**-f** Minimum overlap required as a fraction of A. Default is 1E-9 (i.e. 1bp).
**-f** Minimum overlap required as a fraction of A. Default is 1E-9 (i.e. 1bp).
**-s** Force "strandedness". That is, only report hits in B that overlap A on the same strand. By default, overlaps are reported without respect to strand.
**-s** Force "strandedness". That is, only report hits in B that overlap A on the same strand. By default, overlaps are reported without respect to strand.
**-S** Require different strandedness. That is, only report hits in B that overlap A on the _opposite_ strand. By default, overlaps are reported without respect to strand.
**-S** Require different strandedness. That is, only report hits in B that overlap A on the _opposite_ strand. By default, overlaps are reported without respect to strand.
**-A** Remove entire feature if any overlap. That is, by default, only subtract the portion of A that overlaps B. Here, if any overlap is found (or ``-f`` amount), the entire feature is removed.
**-A** Remove entire feature if any overlap. That is, by default, only subtract the portion of A that overlaps B. Here, if any overlap is found (or ``-f`` amount), the entire feature is removed.
**-N** Same as -A except when used with -f, the amount is the sum
**-N** Same as -A except when used with -f, the amount is the sum of all features (not any single feature).
