Examples of org.broadinstitute.gatk.tools.walkers.haplotypecaller.Kmer.bases()

Package org.broadinstitute.gatk.tools.walkers.haplotypecaller

Class org.broadinstitute.gatk.tools.walkers.haplotypecaller.Kmer

Examples of org.broadinstitute.gatk.tools.walkers.haplotypecaller.Kmer.bases()

org.broadinstitute.gatk.tools.walkers.haplotypecaller.Kmer.bases()
Get the bases of this kmer. May create a copy of the bases, depending on how this kmer was constructed. Note that this function is efficient in that if it needs to copy the bases this only occurs once. @return a non-null byte[] containing length() bases of this kmer, regardless of how this kmer was created

            if (--pendingChildrenCounts[indexByVertex.get(p)] == 0)
                ready.add(p);


        final Kmer mergedKmer = new Kmer(sequence);
        if (uniqueKmers.containsKey(mergedKmer)) {
            uniqueKmersToUpdate.add(new Kmer(mergedKmer.bases().clone()));
            uniqueKmers.remove(mergedKmer);
        }
        boolean foundMergedVertex = false;
        for (final MultiDeBruijnVertex v : vertices)
            if (v == vertexToKeep)

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