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Merge pull request #737 from broadinstitute/rp_VariantContextUtils_warning_message 

This warning message actually happens all the time in AssessNA12878 when...
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rpoplin 2014-09-29 14:49:32 -04:00
parent f7fc9cd839 ac1a397024
commit ff887f5674
1 changed files with 1 additions and 1 deletions
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2
public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtils.java
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@ -706,7 +706,7 @@ public class GATKVariantContextUtils {
if ( likelihoodIndexesToUse == null ) { if ( likelihoodIndexesToUse == null ) {
newLikelihoods = originalLikelihoods; newLikelihoods = originalLikelihoods;
} else if ( originalLikelihoods.length != expectedNumLikelihoods ) { } else if ( originalLikelihoods.length != expectedNumLikelihoods ) {
logger.warn("Wrong number of likelihoods in sample " + g.getSampleName() + " at " + vc + " got " + g.getLikelihoodsString() + " but expected " + expectedNumLikelihoods); logger.debug("Wrong number of likelihoods in sample " + g.getSampleName() + " at " + vc + " got " + g.getLikelihoodsString() + " but expected " + expectedNumLikelihoods);
newLikelihoods = null; newLikelihoods = null;
} else { } else {
newLikelihoods = new double[likelihoodIndexesToUse.size()]; newLikelihoods = new double[likelihoodIndexesToUse.size()];