private boolean overlaps(SAMRecord r) {
if (intervals == null
|| (r.getReadUnmappedFlag() && r.getAlignmentStart() == SAMRecord.NO_ALIGNMENT_START)) {
return true;
}
if (r.getReadUnmappedFlag()) { // special case for unmapped reads with coordinate set
for (Locatable interval : intervals) {
if (interval.getStart() <= r.getStart() && interval.getEnd() >= r.getStart()) {
// This follows the behavior of htsjdk's SamReader which states that
// "an unmapped read will be returned by this call if it has a coordinate for
// the purpose of sorting that is in the query region".
return true;
}
}
}
final Interval interval = new Interval(r.getContig(), r.getStart(), r.getEnd());
Collection<Interval> overlaps = overlapDetector.getOverlaps(interval);
return !overlaps.isEmpty();
}
