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Minor typo in comments fixed

This commit is contained in:
Karthik Gururaj 2014-01-16 19:58:04 -08:00
parent e90405cd1f
commit 90938b8610
1 changed files with 1 additions and 77 deletions
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78
org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM.cc
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@ -316,7 +316,7 @@ JNIEXPORT void JNICALL Java_org_broadinstitute_sting_utils_pairhmm_JNILoglessPai
jdouble* likelihoodDoubleArray = (jdouble*)GET_DOUBLE_ARRAY_ELEMENTS(likelihoodArray, &is_copy);
assert(likelihoodDoubleArray && "likelihoodArray is NULL");
assert(env->GetArrayLength(likelihoodArray) == numTestCases);
#pragma omp parallel for schedule (guided,2) private(tc_idx) num_threads(maxNumThreadsToUse)
#pragma omp parallel for schedule (dynamic,10) private(tc_idx) num_threads(maxNumThreadsToUse)
for(tc_idx=0;tc_idx<numTestCases;++tc_idx)
{
double result_avxd = GEN_INTRINSIC(compute_full_prob_avx, d)<double>(&(tc_array[tc_idx]));
@ -347,79 +347,3 @@ JNIEXPORT void JNICALL Java_org_broadinstitute_sting_utils_pairhmm_JNILoglessPai
tc_array.clear();
}
/*
protected final double computeReadLikelihoodGivenHaplotypeLog10( final byte[] haplotypeBases,
final byte[] readBases,
final byte[] readQuals,
final byte[] insertionGOP,
final byte[] deletionGOP,
final byte[] overallGCP,
final boolean recacheReadValues,
final byte[] nextHaploytpeBases) {
paddedReadLength = readBases.length + 1;
paddedHaplotypeLength = haplotypeBases.length + 1;
double result = subComputeReadLikelihoodGivenHaplotypeLog10(haplotypeBases, readBases, readQuals, insertionGOP, deletionGOP, overallGCP, 0, true, 0);
if ( ! MathUtils.goodLog10Probability(result) )
throw new IllegalStateException("PairHMM Log Probability cannot be greater than 0: " + String.format("haplotype: %s, read: %s, result: %f", Arrays.toString(haplotypeBases), Arrays.toString(readBases), result));
// Warning: Careful if using the PairHMM in parallel! (this update has to be taken care of).
// Warning: This assumes no downstream modification of the haplotype bases (saves us from copying the array). It is okay for the haplotype caller and the Unified Genotyper.
// KG: seems pointless is not being used anywhere
previousHaplotypeBases = haplotypeBases;
return result;
return 0;
}*/
//public PerReadAlleleLikelihoodMap computeLikelihoods(final List<GATKSAMRecord> reads, final Map<Allele, Haplotype> alleleHaplotypeMap, final Map<GATKSAMRecord, byte[]> GCPArrayMap)
//{
////PerReadAlleleLikelihoodMap retValue = super.computeLikelihoods(reads, alleleHaplotypeMap, GCPArrayMap);
//// (re)initialize the pairHMM only if necessary
//final int readMaxLength = findMaxReadLength(reads);
//final int haplotypeMaxLength = findMaxHaplotypeLength(alleleHaplotypeMap);
//if (!initialized || readMaxLength > maxReadLength || haplotypeMaxLength > maxHaplotypeLength)
//{ initialize(readMaxLength, haplotypeMaxLength); }
//if ( ! initialized )
//throw new IllegalStateException("Must call initialize before calling jniComputeLikelihoods");
//final PerReadAlleleLikelihoodMap likelihoodMap = new PerReadAlleleLikelihoodMap();
//jniComputeLikelihoods(reads, alleleHaplotypeMap, GCPArrayMap, likelihoodMap);
//for(GATKSAMRecord read : reads){
//final byte[] readBases = read.getReadBases();
//final byte[] readQuals = read.getBaseQualities();
//final byte[] readInsQuals = read.getBaseInsertionQualities();
//final byte[] readDelQuals = read.getBaseDeletionQualities();
//final byte[] overallGCP = GCPArrayMap.get(read);
//// peak at the next haplotype in the list (necessary to get nextHaplotypeBases, which is required for caching in the array implementation)
//byte[] currentHaplotypeBases = null;
//boolean isFirstHaplotype = true;
//Allele currentAllele = null;
//double log10l;
//for (final Allele allele : alleleHaplotypeMap.keySet()){
//final Haplotype haplotype = alleleHaplotypeMap.get(allele);
//final byte[] nextHaplotypeBases = haplotype.getBases();
//if (currentHaplotypeBases != null) {
//log10l = computeReadLikelihoodGivenHaplotypeLog10(currentHaplotypeBases,
//readBases, readQuals, readInsQuals, readDelQuals, overallGCP, isFirstHaplotype, nextHaplotypeBases);
//likelihoodMap.add(read, currentAllele, log10l);
//}
//// update the current haplotype
//currentHaplotypeBases = nextHaplotypeBases;
//currentAllele = allele;
//}
//// process the final haplotype
//if (currentHaplotypeBases != null) {
//// there is no next haplotype, so pass null for nextHaplotypeBases.
//log10l = computeReadLikelihoodGivenHaplotypeLog10(currentHaplotypeBases,
//readBases, readQuals, readInsQuals, readDelQuals, overallGCP, isFirstHaplotype, null);
//likelihoodMap.add(read, currentAllele, log10l);
//}
//}
//if(debug)
//debugClose();
//return likelihoodMap;
//}