Package htsjdk.tribble

Examples of htsjdk.tribble.FeatureCodec

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    public FeatureManager(final boolean lenientVCFProcessing) {
        this.lenientVCFProcessing = lenientVCFProcessing;
        pluginManager = new PluginManager<FeatureCodec>(FeatureCodec.class, "Codecs", "Codec");

        for (final String rawName: pluginManager.getPluginsByName().keySet()) {
            FeatureCodec codec = pluginManager.createByName(rawName);
            String name = rawName.toUpperCase();
            FeatureDescriptor featureDescriptor = new FeatureDescriptor(name, codec);
            featureDescriptors.add(featureDescriptor);
        }
    }
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     */
    @Requires({"descriptor != null", "name != null", "genomeLocParser != null"})
    @Ensures("result != null")
    public FeatureCodec createCodec(final FeatureDescriptor descriptor, final String name, final GenomeLocParser genomeLocParser,
                                    final String remappedSampleName) {
        FeatureCodec codex = pluginManager.createByType(descriptor.getCodecClass());
        if ( codex instanceof NameAwareCodec )
            ((NameAwareCodec)codex).setName(name);
        if ( codex instanceof ReferenceDependentFeatureCodec )
            ((ReferenceDependentFeatureCodec)codex).setGenomeLocParser(genomeLocParser);
        if ( codex instanceof AbstractVCFCodec ) {
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            // that way we don't assume it's a specific type
            final FeatureManager.FeatureDescriptor fd = new FeatureManager().getByFiletype(file);
            if ( fd == null )
                throw new UserException.LocalParallelizationProblem(file);

            final FeatureCodec codec = fd.getCodec();
            final AbstractFeatureReader<Feature, ?> source = AbstractFeatureReader.getFeatureReader(file.getAbsolutePath(), codec, false);

            for ( final Feature vc : source.iterator() ) {
                target.writer.add((VariantContext) vc);
            }
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    @Test
    public void testCodecCreation() {
        FeatureManager.FeatureDescriptor descriptor = manager.getByName("vcf");
        Assert.assertNotNull(descriptor, "Couldn't find VCF feature descriptor!");

        FeatureCodec c = manager.createCodec(descriptor, "foo", genomeLocParser, null);
        Assert.assertNotNull(c, "Couldn't create codec");
        Assert.assertEquals(c.getClass(), descriptor.getCodecClass());
        Assert.assertEquals(c.getFeatureType(), descriptor.getFeatureClass());
    }
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    @Override
    public RMDTrack createInstanceOfTrack(RMDTriplet fileDescriptor) {
        String name = fileDescriptor.getName();
        File inputFile = new File(fileDescriptor.getFile());
        FeatureManager.FeatureDescriptor descriptor = getFeatureManager().getByTriplet(fileDescriptor);
        FeatureCodec codec = getFeatureManager().createCodec(descriptor, name, genomeLocParser, null);
        TestFeatureReader featureReader;
        Index index;
        try {
            // Create a feature reader that creates checkable tribble iterators.
            index = loadIndex(inputFile, codec);
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        if ( featureIntervals != null ) {
            intervals = new ArrayList<>();

            // TODO -- after ROD system cleanup, go through the ROD system so that we can handle things like gzipped files

            final FeatureCodec codec = new FeatureManager().getByName(featureIntervals.getTribbleType()).getCodec();
            if ( codec instanceof ReferenceDependentFeatureCodec )
                ((ReferenceDependentFeatureCodec)codec).setGenomeLocParser(genomeLocParser);
            try {
                FeatureReader<Feature> reader = AbstractFeatureReader.getFeatureReader(featureIntervals.getSource(), codec, false);
                for ( Feature feature : reader.iterator() )
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Related Classes of htsjdk.tribble.FeatureCodec

  • org.broad.igv.data.GenomeSummaryDataTest
  • org.broad.igv.dev.db.SQLCodecSource
  • org.broad.igv.dev.db.SQLInputStreamTest
  • org.broad.igv.feature.AbstractFeatureParser
  • org.broad.igv.feature.exome.ExomeUtilsTest
  • org.broad.igv.feature.FeatureUtilsTest
  • org.broad.igv.feature.tribble.CachingFeatureReaderTest
  • org.broad.igv.feature.tribble.UCSCGeneTableCodecTest
  • org.broad.igv.plugin.mongocollab.MongoCollabPlugin
  • org.broad.igv.tools.IgvTools
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