@Test public static void testQueryUnmapped() { int counter = 0; CloseableIterator<SAMRecord> baiIterator = bamFileReaderBAI.queryUnmapped(); CloseableIterator<SAMRecord> csiIterator = bamFileReaderCSI.queryUnmapped(); Assert.assertTrue(baiIterator.hasNext()); while (baiIterator.hasNext()) { Assert.assertTrue(csiIterator.hasNext()); SAMRecord r1 = baiIterator.next(); SAMRecord r2 = csiIterator.next(); Assert.assertEquals(r1.getReadName(), r2.getReadName()); Assert.assertEquals(r1.getBaseQualityString(), r2.getBaseQualityString()); counter++; } Assert.assertFalse(csiIterator.hasNext()); Assert.assertEquals(counter, nofUnmappedReads); baiIterator.close(); csiIterator.close(); }
} else if (boundedTraversal && split.getIntervalFilePointers() == null) { iterator = bamFileReader.queryUnmapped(); } else {
} else if (boundedTraversal && split.getIntervalFilePointers() == null) { iterator = bamFileReader.queryUnmapped(); } else {