Package htsjdk.tribble

Examples of htsjdk.tribble.AbstractFeatureReader.query()

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        // Interval index
        TestUtils.createIndex(bedFile, IgvTools.INTERVAL_INDEX, 100);

        AbstractFeatureReader bfr = AbstractFeatureReader.getFeatureReader(bedFile, codec);
        Iterator<Feature> iter = bfr.query("chr1", 0, Integer.MAX_VALUE);
        int count = 0;
        while (iter.hasNext()) {
            Feature feat = iter.next();
            if (count == 0) {
                //Check we don't skip first line
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        String chr = "chr2";
        int start = 178707289 / 2;
        int end = 179973464 * 2;

        AbstractFeatureReader bfr = AbstractFeatureReader.getFeatureReader(bedFile, codec);
        Iterator<Feature> iter = bfr.query(chr, start, end);
        int count = 0;
        while (iter.hasNext()) {
            Feature feat = iter.next();
            if (count == 0) {
                //Check we don't skip first line
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        //Re-query with some restrictions
        count = 0;
        start = 178709699;
        end = 179721089;
        iter = bfr.query(chr, start, end);
        while (iter.hasNext()) {
            Feature feat = iter.next();
            check_feat_unigene(feat, chr, start, end);
            count++;
        }
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        int end = 1748915;
        int[] expectedStarts = {1718547, 1718829, 1723079, 1724830, 1731376, 1733967, 1735586, 1736016, 1738594,
                1739272, 1741124, 1742815, 1743224, 1748886, 1748914};

        AbstractFeatureReader bfr = AbstractFeatureReader.getFeatureReader(testFile, codec);
        Iterator<VariantContext> iter = bfr.query(chr, start, end);
        int count = 0;
        while (iter.hasNext()) {
            VariantContext feat = iter.next();
            int expStart = expectedStarts[count];
            assertEquals(expStart, feat.getStart());
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    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);
    }

    /**
     * Build GenomeSummaryData from sorted (by chromosome and start position) set of features
     * @param genome
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        // Interval index
        TestUtils.createIndex(bedFile, IgvTools.LINEAR_INDEX, 500);

        AbstractFeatureReader bfr = AbstractFeatureReader.getFeatureReader(bedFile, new IGVBEDCodec());
        Iterator<BasicFeature> iter = bfr.query(chr, start, end);
        int countInterval = 0;
        while (iter.hasNext()) {
            BasicFeature feature = iter.next();
            Assert.assertTrue(feature.getEnd() >= start && feature.getStart() <= end);
            Assert.assertTrue(expectedNames.contains(feature.getName()));
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        // Interval index
        TestUtils.createIndex(bedFile, IgvTools.INTERVAL_INDEX, 1);

        AbstractFeatureReader bfr = AbstractFeatureReader.getFeatureReader(bedFile, new IGVBEDCodec());
        Iterator<BasicFeature> iter = bfr.query(chr, start, end);
        int countInterval = 0;
        while (iter.hasNext()) {
            BasicFeature feature = iter.next();
            Assert.assertTrue(feature.getEnd() >= start && feature.getStart() <= end);
            Assert.assertTrue(expectedNames.contains(feature.getName()));
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        // Linear index
        TestUtils.createIndex(file);

        // First test query
        AbstractFeatureReader bfr = AbstractFeatureReader.getFeatureReader(file, new VCFCodec());
        Iterator<htsjdk.variant.variantcontext.VariantContext> iter = bfr.query(chr, 5073767 - 5, 5073767 + 5);
        int count = 0;
        while (iter.hasNext()) {
            htsjdk.variant.variantcontext.VariantContext feat = iter.next();
            assertEquals("chr9", feat.getChr());
            assertEquals(feat.getStart(), 5073767);
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        chr = "1";
        // Linear index
        TestUtils.createIndex(file);

        bfr = AbstractFeatureReader.getFeatureReader(file, new VCFCodec());
        iter = bfr.query(chr, 984163 - 5, 984163 + 5);
        count = 0;
        while (iter.hasNext()) {
            htsjdk.variant.variantcontext.VariantContext feat = iter.next();
            assertEquals(chr, feat.getChr());
            if (count == 0) {
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