rsomics-bed-shift

Shift BED coordinates by a fixed offset — bedtools shift equivalent in pure Rust.

Install

cargo install rsomics-bed-shift

Usage

rsomics-bed-shift -s 100 input.bed                          # shift all features 100 bp downstream
rsomics-bed-shift -s 500 -g hg38.genome input.bed           # clamp to chromosome boundaries
rsomics-bed-shift -p 100 -m -100 input.bed                  # strand-aware shift
rsomics-bed-shift -s -50 -g hg38.genome < input.bed         # stdin

Options

Flag	Description
-s <INT>	Bases to shift (positive = downstream, negative = upstream; default: 0)
-p <INT>	Per-strand override: shift for + strand features
-m <INT>	Per-strand override: shift for - strand features
-g <FILE>	Genome sizes file (chrom<TAB>size); clamps coordinates and drops off-end records
--out <FILE>	Output path (default: stdout)

Origin

This crate is an independent Rust reimplementation of bedtools shift based on:

• The bedtools2 documentation
• The BED format specification
• Black-box behaviour testing against bedtools shift

License: MIT OR Apache-2.0
Upstream credit: bedtools2 (MIT)