pair-to-pair

name	pair-to-pair
description	Use when comparing two paired-end BEDPE files to find overlapping pairs. Requires -a and -b BEDPE input files.
disable-model-invocation	true
user-invocable	true

pair-to-pair

Quick Start

• Command: pairToPair -a A.bedpe -b B.bedpe [options]
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/pairToPair
• Full reference: See references/help.md

When To Use This Tool

• Compare one BEDPE pair set against another BEDPE pair set.
• Require overlap on both ends, either end, neither end, or not-both.
• Add positional tolerance to each pair footprint with -slop.
• Enforce or ignore strand agreement depending on the assay design.

Common Patterns

# 1) Require both ends of A to overlap B
pairToPair \
  -a loops_A.bedpe \
  -b loops_B.bedpe \
  -type both

# 2) Allow either end to match with 500 bp slop
pairToPair \
  -a loops_A.bedpe \
  -b loops_B.bedpe \
  -type either \
  -slop 500

# 3) Ignore strand and avoid self-matches by name
pairToPair \
  -a pairs.bedpe \
  -b pairs.bedpe \
  -is \
  -rdn

Recommended Workflow

1. Confirm both files are valid BEDPE and represent the same conceptual pair geometry.
2. Choose -type based on whether one-end hits are sufficient or both anchors must agree.
3. Add -slop only when you intentionally want fuzzy anchor matching.
4. Use -rdn when self-hits or same-name artifacts would pollute the comparison.

Guardrails

• -a and -b are both required.
• Strands are enforced by default; add -is to ignore them.
• -slop expands each footprint of A before matching, which can materially change reported overlap rates.
• -type both is the default and is stricter than many users expect.
• Prefer -h for help; GNU-style --help / --version calls on these wrappers are noisy.