get-overlap

name	get-overlap
description	Use when you need to append the overlap size or gap distance between two intervals that already appear on the same line, such as paired output from `bedtools window`.
disable-model-invocation	true
user-invocable	true

get-overlap

Quick Start

• Command: getOverlap -i <input> -cols start1,end1,start2,end2
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/getOverlap
• Full reference: See references/help.md

When To Use This Tool

• Quantify how much two intervals overlap after another tool has already paired them on the same row.
• Turn bedtools window-style output into a table with a final numeric overlap or distance column.
• Score candidate interval pairs before thresholding or ranking them downstream.
• Add a simple overlap metric without rerunning a full interval join.

Common Patterns

# 1) Measure overlap or gap after bedtools window
windowBed \
  -a A.bed \
  -b B.bed \
  -w 10 \
  | getOverlap -i stdin -cols 2,3,6,7

# 2) Append overlap to a precomputed paired table
getOverlap \
  -i paired-intervals.tsv \
  -cols 2,3,6,7

Recommended Workflow

1. Generate or prepare a table where each row already contains the two intervals you want to compare.
2. Determine the exact 1-based column numbers for start1,end1,start2,end2 in that table.
3. Run getOverlap on the file or use the literal input name stdin when streaming from a pipe.
4. Interpret the appended value before downstream filtering: positive means overlap, negative means separation, and zero means the intervals touch without overlapping.

Guardrails

• -cols must be given in the exact order start1,end1,start2,end2; swapping them changes the result.
• This tool does not pair records for you; it only computes a metric from coordinates already present on the same line.
• Use the literal token stdin with -i when piping from another command.
• Prefer -h for help; GNU-style --help and --version emit wrapper errors before usage text.