capcruncher-tools 0.2.5

Extra utilities to enhance CapCruncher

CapCruncherTools

Overview

A collection of Rust tools to speed up the Python-based functionality of the CapCruncher project. Python bindings have been generated to allow for easy integration into the existing Python code base.

Development

This project uses uv for Python dependency management and environment setup. Dependencies are declared in pyproject.toml and resolved in uv.lock.

Create or update the local environment:

uv sync --dev

Build the Rust extension into the uv environment:

uv run maturin develop --release

Run the test suite:

uv run pytest

Refresh locked dependencies after editing pyproject.toml:

uv lock --upgrade

Release version bumps are managed by release-plz. After conventional commits land on the default branch, the release workflow opens or updates a release PR that bumps Cargo.toml, updates Cargo.lock, and maintains the changelog. Merge that PR, then create a vX.Y.Z GitHub release from the merged commit to publish the Python distributions.

Runtime dependency ranges are intentionally broad so capcruncher-tools can install inside CapCruncher pipeline environments without forcing shared libraries such as Click, pandas, or Polars to a single version. Build and development tools remain pinned for reproducible local builds. CapCruncher itself is expected to be supplied by the parent pipeline or CLI environment.

Current Accelerators

FASTQ deduplication

This tool takes paired FASTQ files and removes any duplicate fragments.

Use it through the CapCruncher CLI or Python API; this package provides the compiled acceleration layer.

Restriction digestion of FASTA

This tool takes a FASTA file and a list of restriction enzymes and produces a list of fragments in BED format.

Use it through the CapCruncher CLI or Python API; this package does not install a separate capcruncher-tools command.

Count restriction fragments

This tool counts the number of interactions between a fragment (in silico digested read).

Use it through CapCruncher's interaction-counting API; cooler creation and workflow orchestration live in CapCruncher.