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getBestGenotype() does not necessarily return hets in alphabetical order; 

the string (unfortunately) needs to be sorted for lookup in the table (otherwise we throw a NullPointerException)
TO DO: have the table be smarter instead of sorting each genotype string


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1298 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-07-23 01:58:47 +00:00
parent ee8ed534e0
commit f8b1dbe3b3
1 changed files with 7 additions and 1 deletions
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8
java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/RatioFilter.java
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@ -267,7 +267,7 @@ public abstract class RatioFilter implements VariantExclusionCriterion {
ReadBackedPileup pileup = new ReadBackedPileup(ref, context); ReadBackedPileup pileup = new ReadBackedPileup(ref, context);
if ( applyToVariant(variant) ) { if ( applyToVariant(variant) ) {
Pair<Integer, Integer> counts = scoreVariant(ref, pileup, variant); Pair<Integer, Integer> counts = scoreVariant(ref, pileup, variant);
GenotypeFeatureData gfd = dataTable.get(variant.getBestGenotype()); GenotypeFeatureData gfd = dataTable.get(orderedBases(variant.getBestGenotype()));
if (integrateOverSamplingProbabilities) if (integrateOverSamplingProbabilities)
exclude = integralExclude(gfd, counts); exclude = integralExclude(gfd, counts);
@ -314,4 +314,10 @@ public abstract class RatioFilter implements VariantExclusionCriterion {
//double value = counts.first / (1.0 * Math.max(counts.second, 1.0)); //double value = counts.first / (1.0 * Math.max(counts.second, 1.0));
return ! gfd.passesThreshold(value); return ! gfd.passesThreshold(value);
} }
private String orderedBases(String s) {
char[] charArray = s.toCharArray();
java.util.Arrays.sort(charArray);
return new String(charArray);
}
} }