Package org.broadinstitute.gatk.utils.commandline

Examples of org.broadinstitute.gatk.utils.commandline.Tags

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        assertTrue(doRemoveProgramRecords.isEmpty(), "testRemoveProgramRecords: program records not cleared when removeProgramRecords = true");
    }

    @Test(expectedExceptions = UserException.class)
    public void testFailOnReducedReads() {
        readers.add(new SAMReaderID(new File(privateTestDir + "old.reduced.bam"), new Tags()));

        SAMDataSource data = new SAMDataSource(readers,
                new ThreadAllocation(),
                null,
                genomeLocParser,
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                false);
    }

    @Test(expectedExceptions = UserException.class)
    public void testFailOnReducedReadsRemovingProgramRecords() {
        readers.add(new SAMReaderID(new File(privateTestDir + "old.reduced.bam"), new Tags()));

        SAMDataSource data = new SAMDataSource(readers,
                new ThreadAllocation(),
                null,
                genomeLocParser,
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    @Test(expectedExceptions=UserException.class)
    public void testDuplicateSamFileHandlingSingleDuplicate() throws Exception {
        GenomeAnalysisEngine testEngine = new GenomeAnalysisEngine();

        Collection<SAMReaderID> samFiles = new ArrayList<SAMReaderID>();
        samFiles.add(new SAMReaderID(new File(publicTestDir + "exampleBAM.bam"), new Tags()));
        samFiles.add(new SAMReaderID(new File(publicTestDir + "exampleBAM.bam"), new Tags()));

        testEngine.setSAMFileIDs(samFiles);
        testEngine.checkForDuplicateSamFiles();
    }
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    @Test(expectedExceptions=UserException.class)
    public void testDuplicateSamFileHandlingMultipleDuplicates() throws Exception {
        GenomeAnalysisEngine testEngine = new GenomeAnalysisEngine();

        Collection<SAMReaderID> samFiles = new ArrayList<SAMReaderID>();
        samFiles.add(new SAMReaderID(new File(publicTestDir + "exampleBAM.bam"), new Tags()));
        samFiles.add(new SAMReaderID(new File(publicTestDir + "exampleNORG.bam"), new Tags()));
        samFiles.add(new SAMReaderID(new File(publicTestDir + "exampleBAM.bam"),  new Tags()));
        samFiles.add(new SAMReaderID(new File(publicTestDir + "exampleNORG.bam"), new Tags()));

        testEngine.setSAMFileIDs(samFiles);
        testEngine.checkForDuplicateSamFiles();
    }
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        GenomeAnalysisEngine testEngine = new GenomeAnalysisEngine();

        final File relativePathToBAMFile = new File(publicTestDir + "exampleBAM.bam");
        final File absolutePathToBAMFile = new File(relativePathToBAMFile.getAbsolutePath());
        Collection<SAMReaderID> samFiles = new ArrayList<SAMReaderID>();
        samFiles.add(new SAMReaderID(relativePathToBAMFile, new Tags()));
        samFiles.add(new SAMReaderID(absolutePathToBAMFile, new Tags()));

        testEngine.setSAMFileIDs(samFiles);
        testEngine.checkForDuplicateSamFiles();
    }
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    public void testGettersAsRodBindings(MyTest test) {
        logger.warn("Testing " + test + " for get() methods as RodBindings");
        RefMetaDataTracker tracker = test.makeTracker();

        for ( String nameAsString : Arrays.asList("A", "B") ) {
            RodBinding<Feature> binding = new RodBinding<Feature>(Feature.class, nameAsString, "none", "vcf", new Tags());
            List<Feature> v1 = tracker.getValues(binding);
            testGetter(nameAsString, v1, test.expected(nameAsString), true, tracker);

            List<Feature> v2 = tracker.getValues(binding, locus);
            testGetter(nameAsString, v2, startingHere(test.expected(nameAsString)), true, tracker);
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    public void testGettersAsListOfRodBindings(MyTest test) {
        logger.warn("Testing " + test + " for get() methods for List<RodBindings>");
        RefMetaDataTracker tracker = test.makeTracker();

        String nameAsString = "A+B";
        RodBinding<Feature> A = new RodBinding<Feature>(Feature.class, "A", "none", "vcf", new Tags());
        RodBinding<Feature> B = new RodBinding<Feature>(Feature.class, "B", "none", "vcf", new Tags());
        List<RodBinding<Feature>> binding = Arrays.asList(A, B);

        List<Feature> v1 = tracker.getValues(binding);
        testGetter(nameAsString, v1, test.expected(nameAsString), true, tracker);
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                                               publicTestDir + "exampleBAM.bam",
                                               "         "
                                              );

        List<SAMReaderID> expectedBAMFileListAfterUnpacking = new ArrayList<SAMReaderID>();
        expectedBAMFileListAfterUnpacking.add(new SAMReaderID(new File(publicTestDir + "exampleBAM.bam"), new Tags()));

        performBAMListFileUnpackingTest(tempListFile, expectedBAMFileListAfterUnpacking);
    }
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                                               "#" + publicTestDir + "foo.bam",
                                               "      # " + publicTestDir + "bar.bam"
                                              );

        List<SAMReaderID> expectedBAMFileListAfterUnpacking = new ArrayList<SAMReaderID>();
        expectedBAMFileListAfterUnpacking.add(new SAMReaderID(new File(publicTestDir + "exampleBAM.bam"), new Tags()));

        performBAMListFileUnpackingTest(tempListFile, expectedBAMFileListAfterUnpacking);
    }
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    private List<LocusShardDataProvider> createDataProviders(TraverseActiveRegions traverseActiveRegions, final Walker walker, List<GenomeLoc> intervals, File bamFile) {
        GenomeAnalysisEngine engine = new GenomeAnalysisEngine();
        engine.setGenomeLocParser(genomeLocParser);

        Collection<SAMReaderID> samFiles = new ArrayList<SAMReaderID>();
        SAMReaderID readerID = new SAMReaderID(bamFile, new Tags());
        samFiles.add(readerID);

        SAMDataSource dataSource = new SAMDataSource(samFiles, new ThreadAllocation(), null, genomeLocParser,
                false,
                ValidationStringency.STRICT,
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Related Classes of org.broadinstitute.gatk.utils.commandline.Tags

  • org.broadinstitute.gatk.engine.datasources.providers.ReferenceOrderedViewUnitTest
  • org.broadinstitute.gatk.engine.datasources.reads.GATKWalkerBenchmark
  • org.broadinstitute.gatk.engine.datasources.reads.ReadShardBalancerUnitTest$ReadShardBalancerTest
  • org.broadinstitute.gatk.engine.datasources.reads.SAMDataSourceUnitTest
  • org.broadinstitute.gatk.engine.datasources.reads.SAMReaderIDUnitTest
  • org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedDataPoolUnitTest
  • org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedQueryDataPoolUnitTest
  • org.broadinstitute.gatk.engine.GenomeAnalysisEngineUnitTest
  • org.broadinstitute.gatk.engine.ReadMetricsUnitTest
  • org.broadinstitute.gatk.engine.refdata.RefMetaDataTrackerUnitTest
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