Metadata-Version: 2.4
Name: wasp2
Version: 1.3.3
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
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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://pypi.org/project/wasp2/">
    <img src="https://img.shields.io/pypi/v/wasp2" alt="PyPI">
  </a>
  <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/master/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>

---

## Installation

```bash
pip install wasp2
```

Pre-built wheels are available for Linux (x86_64, aarch64) and macOS (Intel, Apple Silicon) with Python 3.10-3.12. The Rust extension and htslib are bundled — no additional dependencies required.

## Quick Start

WASP2 has three steps that run in order:

**Step 1: Remap reads** to correct mapping bias

```bash
wasp2-map make-reads input.bam variants.vcf.gz -s sample1 -o remap_dir/
# Realign the swapped-allele reads with your aligner, then:
wasp2-map filter-remapped remapped.bam -j remap_dir/sample1_wasp_data_files.json -o filtered.bam
```

**Step 2: Count alleles** at heterozygous SNPs

```bash
wasp2-count count-variants filtered.bam variants.vcf.gz -s sample1
```

**Step 3: Test for allelic imbalance**

```bash
wasp2-analyze find-imbalance counts.tsv -o results.tsv
```

See the [documentation](https://mcvickerlab.github.io/WASP2/) for detailed usage, single-cell workflows, and supported variant formats (VCF, BCF, PGEN).

## 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).

