Pair To Bed

# 2) Keep only pairs where both ends overlap annotation
pairToBed \
  -a pairs.bedpe \
  -b exons.bed \
  -type both

# 3) Test whether the outer span of each pair overlaps a region set
pairToBed \
  -a pairs.bedpe \
  -b blacklist.bed \
  -type ospan

Recommended Workflow

1. Decide whether the biology is about pair ends separately (either, both, xor) or about the fragment span (ispan, ospan).
2. Use BEDPE if you already have pair geometry extracted; otherwise consider -abam with query-grouped BAM input.
3. Add -f only when a minimal fractional overlap is biologically justified.
4. Apply strand constraints only for end-wise overlap modes where strand meaningfully applies.

Guardrails

• -a or -abam plus -b is required.
• -abam requires BAM grouped or sorted by query name.
• ispan, ospan, notispan, and notospan ignore records whose mates are on different chromosomes.
• -s and -S do not apply to ispan / ospan modes.
• With BAM input, the default output stays BAM unless you request -bedpe or -ubam.