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Contributing to snpick

Thank you for your interest in contributing to snpick! We welcome contributions that help improve the tool, fix bugs, or enhance the documentation. This document outlines the process for contributing and the guidelines to follow.

Table of Contents

Project Description

snpick is a fast, memory-efficient tool for extracting variable (SNP) sites from whole-genome FASTA alignments. It produces reduced alignments ready for phylogenetic inference with ascertainment-bias correction (ASC) in IQ-TREE and RAxML, and can optionally emit a VCF file. Its zero-copy, memory-mapped architecture scales to thousands of genomes in seconds with minimal RAM, where matrix-in-memory tools such as snp-sites struggle.

Scope

  • Input is a FASTA alignment: every sequence must have the same length. The first sequence is used as the reference for REF/ALT polarization.
  • Standard bases A/C/G/T (case-insensitive) define variability; IUPAC ambiguous bases (N, R, Y, …) are treated as missing data rather than alleles.
  • Gaps (-) are ignored by default and can be included as a 5th character with -g.

How to Contribute

We appreciate all contributions, whether it’s fixing bugs, proposing new features, improving the documentation, or suggesting a new direction for the tool.

Reporting Issues

If you encounter a bug, have a question, or want to request a feature, please open an issue on our GitHub repository. When reporting an issue, please include: - A detailed description of the problem. - Steps to reproduce the issue. - Any relevant logs or screenshots. - Version information of snpick and your operating system.

Feature Requests

We welcome suggestions for new features and improvements! Please open an issue labeled Feature Request and provide as much detail as possible regarding your suggestion and its potential use cases.

Contributing Code

If you’d like to contribute code, follow these steps: 1. Fork the repository. 2. Create a new branch for your feature or bugfix (git checkout -b feature/new-feature). 3. Make your changes. 4. Test your code. 5. Submit a pull request following the guidelines in the Submitting a Pull Request section.

Coding Guidelines

  • Code Style: Follow Rust’s official Rustfmt style guide for formatting.
  • Testing: Ensure that your code changes include relevant tests. Use cargo test to run tests locally before submitting a pull request.
  • Documentation: Document all public methods, structs, and modules using doc comments (///).

Setting Up the Development Environment

  1. Clone the repository: 

    git clone https://github.com/PathoGenOmics-Lab/snpick.git
cd snpick

  2. Install the necessary dependencies using cargo: 

    cargo build

  3. Run the tests to ensure everything is set up correctly: 

    cargo test

  4. You’re ready to start contributing!

Submitting a Pull Request

  1. Ensure that your code follows the coding guidelines and passes all tests.
  2. Write a clear commit message detailing what your change does.
  3. Submit a pull request (PR) and fill in the PR template. Include a summary of the changes, why they are necessary, and any relevant issue numbers.
  4. A project maintainer will review your PR and provide feedback if needed.

Code of Conduct

This project follows the Contributor Covenant Code of Conduct. By participating, you agree to abide by its terms. Please be respectful and professional in all interactions.

We look forward to your contributions!