Package htsjdk.tribble

Examples of htsjdk.tribble.FeatureCodec

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    }

    @Test
    public void testWriteHeader() throws Exception {

        FeatureCodec codec = CodecFactory.getCodec(inpath, genome);
        AbstractFeatureReader<Feature, ?> bfs = AbstractFeatureReader.getFeatureReader(inpath, codec, false);
        VCFHeader header0 = (VCFHeader) bfs.getHeader();

        VariantContextWriter writer = getWriter();
        writer.writeHeader(header0);
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    }

    @Test
    public void testWriteRecords() throws Exception {

        FeatureCodec codec = CodecFactory.getCodec(inpath, genome);
        AbstractFeatureReader<VCFVariant, ?> bfs = AbstractFeatureReader.getFeatureReader(inpath, codec, false);
        Iterable<VCFVariant> iter0 = bfs.iterator();
        List<VCFVariant> list0 = new ArrayList<VCFVariant>();
        VCFHeader header0 = (VCFHeader) bfs.getHeader();
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    static Map<String, List<Feature>> loadTestFeatures() throws IOException {

        Map<String, List<Feature>> allFeatures = new HashMap<String, List<Feature>>();

        String file = TestUtils.DATA_DIR + "gene/UCSCgenes_sample.gene";
        FeatureCodec codec = CodecFactory.getCodec(file, null);
        AbstractFeatureReader<Feature, ?> bfs = AbstractFeatureReader.getFeatureReader(file, codec, false);
        Iterable<Feature> iter = bfs.iterator();
        for (Feature f : iter) {
            List<Feature> flist = allFeatures.get(f.getChr());
            if (flist == null) {
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    @Test
    public void testGffTags() throws Exception {
        String bedFile = TestUtils.DATA_DIR + "bed/gene.bed";
        Genome genome = TestUtils.loadGenome();

        FeatureCodec codec1 = CodecFactory.getCodec(bedFile, genome);
        assertTrue(codec1 instanceof IGVBEDCodec);
        IGVBEDCodec codec = (IGVBEDCodec) codec1;

        AbstractFeatureReader bfr = AbstractFeatureReader.getFeatureReader(bedFile, codec, false);
        FeatureFileHeader header = (FeatureFileHeader) bfr.getHeader();
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    @Test
    public void testLength1Feature() throws Exception {
        String bedFile = TestUtils.DATA_DIR + "bed/snp_calls.bed";
        TestUtils.createIndex(bedFile, IgvTools.LINEAR_INDEX, 10000);
        FeatureCodec codec = CodecFactory.getCodec(bedFile, null);

        AbstractFeatureReader<Feature, ?> bfr = AbstractFeatureReader.getFeatureReader(bedFile, codec);
        for (Feature feat : bfr.iterator()) {
            BasicFeature f = (BasicFeature) feat;
            assertEquals(1, f.getLength());
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    }

    @Test
    public void testIntervalIndex33() throws Exception {
        String testFile = TestUtils.LARGE_DATA_DIR + "CEU.SRP000032.2010_03_v3.3.genotypes.head.vcf";
        FeatureCodec codec = new VCF3Codec();
        tstIntervalIndex(testFile, codec);
    }
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    }

    @Test
    public void testIntervalIndex40() throws Exception {
        String testFile = TestUtils.LARGE_DATA_DIR + "CEU.SRP000032.2010_03_v4.0.genotypes.head.vcf";
        FeatureCodec codec = new VCFCodec();
        tstIntervalIndex(testFile, codec);
    }
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        File idxFi = new File(indexFile);
        assertTrue(idxFi.exists());
        idxFi.deleteOnExit();

        Genome genome = IgvTools.loadGenome(fasta_file);
        FeatureCodec codec = CodecFactory.getCodec(infile, genome);
        AbstractFeatureReader<Feature, ?> reader = AbstractFeatureReader.getFeatureReader(infile, codec, true);
        String chr = "NC_000913_bb";
        Iterator<Feature> features = reader.query(chr, 5085, 5091);
        int count = 0;
        while (features.hasNext() && count < 100) {
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        super.setUp();
        TestUtils.createIndex(testDataPath);
    }

    private Iterable getFeatures(String chr) throws Exception {
        FeatureCodec codec = CodecFactory.getCodec(testDataPath, genome);
        AbstractFeatureReader bfs = AbstractFeatureReader.getFeatureReader(testDataPath, codec, true);
        if(chr == null) return bfs.iterator();
        return bfs.query(chr, 0, Integer.MAX_VALUE);
    }
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    @Test
    public void testFeatureLookupInSmallVCF() throws IOException {
        String vcfFile = TestUtils.DATA_DIR + "vcf/example4-last-gsnap-2_fixed.vcf";
        Genome genome = null; // <= Don't do chromosome conversion
        FeatureCodec codec = CodecFactory.getCodec(vcfFile, genome);
        boolean isVCF = codec.getClass().isAssignableFrom(VCFCodec.class);

        TestUtils.createIndex(vcfFile);

        AbstractFeatureReader basicReader = AbstractFeatureReader.getFeatureReader(vcfFile, codec, true);
        CloseableTribbleIterator it = basicReader.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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