Examples with ReadDataHolder org.broadinstitute.gatk.nativebindings.pairhmm.ReadDataHolder used on opensource projects

Example 1 with ReadDataHolder

use of org.broadinstitute.gatk.nativebindings.pairhmm.ReadDataHolder in project gatk by broadinstitute.

the class VectorLoglessPairHMM method computeLog10Likelihoods.

/**
     * {@inheritDoc}
     */
@Override
public void computeLog10Likelihoods(final LikelihoodMatrix<Haplotype> logLikelihoods, final List<GATKRead> processedReads, final Map<GATKRead, byte[]> gcp) {
    if (processedReads.isEmpty()) {
        return;
    }
    if (doProfiling) {
        startTime = System.nanoTime();
    }
    int readListSize = processedReads.size();
    int numHaplotypes = logLikelihoods.numberOfAlleles();
    ReadDataHolder[] readDataArray = new ReadDataHolder[readListSize];
    int idx = 0;
    for (GATKRead read : processedReads) {
        readDataArray[idx] = new ReadDataHolder();
        readDataArray[idx].readBases = read.getBases();
        readDataArray[idx].readQuals = read.getBaseQualities();
        readDataArray[idx].insertionGOP = ReadUtils.getBaseInsertionQualities(read);
        readDataArray[idx].deletionGOP = ReadUtils.getBaseDeletionQualities(read);
        readDataArray[idx].overallGCP = gcp.get(read);
        ++idx;
    }
    //to store results
    mLogLikelihoodArray = new double[readListSize * numHaplotypes];
    if (doProfiling) {
        threadLocalSetupTimeDiff = (System.nanoTime() - startTime);
    }
    //for(reads)
    //   for(haplotypes)
    //       compute_full_prob()
    pairHmm.computeLikelihoods(readDataArray, mHaplotypeDataArray, mLogLikelihoodArray);
    int readIdx = 0;
    for (int r = 0; r < readListSize; r++) {
        int hapIdx = 0;
        for (final Haplotype haplotype : logLikelihoods.alleles()) {
            //Since the order of haplotypes in the List<Haplotype> and alleleHaplotypeMap is different,
            //get idx of current haplotype in the list and use this idx to get the right likelihoodValue
            final int idxInsideHaplotypeList = haplotypeToHaplotypeListIdxMap.get(haplotype);
            logLikelihoods.set(hapIdx, r, mLogLikelihoodArray[readIdx + idxInsideHaplotypeList]);
            ++hapIdx;
        }
        readIdx += numHaplotypes;
    }
    if (doProfiling) {
        threadLocalPairHMMComputeTimeDiff = (System.nanoTime() - startTime);
        pairHMMComputeTime += threadLocalPairHMMComputeTimeDiff;
        pairHMMSetupTime += threadLocalSetupTimeDiff;
    }
}