map-bed

name	map-bed
description	Use when you need to apply aggregation functions (sum, mean, count, etc.) to values from overlapping intervals in one file and map them onto intervals from another file.
disable-model-invocation	true
user-invocable	true

map-bed

Quick Start

• Command: mapBed -a A.bed -b B.bed -c <B_col> -o <op> [options]
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/mapBed
• Full reference: See references/help.md

When To Use This Tool

• Aggregate values from overlapping B intervals onto each A interval.
• Summarize signal tracks, counts, names, or scores across target intervals.
• Attach mean, sum, min, max, count, or distinct summaries to an interval set.
• Constrain which overlaps contribute with strand or reciprocal-overlap rules.

Common Patterns

# 1) Mean signal from B column 5 over each A interval
mapBed \
  -a exons.bed \
  -b signal.bed \
  -c 5 \
  -o mean

# 2) Count distinct overlapping labels
mapBed \
  -a peaks.bed \
  -b annotations.bed \
  -c 4 \
  -o count_distinct

# 3) Map multiple B columns with matching operations
mapBed \
  -a peaks.bed \
  -b signal.bed \
  -c 4,5 \
  -o distinct,mean

Recommended Workflow

1. Sort both files by chromosome and start coordinate before running mapBed.
2. Decide which B columns carry the statistic you actually want to summarize.
3. Choose aggregation operators that match the column type: numeric ops for numeric columns, collapse / distinct for labels.
4. Add -s, -S, -f, -F, -r, or -e only if overlap eligibility needs to be biologically constrained.

Guardrails

• Both inputs must be sorted by chromosome then start.
• -c refers to columns in B, not A.
• If you provide multiple -c columns and multiple -o operators, the counts must align unless you intentionally rely on the single-column / single-op broadcast behavior.
• collapse keeps duplicates whereas distinct removes them.
• Prefer -h for help; GNU-style --help / --version calls on these wrappers are noisy.