Metadata-Version: 2.4
Name: wasp2
Version: 1.3.2
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: POSIX :: Linux
Classifier: Operating System :: MacOS
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Typing :: Typed
Requires-Dist: numpy>=1.21.0
Requires-Dist: pandas>=1.5.0,<3.0.0
Requires-Dist: polars>=0.19.0
Requires-Dist: scipy>=1.10.0
Requires-Dist: pysam>=0.21.0
Requires-Dist: pybedtools>=0.9.0
Requires-Dist: anndata>=0.8.0,<0.12.0
Requires-Dist: scanpy>=1.9.0
Requires-Dist: typer>=0.12.0
Requires-Dist: rich>=13.0.0
Requires-Dist: pytest-benchmark>=4.0 ; extra == 'benchmark'
Requires-Dist: memory-profiler>=0.61 ; extra == 'benchmark'
Requires-Dist: matplotlib>=3.7.0 ; extra == 'benchmark'
Requires-Dist: seaborn>=0.12.0 ; extra == 'benchmark'
Requires-Dist: cyvcf2>=0.31.0 ; extra == 'cyvcf2'
Requires-Dist: pytest>=7.0 ; extra == 'dev'
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Requires-Dist: build>=0.10 ; extra == 'dev'
Requires-Dist: twine>=4.0 ; extra == 'dev'
Requires-Dist: maturin>=1.4 ; extra == 'dev'
Requires-Dist: bandit[toml]>=1.8.0 ; extra == 'dev'
Requires-Dist: pip-audit>=2.7.0 ; extra == 'dev'
Requires-Dist: sphinx>=7.0 ; extra == 'docs'
Requires-Dist: pydata-sphinx-theme>=0.15 ; extra == 'docs'
Requires-Dist: sphinx-autodoc-typehints>=1.25 ; extra == 'docs'
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Requires-Dist: sphinx-design>=0.5 ; extra == 'docs'
Requires-Dist: ipython>=8.0 ; extra == 'docs'
Requires-Dist: pgenlib>=0.90 ; extra == 'plink'
Requires-Dist: maturin>=1.0 ; extra == 'rust'
Provides-Extra: benchmark
Provides-Extra: cyvcf2
Provides-Extra: dev
Provides-Extra: docs
Provides-Extra: plink
Provides-Extra: rust
License-File: LICENSE
Summary: Allele-specific analysis of next-generation sequencing data with high-performance multi-format variant support (VCF/cyvcf2/PGEN)
Keywords: bioinformatics,genomics,allele-specific,ngs,sequencing,wasp,allelic-imbalance,plink2,pgen,vcf,cyvcf2,high-performance
Author: Aaron Ho, McVicker Lab
Author-email: Jeff Jaureguy <jeffpjaureguy@gmail.com>
License: MIT
Requires-Python: >=3.10
Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM
Project-URL: Documentation, https://mcvickerlab.github.io/WASP2/
Project-URL: Homepage, https://github.com/mcvickerlab/WASP2
Project-URL: Issues, https://github.com/mcvickerlab/WASP2/issues
Project-URL: Repository, https://github.com/mcvickerlab/WASP2

<p align="center">
  <img src="docs/source/_static/banner.svg" alt="WASP2 - Allele-Specific Analysis Pipeline" width="100%">
</p>

<p align="center">
  <a href="https://github.com/mcvickerlab/WASP2/actions/workflows/ci.yml">
    <img src="https://github.com/mcvickerlab/WASP2/actions/workflows/ci.yml/badge.svg" alt="CI">
  </a>
  <a href="https://mcvickerlab.github.io/WASP2/">
    <img src="https://img.shields.io/badge/docs-GitHub%20Pages-blue" alt="Documentation">
  </a>
  <a href="https://github.com/mcvickerlab/WASP2/blob/main/LICENSE">
    <img src="https://img.shields.io/badge/license-MIT-green" alt="License">
  </a>
</p>

<p align="center">
  <a href="https://mcvickerlab.github.io/WASP2/">Documentation</a> •
  <a href="https://mcvicker.salk.edu/">McVicker Lab</a> •
  <a href="https://github.com/bmvdgeijn/WASP">Original WASP</a>
</p>

---

## Quick Start

```bash
pip install wasp2

wasp2-count count-variants reads.bam variants.vcf.gz -s sample1
```

## Authors

- **Aaron Ho** — Creator of WASP2
- **Jeff Jaureguy** — Developer and maintainer
- **[McVicker Lab](https://mcvicker.salk.edu/)**, Salk Institute

## Citation

If you use WASP2 in your research, please cite our paper (coming soon).

