Package org.broadinstitute.gatk.engine.walkers

Examples of org.broadinstitute.gatk.engine.walkers.Walker

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        walkerManager = new WalkerManager();
    }

    @Test
    public void testPresentWalker() {
        Walker countLociWalker = walkerManager.createByName("CountLoci");
        Assert.assertEquals(CountLoci.class,countLociWalker.getClass());
    }
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    @Test
    public void testAddingVCFHeaderInfo() {
        final VCFHeader header = new VCFHeader();

        final Walker walker1 = new VCFHeaderTestWalker();
        final Walker walker2 = new VCFHeaderTest2Walker();

        final GenomeAnalysisEngine testEngine1 = new GenomeAnalysisEngine();
        testEngine1.setWalker(walker1);

        final GenomeAnalysisEngine testEngine2 = new GenomeAnalysisEngine();
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        // No walker info?  No plugins.
        if (getAnalysisName() == null) return new Class[] {};

        Collection<Class> argumentSources = new ArrayList<Class>();

        Walker walker = engine.getWalkerByName(getAnalysisName());
        engine.setArguments(getArgumentCollection());
        engine.setWalker(walker);
        walker.setToolkit(engine);
        argumentSources.add(walker.getClass());

        Collection<ReadFilter> filters = engine.createFilters();
        for(ReadFilter filter: filters)
            argumentSources.add(filter.getClass());
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    @DataProvider(name = "GATKReportCreationTest")
    public Object[][] makeGATKReportCreationTest() {
        List<Object[]> tests = new ArrayList<Object[]>();

        final Walker readWalker = new CountReads();
        final Walker lociWalker = new CountLoci();
        final Walker rodWalker = new CountRODs();
        final Walker artWalker = new RunReportDummyActiveRegionWalker();

        final Exception noException = null;
        final Exception javaException = new IllegalArgumentException("javaException");
        final Exception stingException = new ReviewedGATKException("GATKException");
        final Exception userException = new UserException("userException");
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Related Classes of org.broadinstitute.gatk.engine.walkers.Walker

  • org.broadinstitute.gatk.engine.CommandLineExecutable
  • org.broadinstitute.gatk.engine.phonehome.GATKRunReportUnitTest
  • org.broadinstitute.gatk.engine.WalkerManagerUnitTest
  • org.broadinstitute.gatk.utils.variant.GATKVCFUtilsUnitTest
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