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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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46
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngine.java
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@ -86,30 +86,31 @@ public class PairHMMLikelihoodCalculationEngine implements LikelihoodCalculation
case EXACT: return new Log10PairHMM(true); case EXACT: return new Log10PairHMM(true);
case ORIGINAL: return new Log10PairHMM(false); case ORIGINAL: return new Log10PairHMM(false);
case LOGLESS_CACHING: case LOGLESS_CACHING:
if (noFpga || !CnyPairHMM.isAvailable()) if (noFpga || !CnyPairHMM.isAvailable())
return new LoglessPairHMM(); return new LoglessPairHMM();
else else
return new CnyPairHMM(); return new CnyPairHMM();
case VECTOR_LOGLESS_CACHING: case VECTOR_LOGLESS_CACHING:
try try
{ {
return new VectorLoglessPairHMM(); return new VectorLoglessPairHMM();
} }
catch(UnsatisfiedLinkError ule) catch(UnsatisfiedLinkError ule)
{ {
logger.warn("Failed to load native library for VectorLoglessPairHMM - using Java implementation of LOGLESS_CACHING"); logger.warn("Failed to load native library for VectorLoglessPairHMM - using Java implementation of LOGLESS_CACHING");
return new LoglessPairHMM(); return new LoglessPairHMM();
} }
case DEBUG_VECTOR_LOGLESS_CACHING: case DEBUG_VECTOR_LOGLESS_CACHING:
return new DebugJNILoglessPairHMM(PairHMM.HMM_IMPLEMENTATION.VECTOR_LOGLESS_CACHING); return new DebugJNILoglessPairHMM(PairHMM.HMM_IMPLEMENTATION.VECTOR_LOGLESS_CACHING);
case ARRAY_LOGLESS: case ARRAY_LOGLESS:
if (noFpga || !CnyPairHMM.isAvailable()) if (noFpga || !CnyPairHMM.isAvailable())
return new ArrayLoglessPairHMM(); return new ArrayLoglessPairHMM();
else else
return new CnyPairHMM(); return new CnyPairHMM();
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",
@ -330,8 +330,8 @@ public class PairHMMLikelihoodCalculationEngine implements LikelihoodCalculation
int X_METRIC_LENGTH = 0; int X_METRIC_LENGTH = 0;
for( final Map.Entry<String, List<GATKSAMRecord>> sample : perSampleReadList.entrySet() ) { for( final Map.Entry<String, List<GATKSAMRecord>> sample : perSampleReadList.entrySet() ) {
for( final GATKSAMRecord read : sample.getValue() ) { for( final GATKSAMRecord read : sample.getValue() ) {
final int readLength = read.getReadLength(); final int readLength = read.getReadLength();
if( readLength > X_METRIC_LENGTH ) { X_METRIC_LENGTH = readLength; } if( readLength > X_METRIC_LENGTH ) { X_METRIC_LENGTH = readLength; }
} }
} }
int Y_METRIC_LENGTH = 0; int Y_METRIC_LENGTH = 0;
@ -360,7 +360,7 @@ public class PairHMMLikelihoodCalculationEngine implements LikelihoodCalculation
// Add likelihoods for each sample's reads to our stratifiedReadMap // Add likelihoods for each sample's reads to our stratifiedReadMap
final Map<String, PerReadAlleleLikelihoodMap> stratifiedReadMap = new LinkedHashMap<>(); final Map<String, PerReadAlleleLikelihoodMap> stratifiedReadMap = new LinkedHashMap<>();
for( final Map.Entry<String, List<GATKSAMRecord>> sampleEntry : perSampleReadList.entrySet() ) { for( final Map.Entry<String, List<GATKSAMRecord>> sampleEntry : perSampleReadList.entrySet() ) {
// evaluate the likelihood of the reads given those haplotypes // evaluate the likelihood of the reads given those haplotypes
final PerReadAlleleLikelihoodMap map = computeReadLikelihoods(haplotypes, sampleEntry.getValue()); final PerReadAlleleLikelihoodMap map = computeReadLikelihoods(haplotypes, sampleEntry.getValue());
map.filterPoorlyModelledReads(EXPECTED_ERROR_RATE_PER_BASE); map.filterPoorlyModelledReads(EXPECTED_ERROR_RATE_PER_BASE);