Examples of org.broadinstitute.gatk.engine.walkers.diffengine.DiffableReader.canRead()

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

Class org.broadinstitute.gatk.engine.walkers.diffengine.DiffableReader

Examples of org.broadinstitute.gatk.engine.walkers.diffengine.DiffableReader.canRead()

org.broadinstitute.gatk.engine.walkers.diffengine.DiffableReader.canRead()
Return true if the file can be read into DiffElement objects with this reader. This should be uniquely true/false for all readers, as the system will use the first reader that can read the file. This routine should never throw an exception. The VCF reader, for example, looks at the first line of the file for the ##format=VCF4.1 header, and the BAM reader for the BAM_MAGIC value @param file @return


    @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);

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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());

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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);

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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());

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