isSNP() )
if ( vcComp.isSNP() ) {
call = snpEngine.calculateLikelihoodsAndGenotypes(tracker, ref, context);
else if ( vcComp.isIndel() ) {
} else if ( vcComp.isIndel() ) {
call = indelEngine.calculateLikelihoodsAndGenotypes(tracker, ref, context);
}
else {
} else if ( bamIsTruth ) {
// assume it's a SNP if no variation is present; this is necessary so that we can test supposed monomorphic sites against the truth bam
call = snpEngine.calculateLikelihoodsAndGenotypes(tracker, ref, context);
} else {
logger.info("Not SNP or INDEL " + vcComp.getChr() + ":" + vcComp.getStart() + " " + vcComp.getAlleles());
return counter;
}

2
public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java
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@ -62,5 +62,5 @@ public class VariantRecalibratorArgumentCollection {
@Argument(fullName="percentBadVariants", shortName="percentBad", doc="What percentage of the worst scoring variants to use when building the Gaussian mixture model of bad variants. 0.07 means bottom 7 percent.", required=false)
public double PERCENT_BAD_VARIANTS = 0.03;
@Argument(fullName="minNumBadVariants", shortName="minNumBad", doc="The minimum amount of worst scoring variants to use when building the Gaussian mixture model of bad variants. Will override -percentBad argument if necessary.", required=false)
public int MIN_NUM_BAD_VARIANTS = 2000;
public int MIN_NUM_BAD_VARIANTS = 2500;
}