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Put back the check that both chip and variant are not null. 

Also, sanity check that ref is not 'N'.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1651 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-09-18 16:03:54 +00:00
parent 94618044e8
commit 7da9ff2a9e
1 changed files with 7 additions and 1 deletions
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8
java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/GenotypeConcordance.java
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@ -2,6 +2,7 @@ package org.broadinstitute.sting.playground.gatk.walkers.varianteval;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.StingException; import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.genotype.DiploidGenotype; import org.broadinstitute.sting.utils.genotype.DiploidGenotype;
import org.broadinstitute.sting.utils.genotype.VariantBackedByGenotype; import org.broadinstitute.sting.utils.genotype.VariantBackedByGenotype;
@ -49,6 +50,10 @@ public class GenotypeConcordance extends BasicVariantAnalysis implements Genotyp
if ((chip != null && !(chip instanceof VariantBackedByGenotype) || (eval != null && !(eval instanceof VariantBackedByGenotype)))) if ((chip != null && !(chip instanceof VariantBackedByGenotype) || (eval != null && !(eval instanceof VariantBackedByGenotype))))
throw new StingException("Failure: trying to analyze genotypes of non-genotype data"); throw new StingException("Failure: trying to analyze genotypes of non-genotype data");
// This shouldn't happen, but let's check anyways
if ( BaseUtils.simpleBaseToBaseIndex(ref) == -1 )
return;
DiploidGenotype g = DiploidGenotype.createHomGenotype(ref); DiploidGenotype g = DiploidGenotype.createHomGenotype(ref);
int truthIndex, callIndex; int truthIndex, callIndex;
if (chip == null) if (chip == null)
@ -79,7 +84,8 @@ public class GenotypeConcordance extends BasicVariantAnalysis implements Genotyp
public String update(Variation eval, RefMetaDataTracker tracker, char ref, AlignmentContext context) { public String update(Variation eval, RefMetaDataTracker tracker, char ref, AlignmentContext context) {
Variation chip = (Variation) tracker.lookup(dbName, null); Variation chip = (Variation) tracker.lookup(dbName, null);
inc(chip, eval, ref); if ( eval != null || chip != null )
inc(chip, eval, ref);
return null; return null;
} }