Package org.broad.igv.sam.reader

Examples of org.broad.igv.sam.reader.BAMFileReader.query()

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        int end = 300000000;
        int start = end / 5;
        int stopafter = 10;
        int counter = 0;
        BAMFileReader bamreader = new BAMFileReader(new File(bamfile));
        CloseableIterator<PicardAlignment> bamiter = bamreader.query(chr, start, end, true);
        while (bamiter.hasNext()) {
            Alignment bamrecord = bamiter.next();
            if (counter >= stopafter) {
                break;
            } else {
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            }
        }
        bamreader.close();
        boolean closeSucceeded = false;
        try {
            CloseableIterator<PicardAlignment> bamiter2 = bamreader.query(chr, start, end, true);
        } catch (NullPointerException npe) {
            closeSucceeded = true;
        }
        assertTrue(closeSucceeded);
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        int end = 300000000;
        int start = end / 5;

        BAMFileReader bamreader = new BAMFileReader(new File(bamfile));
        SAMReader samreader = new SAMReader(samfile);
        CloseableIterator<PicardAlignment> bamiter = bamreader.query(chr, start, end, true);
        CloseableIterator<PicardAlignment> samiter = samreader.iterator();
        int count = 0;
        while (bamiter.hasNext()) {
            Alignment bamrecord = bamiter.next();
            Alignment samrecord = samiter.next();
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