Package htsjdk.samtools

Examples of htsjdk.samtools.TextCigarCodec

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    }


    public int getReferenceLength(String cigarString) {
               // Use htsjdk class for now
        TextCigarCodec codec = new TextCigarCodec();
        Cigar cigar = codec.decode(cigarString);
        return cigar.getReferenceLength();
    }
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    }

    @Test
    public void testWholeTailIsInsertion() {
        final ReadThreadingGraph rtgraph = new ReadThreadingGraph(10);
        final ReadThreadingGraph.DanglingChainMergeHelper result = new ReadThreadingGraph.DanglingChainMergeHelper(null, null, "AXXXXX".getBytes(), "AAAAAA".getBytes(), new TextCigarCodec().decode("5I1M"));
        final int mergeResult = rtgraph.mergeDanglingTail(result);
        Assert.assertEquals(mergeResult, 0);
    }
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Related Classes of htsjdk.samtools.TextCigarCodec

  • org.broad.igv.ga4gh.Ga4ghAlignment
  • org.broadinstitute.gatk.tools.walkers.haplotypecaller.readthreading.DanglingChainMergingGraphUnitTest
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