Create CONTRIBUTING.md

Author: Paururo

.github/CONTRIBUTING.md

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+# Contributing to pathotypr
+
+Thank you for your interest in contributing to **pathotypr**! 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](#project-description)
+- [How to Contribute](#how-to-contribute)
+  - [Reporting Issues](#reporting-issues)
+  - [Feature Requests](#feature-requests)
+  - [Contributing Code](#contributing-code)
+- [Coding Guidelines](#coding-guidelines)
+- [Setting Up the Development Environment](#setting-up-the-development-environment)
+- [Submitting a Pull Request](#submitting-a-pull-request)
+- [Code of Conduct](#code-of-conduct)
+
+## Project Description
+`pathotypr` is a tool designed to identify **Multi-Nucleotide Variants (MNVs)** within the same codon in genomic sequences. MNVs occur when multiple Single Nucleotide Variants (SNVs) are present within the same codon, leading to the translation of a different amino acid. This tool addresses limitations in current annotation programs like **ANNOVAR** or **SnpEff**, which are primarily designed to work with individual SNVs and might overlook the actual amino acid changes resulting from MNVs.
+
+### Current Limitations
+**IMPORTANT**: This script currently works only with **SNVs** against a reference genome. Insertions and deletions that modify the reading frame are not supported yet.
+
+## 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](https://github.com/PathoGenOmics-Lab/pathotypr/issues) 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 `pathotypr` 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](https://github.com/rust-lang/rustfmt) 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:
+   ```bash
+   git clone https://github.com/PathoGenOmics-Lab/pathotypr.git
+   cd pathotypr
+   ```
+
+2. Install the necessary dependencies using `cargo`:
+   ```bash
+   cargo build
+   ```
+
+3. Run the tests to ensure everything is set up correctly:
+   ```bash
+   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](https://www.contributor-covenant.org/version/2/0/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!