mopdepth

A fast BAM/CRAM depth calculation tool written in Crystal, inspired by mosdepth.

This is an experiment to see if well-known tools can be ported to Crystal using “vibe coding”.

Features

• Fast depth calculation for BAM/CRAM files
• Multiple processing modes (fast mode, fragment mode, CIGAR-based)
• Per-base and region-based depth analysis
• BED file support for custom regions
• Window-based analysis
• Comprehensive filtering options (MAPQ, fragment length, flags)

Installation

Prerequisites

• Crystal
• hts-lib (for BAM/CRAM support)

Build from source

git clone https://github.com/kojix2/mopdepth
cd mopdepth
shards install
shares build --release

Usage

./mopdepth [options] <prefix> <BAM-or-CRAM>

Basic example

./mopdepth output sample.bam

Options

• -t, --threads THREADS: BAM decompression threads
• -c, --chrom CHROM: Restrict to chromosome
• -b, --by BY: BED file or numeric window size
• -n, --no-per-base: Skip per-base output
• -Q, --mapq MAPQ: MAPQ threshold
• -l, --min-frag-len MIN: Minimum fragment length
• -u, --max-frag-len MAX: Maximum fragment length
• -x, --fast-mode: Fast mode (read start/end positions only)
• -a, --fragment-mode: Count full fragment (proper pairs only)
• -m, --use-median: Use median for region stats instead of mean
• -M, --mos: Use mosdepth-compatible filenames (mosdepth.); default is depth.
• -v, --version: Show version
• -h, --help: Show help message

Processing modes

• Default mode: CIGAR-based depth calculation (most accurate)
• Fast mode (-x): Uses read start/end positions (faster but less accurate)
• Fragment mode (-a): Counts full fragments for paired-end reads

Note: Fast mode and fragment mode cannot be used together.

Output files

• Summary: <prefix>.(mopdepth|mosdepth).summary.txt
• Per-base: <prefix>.per-base.bed (unless -n)
• Global dist: <prefix>.(mopdepth|mosdepth).global.dist.txt
• Regions: <prefix>.regions.bed (when --by)
• Region dist: <prefix>.(mopdepth|mosdepth).region.dist.txt (when --by)

By default, files are named with the mopdepth.* label. Use -M/--mos to switch to mosdepth.*.

Summary file format

The summary file contains the following columns:

• chrom: Chromosome name
• length: Chromosome length
• sum_depth: Total depth (sum of all depths)
• mean: Mean depth
• min: Minimum depth
• max: Maximum depth

Examples

Basic depth calculation

./mopdepth output sample.bam

With BED regions

./mopdepth -b regions.bed output sample.bam

Window-based analysis (1kb windows)

./mopdepth -b 1000 output sample.bam

Fast mode with MAPQ filtering

./mopdepth -x -Q 20 output sample.bam

Fragment mode for paired-end data

./mopdepth -a -l 100 -u 1000 output sample.bam

License

MIT License