Package org.broad.igv.sam.reader

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

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        int end = 153426154;

        // Test posA query that includes overlaps (contained == false)
        boolean contained = false;
        SAMReader reader = new SAMReader(testFile);
        CloseableIterator<PicardAlignment> iter = reader.query(chr, start, end, contained);
        int count = 0;
        while (iter.hasNext()) {
            Alignment record = iter.next();
            if (record.isMapped()) {
                assertEquals(chr, record.getChr());
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        int end = 125972750;

        // Test posA query that includes overlaps (contained == false)
        boolean contained = false;
        SAMReader reader = new SAMReader(testFile);
        CloseableIterator<PicardAlignment> iter = reader.query(chr, start, end, contained);
        int count = 0;
        while (iter.hasNext()) {
            Alignment record = iter.next();
            assertEquals(chr, record.getChr());
            assertTrue(record.getEnd() >= start);
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        int end = 12550610;

        // Test posA query that includes overlaps (contained == false)
        boolean contained = false;
        SAMReader reader = new SAMReader(testFile);
        CloseableIterator<PicardAlignment> iter = reader.query(chr, start, end, contained);
        int count = 0;
        while (iter.hasNext()) {
            Alignment record = iter.next();
            assertEquals(chr, record.getChr());
            assertTrue(record.getEnd() >= start);
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        // Test posA query that includes overlaps (contained == false)
        boolean contained = false;

        SAMReader reader = new SAMReader(testFile);
        CloseableIterator<PicardAlignment> iter = reader.query(chr, start, end, contained);
        int count = 0;
        while (iter.hasNext()) {
            Alignment record = iter.next();
            assertEquals(chr, record.getChr());
            assertTrue(record.getEnd() >= start);
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