for (Locatable interval : intervals) {
if (r.getReadUnmappedFlag()) {</BUG>
if (interval.getStart() <= r.getStart() && interval.getEnd() >= r.getStart()) {
return true;
}
<BUG>} else if (r.getContig().equals(interval.getContig()) &&
CoordMath.overlaps(r.getStart(), r.getEnd(),
interval.getStart(), interval.getEnd())) {
return true;</BUG>
}

for (Locatable interval : intervals) {
if (interval.getStart() <= r.getStart() && interval.getEnd() >= r.getStart()) {
return true;
