Examples of org.broadinstitute.gatk.tools.walkers.haplotypecaller.AssemblyResultSet

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

Examples of org.broadinstitute.gatk.tools.walkers.haplotypecaller.AssemblyResultSet

org.broadinstitute.gatk.tools.walkers.haplotypecaller.AssemblyResultSet
Collection of read assembly using several kmerSizes.
There could be a different assembly per each kmerSize. In turn, haplotypes are result of one of those assemblies.

Where there is more than one possible kmerSize that generates a haplotype we consider the smaller one.
@author Valentin Ruano-Rubio <valentin@broadinstitute.com>

            if (rtg.hasCycles())
                throw new RuntimeException("there is cycles in the reference with kmer size " + kmerSize + ". Don't use this size for the benchmark or change the reference");


            List<Haplotype> haplotypeList = this.haplotypeList();


            assemblyResultSet = new AssemblyResultSet();
            final AssemblyResult ar = new AssemblyResult((haplotypeList.size() > 1 ?
                    AssemblyResult.Status.ASSEMBLED_SOME_VARIATION : AssemblyResult.Status.JUST_ASSEMBLED_REFERENCE),rtg.convertToSequenceGraph());
            ar.setThreadingGraph(rtg);


            for (final Haplotype h : haplotypeList)

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