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Merge correction

This commit is contained in:
Karthik Gururaj 2014-03-05 10:06:45 -08:00
parent ec54528605
commit b9afe800ae
1 changed files with 23 additions and 23 deletions
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protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngine.java
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@ -110,6 +110,7 @@ public class PairHMMLikelihoodCalculationEngine implements LikelihoodCalculation
default: default:
throw new UserException.BadArgumentValue("pairHMM", "Specified pairHMM implementation is unrecognized or incompatible with the HaplotypeCaller. Acceptable options are ORIGINAL, EXACT, CACHING, LOGLESS_CACHING, and ARRAY_LOGLESS."); throw new UserException.BadArgumentValue("pairHMM", "Specified pairHMM implementation is unrecognized or incompatible with the HaplotypeCaller. Acceptable options are ORIGINAL, EXACT, CACHING, LOGLESS_CACHING, and ARRAY_LOGLESS.");
} }
}
}; };
// Attempted to do as below, to avoid calling pairHMMThreadLocal.get() later on, but it resulted in a NullPointerException // Attempted to do as below, to avoid calling pairHMMThreadLocal.get() later on, but it resulted in a NullPointerException
// private final PairHMM pairHMM = pairHMMThreadLocal.get(); // private final PairHMM pairHMM = pairHMMThreadLocal.get();
@ -179,7 +180,6 @@ public class PairHMMLikelihoodCalculationEngine implements LikelihoodCalculation
pairHMMThreadLocal.get().close(); pairHMMThreadLocal.get().close();
} }
private void writeDebugLikelihoods(final GATKSAMRecord processedRead, final Haplotype haplotype, final double log10l){ private void writeDebugLikelihoods(final GATKSAMRecord processedRead, final Haplotype haplotype, final double log10l){
if ( WRITE_LIKELIHOODS_TO_FILE ) { if ( WRITE_LIKELIHOODS_TO_FILE ) {
likelihoodsStream.printf("%s %s %s %s %s %s %f%n", likelihoodsStream.printf("%s %s %s %s %s %s %f%n",