/** * Create an iterator containing the specified reads * * @param reads the reads * @return iterator for the reads */ public static GATKSAMIterator createReadIterator(SAMRecord... reads) { return createReadIterator(Arrays.asList(reads)); }
@Test(expectedExceptions = ReviewedGATKException.class) public void testMappedAndUnmapped() { new IntervalOverlapFilteringIterator( ArtificialSAMUtils.createReadIterator(testReads), Arrays.asList(firstContig, GenomeLoc.UNMAPPED)); }
@Test(dataProvider = "filteringIteratorTestData") public void testFilteringIterator(List<GenomeLoc> locs, List<SAMRecord> expected) { IntervalOverlapFilteringIterator filterIter = new IntervalOverlapFilteringIterator( ArtificialSAMUtils.createReadIterator(testReads), locs); List<SAMRecord> actual = new ArrayList<SAMRecord>(); while (filterIter.hasNext()) { actual.add(filterIter.next()); } Assert.assertEquals(actual, expected); }