Examples of org.broadinstitute.gatk.engine.walkers.diffengine.DiffNode

        Assert.assertNotNull(diff);


        Assert.assertEquals(diff.getName(), vcfFile.getName());
        Assert.assertSame(diff.getParent(), DiffElement.ROOT);


        DiffNode node = diff.getValueAsNode();
        Assert.assertEquals(node.getElements().size(), 11);


        // chr1    2646    rs62635284      G       A       0.15    PASS    AC=2;AF=1.00;AN=2       GT:AD:DP:GL:GQ  1/1:53,75:3:-12.40,-0.90,-0.00:9.03
        DiffNode rec1 = node.getElement("chr1:2646").getValueAsNode();
        testLeaf(rec1, "CHROM", "chr1");
        testLeaf(rec1, "POS", 2646);
        testLeaf(rec1, "ID", "rs62635284");
        testLeaf(rec1, "REF", Allele.create("G", true));
        testLeaf(rec1, "ALT", Arrays.asList(Allele.create("A")));

        Assert.assertNotNull(diff);


        Assert.assertEquals(diff.getName(), bamFile.getName());
        Assert.assertSame(diff.getParent(), DiffElement.ROOT);


        DiffNode node = diff.getValueAsNode();
        Assert.assertEquals(node.getElements().size(), 33);


        // 30PPJAAXX090125:1:42:512:1817#0 99      chr1    200     0       76M     =
        // 255     -130    ACCCTAACCCTAACCCTAACCCTAACCATAACCCTAAGACTAACCCTAAACCTAACCCTCATAATCGAAATACAAC
        // BBBBC@C?AABCBB<63>=B@>+B9-9+)2B8,+@327B5A>90((>-+''3?(/'''A)(''19('7.,**%)3:
        // PG:Z:0  RG:Z:exampleBAM.bam     SM:Z:exampleBAM.bam


        DiffNode rec1 = node.getElement("30PPJAAXX090125:1:42:512:1817#0_1").getValueAsNode();
        testLeaf(rec1, "NAME", "30PPJAAXX090125:1:42:512:1817#0");
        testLeaf(rec1, "FLAGS", 99);
        testLeaf(rec1, "RNAME", "chr1");
        testLeaf(rec1, "POS", 200);
        testLeaf(rec1, "MAPQ", 0);

Related Classes of org.broadinstitute.gatk.engine.walkers.diffengine.DiffNode

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