Source:
<code>public void testInsertionQualityFilter() { final SAMRecordSetBuilder builder = getRecordBuilder(); final int startPosition = 165; String qualityString = "++++++++++,,,+++++++++++++++++***+++"; for (int i = 0; i < coverage; i++) { builder.addFrag("record" + i, 0, startPosition, true, false, "10M3I17M3I3M", qualityString, 10); } final int insStart1 = 174; final int insStart2 = 194; for (final boolean incIndels : new boolean[] {false, true}) { final SamLocusIterator sli = createSamLocusIterator(builder); sli.setIncludeIndels(incIndels); sli.setQualityScoreCutoff(10); int pos = startPosition; for (final SamLocusIterator.LocusInfo li : sli) { Assert.assertEquals(li.getPosition(), pos++); Assert.assertEquals(li.getRecordAndOffsets().size(), coverage); for (final SamLocusIterator.RecordAndOffset rao : li.getRecordAndOffsets()) { Assert.assertEquals(rao.getAlignmentType(), SamLocusIterator.RecordAndOffset.AlignmentType.Match); } Assert.assertEquals(li.size(), coverage); Assert.assertEquals(li.getDeletedInRecord().size(), 0); if (incIndels && li.getPosition() == insStart1) { Assert.assertEquals(li.getInsertedInRecord().size(), coverage); for (final SamLocusIterator.RecordAndOffset rao : li.getInsertedInRecord()) { Assert.assertEquals(rao.getAlignmentType(), SamLocusIterator.RecordAndOffset.AlignmentType.Insertion); } } else if (incIndels && li.getPosition() == insStart2){ <START> Assert.assertEquals(li.getInsertedInRecord().size(), 0); <END> } else { Assert.assertEquals(li.getInsertedInRecord().size(), 0); } } } }</code><technical_language>final branches do thing. meant assert things</technical_language>

Target:
public void testInsertionQualityFilter() { final SAMRecordSetBuilder builder = getRecordBuilder(); final int startPosition = 165; String qualityString = "++++++++++,,,+++++++++++++++++***+++"; for (int i = 0; i < coverage; i++) { builder.addFrag("record" + i, 0, startPosition, true, false, "10M3I17M3I3M", qualityString, 10); } final int insStart1 = 174; final int insStart2 = 191; for (final int qualityScoreCutoff : new int[] {0, 10}){ final SamLocusIterator sli = createSamLocusIterator(builder); sli.setQualityScoreCutoff(10); sli.setQualityScoreCutoff(qualityScoreCutoff); sli.includeIndels = true; int pos = startPosition; for (final SamLocusIterator.LocusInfo li : sli) { Assert.assertEquals(li.getPosition(), pos++); Assert.assertEquals(li.getRecordAndOffsets().size(), coverage); for (final SamLocusIterator.RecordAndOffset rao : li.getRecordAndOffsets()) { Assert.assertEquals(rao.getAlignmentType(), SamLocusIterator.RecordAndOffset.AlignmentType.Match); } Assert.assertEquals(li.size(), coverage); Assert.assertEquals(li.getDeletedInRecord().size(), 0); if (li.getPosition() == insStart1) { Assert.assertEquals(li.getInsertedInRecord().size(), coverage); for (final SamLocusIterator.RecordAndOffset rao : li.getInsertedInRecord()) { Assert.assertEquals(rao.getAlignmentType(), SamLocusIterator.RecordAndOffset.AlignmentType.Insertion); } } else if ((qualityScoreCutoff == 0) && (li.getPosition() == insStart2)) { Assert.assertEquals(li.getInsertedInRecord().size(), coverage); } else { Assert.assertEquals(li.getInsertedInRecord().size(), 0); } } } }