@Test(dataProvider = "testData")
public void testIntervalPairFilter(
final List<Interval> intervals, final long expectedPassingRecords) {
final IntervalKeepPairFilter filter = new IntervalKeepPairFilter(intervals);
long actualPassingRecords =
StreamSupport.stream(builder.spliterator(), false)
.filter(rec -> !filter.filterOut(rec))
.count();
Assert.assertEquals(actualPassingRecords, expectedPassingRecords);
}
@Test
public void testNotPrimaryReads() {
final List<Interval> intervalList = new ArrayList<>();
final Interval interval1 = new Interval("chr1", 1, 999);
intervalList.add(interval1);
final IntervalKeepPairFilter filter = new IntervalKeepPairFilter(intervalList);
boolean notPrimary =
StreamSupport.stream(builder.spliterator(), false)
.filter(rec -> !filter.filterOut(rec))
.anyMatch(
rec -> rec.getNotPrimaryAlignmentFlag() || rec.getSupplementaryAlignmentFlag());
Assert.assertFalse(notPrimary);
}
@Test
public void testUnmappedPair() {
final List<Interval> intervalList = new ArrayList<>();
final Interval interval1 = new Interval("chr1", 1, 999);
final Interval interval2 = new Interval("chr3", 1, 2);
final Interval interval3 = new Interval("chr2", 1, 2);
final Interval interval4 = new Interval("chr4", 1, 2);
intervalList.addAll(CollectionUtil.makeList(interval1, interval2, interval3, interval4));
final IntervalKeepPairFilter filter = new IntervalKeepPairFilter(intervalList);
boolean unmappedPassed =
StreamSupport.stream(builder.spliterator(), false)
.filter(rec -> !filter.filterOut(rec))
.anyMatch(rec -> rec.getReadName().equals("both_unmapped"));
Assert.assertFalse(unmappedPassed);
}
