public void query( String contig, int start, int stop, boolean contained ) { if (contained) queryContained(contig, start, stop); else queryOverlapping(contig, start, stop); }
@Test public void testWholeChromosomeQuery() { ArtificialSAMQueryIterator iter = ArtificialSAMUtils.queryReadIterator(1, 2, 100); iter.queryContained("chr1", 1, -1); int count = 0; while (iter.hasNext()) { SAMRecord rec = iter.next(); count++; } assertEquals(count, 100); }
@Test public void testContainedQueryStart() { ArtificialSAMQueryIterator iter = ArtificialSAMUtils.queryReadIterator(1, 2, 100); iter.queryContained("chr1", 1, 50); int count = 0; while (iter.hasNext()) { SAMRecord rec = iter.next(); count++; } assertEquals(count, 1); }
@Test public void testContainedQueryMiddle() { ArtificialSAMQueryIterator iter = ArtificialSAMUtils.queryReadIterator(1, 2, 100); iter.queryContained("chr1", 25, 74); int count = 0; while (iter.hasNext()) { SAMRecord rec = iter.next(); count++; } assertEquals(count, 1); }