Package org.broadinstitute.gatk.utils.commandline

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


     * Test a single ROD binding.
     */
    @Test
    public void testSingleBinding() {
        String fileName = privateTestDir + "TabularDataTest.dat";
        RMDTriplet triplet = new RMDTriplet("tableTest","Table",fileName,RMDStorageType.FILE,new Tags());
        ReferenceOrderedDataSource dataSource = new ReferenceOrderedDataSource(triplet,builder,seq.getSequenceDictionary(),genomeLocParser,false);

        Shard shard = new MockLocusShard(genomeLocParser,Collections.singletonList(genomeLocParser.createGenomeLoc("chrM",1,30)));

        LocusShardDataProvider provider = new LocusShardDataProvider(shard, null, genomeLocParser, shard.getGenomeLocs().get(0), null, seq, Collections.singletonList(dataSource));
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     */
    @Test
    public void testMultipleBinding() {
        File file = new File(privateTestDir + "TabularDataTest.dat");

        RMDTriplet testTriplet1 = new RMDTriplet("tableTest1","Table",file.getAbsolutePath(),RMDStorageType.FILE,new Tags());
        ReferenceOrderedDataSource dataSource1 = new ReferenceOrderedDataSource(testTriplet1,builder,seq.getSequenceDictionary(),genomeLocParser,false);

        RMDTriplet testTriplet2 = new RMDTriplet("tableTest2","Table",file.getAbsolutePath(),RMDStorageType.FILE,new Tags());
        ReferenceOrderedDataSource dataSource2 = new ReferenceOrderedDataSource(testTriplet2,builder,seq.getSequenceDictionary(),genomeLocParser,false);

        Shard shard = new MockLocusShard(genomeLocParser,Collections.singletonList(genomeLocParser.createGenomeLoc("chrM",1,30)));

        LocusShardDataProvider provider = new LocusShardDataProvider(shard, null, genomeLocParser, shard.getGenomeLocs().get(0), null, seq, Arrays.asList(dataSource1,dataSource2));
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    @BeforeMethod
    public void setUp() {
        String fileName = privateTestDir + "TabularDataTest.dat";

        triplet = new RMDTriplet("tableTest","Table",fileName,RMDStorageType.FILE,new Tags());
        // disable auto-index creation/locking in the RMDTrackBuilder for tests
        builder = new RMDTrackBuilder(seq.getSequenceDictionary(),genomeLocParser,null,true,null);
    }
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            for ( SAMRecord read : artificialReads ) {
                bamWriter.addAlignment(read);
            }
            bamWriter.close();

            testBAM =  new SAMReaderID(testBAMFile, new Tags());

            new File(testBAM.getSamFilePath().replace(".bam", ".bai")).deleteOnExit();
            new File(testBAM.getSamFilePath() + ".bai").deleteOnExit();
        }
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public class ReferenceOrderedQueryDataPoolUnitTest extends BaseTest{
    @Test
    public void testCloseFilePointers() throws IOException {
        // Build up query parameters
        File file = new File(BaseTest.privateTestDir + "NA12878.hg19.example1.vcf");
        RMDTriplet triplet = new RMDTriplet("test", "VCF", file.getAbsolutePath(), RMDTriplet.RMDStorageType.FILE, new Tags());
        IndexedFastaSequenceFile seq = new CachingIndexedFastaSequenceFile(new File(BaseTest.hg19Reference));
        GenomeLocParser parser = new GenomeLocParser(seq);
        GenomeLoc loc = parser.createGenomeLoc("20", 1, 100000);
        TestRMDTrackBuilder builder = new TestRMDTrackBuilder(seq.getSequenceDictionary(), parser);
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     * @return a flattened list of the bam files provided
     */
    public static List<SAMReaderID> unpackBAMFileList(final List<String> samFiles, final ParsingEngine parser) {
        List<SAMReaderID> unpackedReads = new ArrayList<SAMReaderID>();
        for( String inputFileName: samFiles ) {
            Tags inputFileNameTags = parser.getTags(inputFileName);
            inputFileName = expandFileName(inputFileName);
            if (inputFileName.toLowerCase().endsWith(".list") ) {
                try {
                    for ( String fileName : new XReadLines(new File(inputFileName), true, LIST_FILE_COMMENT_START) ) {
                        unpackedReads.add(new SAMReaderID(fileName,parser.getTags(inputFileName)));
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    public static Collection<RMDTriplet> unpackRODBindingsOldStyle(final Collection<String> RODBindings, final ParsingEngine parser) {
        // todo -- this is a strange home for this code.  Move into ROD system
        Collection<RMDTriplet> rodBindings = new ArrayList<RMDTriplet>();

        for (String fileName: RODBindings) {
            final Tags tags = parser.getTags(fileName);
            fileName = expandFileName(fileName);

            List<String> positionalTags = tags.getPositionalTags();
            if(positionalTags.size() != 2)
                throw new UserException("Invalid syntax for -B (reference-ordered data) input flag.  " +
                        "Please use the following syntax when providing reference-ordered " +
                        "data: -B:<name>,<type> <filename>.");
            // Assume that if tags are present, those tags are name and type.
            // Name is always first, followed by type.
            String name = positionalTags.get(0);
            String type = positionalTags.get(1);

            RMDTriplet.RMDStorageType storageType;
            if(tags.getValue("storage") != null)
                storageType = Enum.valueOf(RMDTriplet.RMDStorageType.class,tags.getValue("storage"));
            else if(fileName.toLowerCase().endsWith("stdin"))
                storageType = RMDTriplet.RMDStorageType.STREAM;
            else
                storageType = RMDTriplet.RMDStorageType.FILE;
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