Examples of CountReads

Examples of org.broadinstitute.gatk.tools.walkers.qc.CountReads

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public class GenomeAnalysisEngineUnitTest extends BaseTest {

    @Test(expectedExceptions=UserException.class)
    public void testEmptySamFileListHandling() throws Exception {
        GenomeAnalysisEngine testEngine = new GenomeAnalysisEngine();
        testEngine.setWalker(new CountReads()); //generalizable to any walker requiring reads

        //supply command line args so validateSuppliedReads() knows whether reads were passed in
        GATKArgumentCollection testArgs = new GATKArgumentCollection();
        testArgs.samFiles.add("empty.list");
        testEngine.setArguments(testArgs);
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Examples of org.broadinstitute.gatk.tools.walkers.qc.CountReads

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            fail("Couldn't open the output file");
        }

        bamList = new ArrayList<SAMReaderID>();
        bamList.add(bam);
        countReadWalker = new CountReads();
       
        traversalEngine = new TraverseReadsNano(1);
        traversalEngine.initialize(engine, countReadWalker);
    }
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Examples of org.broadinstitute.gatk.tools.walkers.qc.CountReads

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    private String downloaderAccessKey;
    private String downloaderSecretKey;

    @BeforeClass
    public void setup() throws Exception {
        walker = new CountReads();
        exception = new IllegalArgumentException("javaException");
        engine = new GenomeAnalysisEngine();
        engine.setArguments(new GATKArgumentCollection());

        Properties awsProperties = new Properties();
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Examples of org.broadinstitute.gatk.tools.walkers.qc.CountReads

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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;
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