Genemancer

Genemancer is a Rust CLI toolkit for genomics file processing, built primarily on the noodles ecosystem, with optional GPU acceleration (wgpu) for target-based variant aggregation.

Toolkit

Current subcommands:

• merge-bam (implemented): merge multiple coordinate-sorted, indexed BAM files into one BAM, with optional BED filtering (all|strict|trim), read-group filtering, output index writing, and configurable compression level.
• gff-to-gtf (implemented): convert GFF3 annotations to GTF (stdin/stdout supported).
• call-targets (implemented): call simple SNVs from BAM inputs over BED target intervals and write bgzipped VCF output (.vcf.gz) with index (csi default, optional tbi).
• call-targets-gpu (implemented): same pipeline as call-targets, but attempts GPU initialization and falls back to CPU unless --require-gpu is set.
• split-bam (implemented): split one or more coordinate-sorted BAM files into per-region BAMs from a BED file, with optional unassigned-read output and optional output indexing.

Global options:

• -v/--verbose (repeatable) for log verbosity.
• -t/--threads to control worker threads.

Installation

Install from crates.io:

cargo install genemancer

Or install from the local repository checkout:

cargo install --path .

Build And Run

1. Install a Rust toolchain with edition 2024 support.
2. Build:

   cargo build
   

3. Show CLI help:

   cargo run -- --help
   

You can inspect any command with:

cargo run -- <subcommand> --help

Usage Examples

Examples below assume you provide your own inputs. In this repository, *.bam and /test_data are gitignored.

Merge two BAMs into one BAM with index output:

cargo run -- merge-bam \
  -i /path/to/input1.bam \
  -i /path/to/input2.bam \
  -o test_data/merged.bam \
  --index

Convert GFF3 to GTF:

cargo run -- gff-to-gtf \
  -i input.gff3 \
  -o output.gtf

Call SNVs on target regions (CPU/streaming path):

cargo run -- call-targets \
  -i /path/to/bams_or_directory \
  -r /path/to/reference.fa.gz \
  -T /path/to/targets.bed \
  --rg-map references/rg_map.txt \
  -o test_data/out.vcf.gz

Run the GPU-enabled path (falls back to CPU by default):

cargo run -- call-targets-gpu \
  -i /path/to/bams_or_directory \
  -r /path/to/reference.fa.gz \
  -T /path/to/targets.bed \
  --rg-map references/rg_map.txt \
  --gpu-backend auto \
  -o test_data/out.vcf.gz

Split multiple BAMs by BED regions into an output folder:

cargo run -- split-bam \
  -i /path/to/input1.bam \
  -i /path/to/input2.bam \
  --bed /path/to/targets.bed \
  --out-dir test_data/splits \
  --output-prefix panel \
  --write-indices \
  --unassigned test_data/splits/unassigned.bam

Repository Data

• references: helper scripts and a tracked sample RG map (references/rg_map.txt).
• tests/data: tracked .bai files only.
• Local working datasets are expected under test_data/ (ignored by git).

Ignored Paths

Notes

• call-targets may prepare a sorted/indexed BGZF FASTA companion (*.sorted.fa.gz plus indexes) when the provided reference is not already in an indexed form suitable for random access.

TODO