lastOfPair = !first && second;
if (virtPos == virtualStart && keepReadPairsTogether && !firstOfPair) {
continue;
}
}
<BUG>if (!overlaps(r, intervals)) {
continue;</BUG>
}
key.set(getKey(r));
record.set(r);

lastOfPair = !first && second;
if (virtPos == virtualStart && keepReadPairsTogether && !firstOfPair) {
continue;
}
}
if (!overlaps(r)) {
continue;
}
key.set(getKey(r));
record.set(r);
