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Merge pull request #76 from broadinstitute/md_kb_bugfix_GSA-795 

Bug fixes and optimizations for NA12878 KB
This commit is contained in:
depristo 2013-03-01 10:52:16 -08:00
parent c05d1352b1 0931afab39
commit 6204e6ccc9
1 changed files with 6 additions and 2 deletions
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8
public/java/src/org/broadinstitute/sting/utils/variant/GATKVariantContextUtils.java
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@ -405,6 +405,7 @@ public class GATKVariantContextUtils {
// we need to determine which of the alternate alleles (and hence the likelihoods) to use and carry forward
final int numOriginalAltAlleles = vc.getAlternateAlleles().size();
final int expectedNumLikelihoods = GenotypeLikelihoods.numLikelihoods(vc.getNAlleles(), 2);
final int numNewAltAlleles = allelesToUse.size() - 1;
// which PLs should be carried forward?
@ -444,6 +445,9 @@ public class GATKVariantContextUtils {
double[] newLikelihoods;
if ( likelihoodIndexesToUse == null ) {
newLikelihoods = originalLikelihoods;
} else if ( originalLikelihoods.length != expectedNumLikelihoods ) {
logger.warn("Wrong number of likelihoods in sample " + g.getSampleName() + " at " + vc + " got " + g.getLikelihoodsString() + " but expected " + expectedNumLikelihoods);
newLikelihoods = null;
} else {
newLikelihoods = new double[likelihoodIndexesToUse.size()];
int newIndex = 0;
@ -455,13 +459,13 @@ public class GATKVariantContextUtils {
}
// if there is no mass on the (new) likelihoods, then just no-call the sample
if ( MathUtils.sum(newLikelihoods) > SUM_GL_THRESH_NOCALL ) {
if ( newLikelihoods != null && MathUtils.sum(newLikelihoods) > SUM_GL_THRESH_NOCALL ) {
newGTs.add(GenotypeBuilder.create(g.getSampleName(), NO_CALL_ALLELES));
}
else {
final GenotypeBuilder gb = new GenotypeBuilder(g);
if ( numNewAltAlleles == 0 )
if ( newLikelihoods == null || numNewAltAlleles == 0 )
gb.noPL();
else
gb.PL(newLikelihoods);