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This warning message actually happens all the time in AssessNA12878 when we subset down to biallelic events but I've verified that it is working as intended. Moving the logging level up to debug.

This commit is contained in:
Ryan Poplin 2014-09-29 11:40:10 -04:00
parent f7fc9cd839
commit ac1a397024
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 ) {
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);
logger.debug("Wrong number of likelihoods in sample " + g.getSampleName() + " at " + vc + " got " + g.getLikelihoodsString() + " but expected " + expectedNumLikelihoods);
newLikelihoods = null;
} else {
newLikelihoods = new double[likelihoodIndexesToUse.size()];