Examples of kmerSize()

Examples of org.broadinstitute.gatk.tools.walkers.haplotypecaller.KmerSequence.kmerSize()

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            throw new IllegalArgumentException("the input graph must implement " + KmerSearchableGraph.class.getName());

        final int kmerSize = graph.getKmerSize();
        final KmerSequence haplotypeKmers = new KmerSequence(sequence,kmerSize);

        if (haplotypeKmers.kmerSize() != graph.getKmerSize())
            throw new IllegalArgumentException("incompatible kmer sizes " + graph.getKmerSize() + " != " + haplotypeKmers.kmerSize());

        V vertex = null;
        int i;
        for (i = 0; i < haplotypeKmers.size(); i++)
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Examples of org.broadinstitute.gatk.tools.walkers.haplotypecaller.KmerSequence.kmerSize()

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        final int kmerSize = graph.getKmerSize();
        final KmerSequence haplotypeKmers = new KmerSequence(sequence,kmerSize);

        if (haplotypeKmers.kmerSize() != graph.getKmerSize())
            throw new IllegalArgumentException("incompatible kmer sizes " + graph.getKmerSize() + " != " + haplotypeKmers.kmerSize());

        V vertex = null;
        int i;
        for (i = 0; i < haplotypeKmers.size(); i++)
            if ((vertex = ((KmerSearchableGraph<V,E>)graph).findKmer(haplotypeKmers.get(i))) != null)
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