window-maker

name	window-maker
description	Use when you need to create adjacent or sliding windows across a genome or BED file for binning genomic regions into fixed-size or fixed-count intervals.
disable-model-invocation	true
user-invocable	true

window-maker

Quick Start

• Command: windowMaker [-g genome.txt | -b intervals.bed] [-w size | -n count] [options]
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/windowMaker
• Full reference: See references/help.md

When To Use This Tool

• Tile a genome or interval set into fixed-width windows.
• Create sliding windows by combining -w with -s.
• Split each source interval into a fixed number of windows with -n.
• Add window identifiers for downstream joins, coverage summaries, or matrix construction.

Common Patterns

# 1) Make non-overlapping 1 Mb genome windows
windowMaker \
  -g genome.txt \
  -w 1000000

# 2) Make sliding 10 kb windows with 5 kb step
windowMaker \
  -g genome.txt \
  -w 10000 \
  -s 5000

# 3) Split each BED interval into 20 windows and label by window number
windowMaker \
  -b regions.bed \
  -n 20 \
  -i winnum

Recommended Workflow

1. Choose the source domain first: whole-genome tiling with -g or per-interval tiling with -b.
2. Choose fixed width (-w) versus fixed count (-n) based on the downstream statistical design.
3. Add -s only when you intentionally want overlapping sliding windows.
4. Use -i and optionally -reverse when downstream tools need stable window IDs rather than anonymous coordinates.

Guardrails

• You must provide one interval source: -g or -b.
• You must provide one windowing mode: -w or -n.
• -s is meaningful with -w window-size mode, not as a replacement for -n.
• The genome file is tab-delimited chromosome name plus size; a FASTA .fai works because bedtools reads only the first two columns.
• Prefer -h for help; GNU-style --version on this wrapper emits errors before exiting.