public void query( String contig, int start, int stop, boolean contained ) { if (contained) queryContained(contig, start, stop); else queryOverlapping(contig, start, stop); }
@Test(expectedExceptions=IllegalArgumentException.class) public void testUnknownChromosome() { ArtificialSAMQueryIterator iter = ArtificialSAMUtils.queryReadIterator(1, 2, 100); iter.queryOverlapping("chr621", 25, 74); } }
@Test public void testOverlappingQueryStart() { ArtificialSAMQueryIterator iter = ArtificialSAMUtils.queryReadIterator(1, 2, 100); iter.queryOverlapping("chr1", 1, 50); int count = 0; while (iter.hasNext()) { SAMRecord rec = iter.next(); count++; } assertEquals(count, 50); }
@Test public void testOverlappingQueryMiddle() { ArtificialSAMQueryIterator iter = ArtificialSAMUtils.queryReadIterator(1, 2, 100); iter.queryOverlapping("chr1", 25, 74); int count = 0; while (iter.hasNext()) { SAMRecord rec = iter.next(); count++; } assertEquals(count, 50); }