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N reference base fix for SSG 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1572 348d0f76-0448-11de-a6fe-93d51630548a
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depristo 2009-09-09 21:19:36 +00:00
parent bc9fe31cf5
commit 0093482c62
2 changed files with 17 additions and 9 deletions
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22
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SingleSampleGenotyper.java
View File

@ -92,18 +92,22 @@ public class SingleSampleGenotyper extends LocusWalker<SSGenotypeCall, SingleSam
*/ */
public SSGenotypeCall map(RefMetaDataTracker tracker, ReferenceContext refContext, AlignmentContext context) { public SSGenotypeCall map(RefMetaDataTracker tracker, ReferenceContext refContext, AlignmentContext context) {
char ref = refContext.getBase(); char ref = refContext.getBase();
DiploidGenotypePriors priors = new DiploidGenotypePriors(ref, heterozygosity, DiploidGenotypePriors.PROB_OF_TRISTATE_GENOTYPE); if ( BaseUtils.isRegularBase(ref) ) {
DiploidGenotypePriors priors = new DiploidGenotypePriors(ref, heterozygosity, DiploidGenotypePriors.PROB_OF_TRISTATE_GENOTYPE);
// setup GenotypeLike object // setup GenotypeLike object
GenotypeLikelihoods gl = GenotypeLikelihoodsFactory.makeGenotypeLikelihoods(baseModel, priors, defaultPlatform); GenotypeLikelihoods gl = GenotypeLikelihoodsFactory.makeGenotypeLikelihoods(baseModel, priors, defaultPlatform);
gl.setVerbose(VERBOSE); gl.setVerbose(VERBOSE);
gl.setEnableCacheFlag(! disableCache); gl.setEnableCacheFlag(! disableCache);
ReadBackedPileup pileup = new ReadBackedPileup(ref, context); ReadBackedPileup pileup = new ReadBackedPileup(ref, context);
gl.add(pileup, true); gl.add(pileup, true);
gl.validate(); gl.validate();
return new SSGenotypeCall(!GENOTYPE, context.getLocation(), ref,gl, pileup); return new SSGenotypeCall(!GENOTYPE, context.getLocation(), ref,gl, pileup);
} else {
return null;
}
} }
/** /**

4
java/src/org/broadinstitute/sting/utils/BaseUtils.java
View File

@ -133,6 +133,10 @@ public class BaseUtils {
} }
} }
static public boolean isRegularBase(char base) {
return simpleBaseToBaseIndex(base) != -1;
}
/** /**
* Converts a base index to a simple base * Converts a base index to a simple base
* *