Package org.broad.igv.bbfile

Examples of org.broad.igv.bbfile.BBFileReader

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        String trackName = locator.getTrackName();
        String trackId = locator.getPath();

        String path = locator.getPath();
        BBFileReader reader = new BBFileReader(path);
        BigWigDataSource bigwigSource = new BigWigDataSource(reader, genome);

        if (reader.isBigWigFile()) {
            DataSourceTrack track = new DataSourceTrack(locator, trackId, trackName, bigwigSource);
            newTracks.add(track);
        } else if (reader.isBigBedFile()) {

            if (locator.getPath().contains("RRBS_cpgMethylation") ||
                    locator.getPath().contains("BiSeq_cpgMethylation") ||
                    (reader.getAutoSql() != null && reader.getAutoSql().startsWith("table BisulfiteSeq"))) {
                loadMethylTrack(locator, reader, newTracks, genome);
            } else {
                FeatureTrack track = new FeatureTrack(locator, trackId, trackName, bigwigSource);
                newTracks.add(track);
            }
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        String chr = "chr11";
        int start = 10001654;
        int end = 10001754;

        BBFileReader reader = new BBFileReader(testFile);
        MethylDataSource source = new BBMethylDataSource(reader, BBMethylDataSource.Type.USC, genome);
        Iterator<MethylScore> iter = source.query(chr, start, end);

        int i = 0;
        while (iter.hasNext()) {
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        String chr = "chr7";
        int start = 26133475;
        int end = 27333475;
        Genome genome = null;

        BBFileReader reader = new BBFileReader(testFile);
        MethylDataSource source = new BBMethylDataSource(reader, BBMethylDataSource.Type.ZILLER, genome);
        Iterator<MethylScore> iter = source.query(chr, start, end);

        // Should find at least 1 score.
        assertTrue(iter.hasNext());
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        String chr = "chr7";
        int start = 26133475;
        int end = 27333475;
        Genome genome = null;

        BBFileReader reader = new BBFileReader(testFile);
        MethylDataSource source = new BBMethylDataSource(reader, BBMethylDataSource.Type.ZILLER, genome);
        Iterator<MethylScore> iter = source.query(chr, start, end);
        List<MethylScore> nonCachedScores = new ArrayList<MethylScore>();
        while (iter.hasNext()) {
            nonCachedScores.add(iter.next());
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    private RawDataInterval currentInterval = null;


    public ZillerDataSource2(String path, Genome genome) throws IOException {
        super(genome);
        reader = new BBFileReader(path);
        init(genome);
    }
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Related Classes of org.broad.igv.bbfile.BBFileReader

  • org.broad.igv.methyl.BBMethylDataSourceTest
  • org.broad.igv.methyl.ZillerDataSource2
  • org.broad.igv.track.TrackLoader
  • org.broad.igv.util.stream.IGVSeekableBufferedStream
  • java.io.ByteArrayOutputStream
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