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

Example 1 with HaplotypeDataHolder

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

the class VectorLoglessPairHMM method initialize.

/**
     * {@inheritDoc}
     */
@Override
public void initialize(final List<Haplotype> haplotypes, final Map<String, List<GATKRead>> perSampleReadList, final int readMaxLength, final int haplotypeMaxLength) {
    // do not need to call super.initialize()
    int numHaplotypes = haplotypes.size();
    mHaplotypeDataArray = new HaplotypeDataHolder[numHaplotypes];
    int idx = 0;
    haplotypeToHaplotypeListIdxMap.clear();
    for (final Haplotype currHaplotype : haplotypes) {
        mHaplotypeDataArray[idx] = new HaplotypeDataHolder();
        mHaplotypeDataArray[idx].haplotypeBases = currHaplotype.getBases();
        haplotypeToHaplotypeListIdxMap.put(currHaplotype, idx);
        ++idx;
    }
}