Examples of GATKArgumentCollection

Examples of org.broadinstitute.gatk.engine.arguments.GATKArgumentCollection

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     * Verifies that the supplied set of reads files mesh with what the walker says it requires;
     * also makes sure that list of SAM files specified on the command line is not empty and contains
     * no duplicates.
     */
    protected void validateSuppliedReads() {
        GATKArgumentCollection arguments = this.getArguments();
        final Boolean samFilesArePresent = (arguments.samFiles != null && !arguments.samFiles.isEmpty());

        // Check what the walker says is required against what was provided on the command line.
        if (WalkerManager.isRequired(walker, DataSource.READS) && !samFilesArePresent)
            throw new ArgumentException("Walker requires reads but none were provided.");
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Examples of org.broadinstitute.gatk.engine.arguments.GATKArgumentCollection

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    /**
     * Verifies that the supplied reference file mesh with what the walker says it requires.
     */
    protected void validateSuppliedReference() {
        GATKArgumentCollection arguments = this.getArguments();
        // Check what the walker says is required against what was provided on the command line.
        // TODO: Temporarily disabling WalkerManager.isRequired check on the reference because the reference is always required.
        if (/*WalkerManager.isRequired(walker, DataSource.REFERENCE) &&*/ arguments.referenceFile == null)
            throw new ArgumentException("Walker requires a reference but none was provided.");

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Examples of org.broadinstitute.gatk.engine.arguments.GATKArgumentCollection

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        binding.getIntervals(toolkit);
    }

    @DataProvider(name="invalidIntervalTestData")
    public Object[][] invalidIntervalDataProvider() throws Exception {
        GATKArgumentCollection argCollection = new GATKArgumentCollection();
        File fastaFile = new File(publicTestDir + "exampleFASTA.fasta");
        GenomeLocParser genomeLocParser = new GenomeLocParser(new IndexedFastaSequenceFile(fastaFile));

        return new Object[][] {
                new Object[] {argCollection, genomeLocParser, "chr1", 10000000, 20000000},
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Examples of org.broadinstitute.gatk.engine.arguments.GATKArgumentCollection

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

        Properties awsProperties = new Properties();
        awsProperties.load(new FileInputStream(AWS_DOWNLOADER_CREDENTIALS_PROPERTIES_FILE));
        downloaderAccessKey = awsProperties.getProperty("accessKey");
        downloaderSecretKey = awsProperties.getProperty("secretKey");
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Examples of org.broadinstitute.gatk.engine.arguments.GATKArgumentCollection

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        final Exception javaException = new IllegalArgumentException("javaException");
        final Exception stingException = new ReviewedGATKException("GATKException");
        final Exception userException = new UserException("userException");

        final GenomeAnalysisEngine engine = new GenomeAnalysisEngine();
        engine.setArguments(new GATKArgumentCollection());

        for ( final Walker walker : Arrays.asList(readWalker, lociWalker, rodWalker, artWalker) ) {
            for ( final Exception exception : Arrays.asList(noException,  javaException, stingException, userException) ) {
                tests.add(new Object[]{walker, exception, engine});
            }
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