Package org.broadinstitute.gatk.engine.walkers.diffengine

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

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    }

    @Test(enabled = true, dependsOnMethods = "testPluggableDiffableReaders")
    public void testVCF1() {
        logger.warn("testVCF1");
        DiffableReader vcfReader = engine.getReader("VCF");
        Assert.assertTrue(vcfReader.canRead(vcfFile));
        Assert.assertFalse(vcfReader.canRead(bamFile));

        DiffElement diff = vcfReader.readFromFile(vcfFile, -1);
        Assert.assertNotNull(diff);

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

    @Test(enabled = true, dependsOnMethods = "testPluggableDiffableReaders")
    public void testBAM() {
        logger.warn("testBAM");
        DiffableReader bamReader = engine.getReader("BAM");
        Assert.assertTrue(bamReader.canRead(bamFile));
        Assert.assertFalse(bamReader.canRead(vcfFile));

        DiffElement diff = bamReader.readFromFile(bamFile, -1);
        Assert.assertNotNull(diff);

        Assert.assertEquals(diff.getName(), bamFile.getName());
        Assert.assertSame(diff.getParent(), DiffElement.ROOT);
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Related Classes of org.broadinstitute.gatk.engine.walkers.diffengine.DiffableReader

  • org.broadinstitute.gatk.engine.walkers.diffengine.DiffableReaderUnitTest
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