diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngine.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngine.java index 01accfee8..c1a1f68f1 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngine.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngine.java @@ -180,6 +180,7 @@ public class PairHMMLikelihoodCalculationEngine implements LikelihoodCalculation pairHMMThreadLocal.get().close(); } + private void writeDebugLikelihoods(final GATKSAMRecord processedRead, final Haplotype haplotype, final double log10l){ if ( WRITE_LIKELIHOODS_TO_FILE ) { likelihoodsStream.printf("%s %s %s %s %s %s %f%n",