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Merge pull request #697 from broadinstitute/ldg_inbreedingCoeffForMultiallelics 

Fix nullPointerException
This commit is contained in:
ldgauthier 2014-08-07 11:57:39 -04:00
parent 0b72f7a16d f532f1f843
commit 683baff375
1 changed files with 2 additions and 0 deletions
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2
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/InbreedingCoeff.java
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@ -108,6 +108,8 @@ public class InbreedingCoeff extends InfoFieldAnnotation implements StandardAnno
for ( final Genotype g : genotypes ) { for ( final Genotype g : genotypes ) {
if ( g.isCalled() && g.hasLikelihoods() && g.getPloidy() == 2) // only work for diploid samples if ( g.isCalled() && g.hasLikelihoods() && g.getPloidy() == 2) // only work for diploid samples
sampleCount++; sampleCount++;
else
continue;
final double[] normalizedLikelihoods = MathUtils.normalizeFromLog10( g.getLikelihoods().getAsVector() ); final double[] normalizedLikelihoods = MathUtils.normalizeFromLog10( g.getLikelihoods().getAsVector() );
if (doMultiallelicMapping) if (doMultiallelicMapping)
{ {