Package htsjdk.tribble

Examples of htsjdk.tribble.Feature

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        AsciiFeatureCodec codec2 = new EncodePeakCodec();

        assertTrue(codec.getClass() == codec2.getClass());

        Feature feature =  codec.decode(line);
        Feature feature2 = codec2.decode(line);

        assertEquals("chr22", feature.getChr());


    }
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*/
public class TestLoadGeneManager extends AbstractHeadlessTest {

    @Test
    public void main() throws IOException {
        Feature feature = FeatureDB.getFeature("EGFR");
        assertNotNull(feature);
    }
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        FeatureCodec featCodec = new ExampleBinaryCodec();
        PositionalBufferedStream pbs = new PositionalBufferedStream(is);
        int count = 0;
        while (!rs.isAfterLast()) {
            Feature feat = featCodec.decode(pbs);
            checkFeatureIntegrity(feat, "chr2");
            count++;
        }
        assertEquals(72, count);
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        BufferedReader in = new BufferedReader(new InputStreamReader(is));
        int totalLines = 0;
        String val = "";
        AsciiFeatureCodec featureCodec = new IGVBEDCodec(genome);
        while ((val = in.readLine()) != null) {
            Feature feat = featureCodec.decode(val);
            checkFeatureIntegrity(feat, "chr2");
            totalLines += 1;
        }
        assertEquals(72, totalLines);
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        AbstractFeatureReader bfr = AbstractFeatureReader.getFeatureReader(bedFile, codec, false);
        Iterator<Feature> fileFeatures = bfr.iterator();

        int count = 0;
        while (SQLFeatures.hasNext()) {
            Feature f = SQLFeatures.next();
            Feature fileFeature = fileFeatures.next();
            TestUtils.assertFeaturesEqual(fileFeature, f);
            count++;
        }

        Assert.assertEquals(72, count);
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        Iterator<Feature> features0 = source0.iterator();
        Iterator<Feature> features1 = source1.iterator();

        while (features0.hasNext()) {
            Feature act_feat = features0.next();
            Feature exp_feat = features1.next();
            TestUtils.assertFeaturesEqual(exp_feat, act_feat);
        }

    }
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        int end = 100000;
        Iterator<Feature> feats = source.getFeatures("chr1", start, end);
        int count = 0;

        while (feats.hasNext()) {
            Feature f = feats.next();
            assertTrue(f.getStart() >= start);
            assertTrue(f.getStart() < end);
            count++;
        }

        assertTrue("No data retrieved", count > 0);
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        int count = 0;
        while (binFeats.hasNext()) {
            assertTrue(noBinFeats.hasNext());

            Feature bf = binFeats.next();
            Feature nbf = noBinFeats.next();

            assertEquals(chr, bf.getChr());
            assertTrue(bf.getStart() >= start);
            assertTrue(bf.getStart() < end);

            assertEquals(nbf.getChr(), bf.getChr());
            assertEquals(nbf.getStart(), bf.getStart());
            assertEquals(nbf.getEnd(), bf.getEnd());

            count++;
        }

        assertFalse(noBinFeats.hasNext());
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        public boolean hasNext() {
            return nextRecord != null;
        }

        public Feature next() {
            Feature ret = nextRecord;

            advanceToNextRecord();

            return ret;
        }
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        CloseableTribbleIterator<Feature> iter = null;
        try {
            iter = wrappedReader.query(chr, start, end);
            List<Feature> featureList = new ArrayList<Feature>();
            while (iter.hasNext()) {
                Feature f = iter.next();
                if (f.getStart() > end) {
                    break;
                } else if (f.getEnd() < start) {
                    continue;
                } else {
                    featureList.add(f);
                }
            }
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