Package org.broadinstitute.gatk.engine.refdata.utils

Examples of org.broadinstitute.gatk.engine.refdata.utils.RMDTriplet

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        final FeatureManager.FeatureDescriptor descriptor = getFeatureManager().getByCodec(codecClass);

        if (descriptor == null)
            throw new ReviewedGATKException("Unable to find type name for codec class " + codecClass.getName());

        return createInstanceOfTrack(new RMDTriplet("anonymous",descriptor.getName(),inputFile.getAbsolutePath(),RMDStorageType.FILE,new Tags()));
    }
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     * 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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            else if(fileName.toLowerCase().endsWith("stdin"))
                storageType = RMDTriplet.RMDStorageType.STREAM;
            else
                storageType = RMDTriplet.RMDStorageType.FILE;

            rodBindings.add(new RMDTriplet(name,type,fileName,storageType,tags));
        }

        return rodBindings;
    }
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            else if(fileName.toLowerCase().endsWith("stdin"))
                storageType = RMDTriplet.RMDStorageType.STREAM;
            else
                storageType = RMDTriplet.RMDStorageType.FILE;

            RMDTriplet triplet = new RMDTriplet(name,type,fileName,storageType,rodBinding.getTags());

            // validate triplet type
            FeatureManager.FeatureDescriptor descriptor = builderForValidation.getByTriplet(triplet);
            if ( descriptor == null )
                throw new UserException.UnknownTribbleType(rodBinding.getTribbleType(),
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Related Classes of org.broadinstitute.gatk.engine.refdata.utils.RMDTriplet

  • org.broadinstitute.gatk.engine.datasources.providers.ReferenceOrderedViewUnitTest
  • org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedDataPoolUnitTest
  • org.broadinstitute.gatk.engine.refdata.tracks.RMDTrackBuilder
  • org.broadinstitute.gatk.utils.text.ListFileUtils
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