@Test public void testFilterNames() { SAMRecordSetBuilder builder = new SAMRecordSetBuilder(); names.forEach(builder::addUnmappedFragment); FilteringSamIterator filteringSamIterator = new FilteringSamIterator(builder.getRecords().iterator(), new ReadNameFilter(new File(TEST_DIR, "names.txt"), true)); Assert.assertEquals(filteringSamIterator.stream() .peek(s -> Assert.assertTrue(s.getReadName().contains("filter"))) .count(), 3); }
@Test(dataProvider = "TrueFalse") public void testFilterNamesEmptySetTrue(boolean include) { SAMRecordSetBuilder builder = new SAMRecordSetBuilder(); names.forEach(builder::addUnmappedFragment); FilteringSamIterator filteringSamIterator = new FilteringSamIterator(builder.getRecords().iterator(), new ReadNameFilter(Collections.emptySet(), include)); Assert.assertEquals(filteringSamIterator.hasNext(), !include); Assert.assertEquals(filteringSamIterator.stream().count(), include ? 0 : names.size()); } }
case includeReadList: filteringIterator = new FilteringSamIterator(samReader.iterator(), new ReadNameFilter(READ_LIST_FILE, true)); break; case excludeReadList: filteringIterator = new FilteringSamIterator(samReader.iterator(), new ReadNameFilter(READ_LIST_FILE, false)); break; case includeJavascript:
case includeReadList: filteringIterator = new FilteringSamIterator(samReader.iterator(), new ReadNameFilter(READ_LIST_FILE, true)); break; case excludeReadList: filteringIterator = new FilteringSamIterator(samReader.iterator(), new ReadNameFilter(READ_LIST_FILE, false)); break; case includeJavascript: