Package htsjdk.tribble

Examples of htsjdk.tribble.AsciiFeatureCodec.decode()

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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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        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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            while ((nextLine = br.readLine()) != null) {
                if (nextLine.startsWith("track")) {
                    props = new TrackProperties();
                    ParsingUtils.parseTrackLine(nextLine, props);
                } else {
                    BasicFeature f = (BasicFeature) codec.decode(nextLine);
                    if (f != null) {
                        String chr = f.getChr();
                        List<BasicFeature> featureList = featureMap.get(chr);
                        if (featureList == null) {
                            featureList = new ArrayList<BasicFeature>();
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