Metadata-Version: 2.4
Name: qualrepair
Version: 1.0.0
Summary: Update the FASTQ quality scores from a subsequence FASTQ.
Project-URL: homepage, https://github.com/clintval/qualrepair
Project-URL: repository, https://github.com/clintval/qualrepair
Project-URL: Bug Tracker, https://github.com/clintval/qualrepair/issues
Author-email: Clint Valentine <valentine.clint@gmail.com>
License-Expression: MIT
License-File: LICENSE
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Classifier: Typing :: Typed
Requires-Python: >=3.11
Requires-Dist: pysam~=0.23.3
Requires-Dist: syncup~=0.1.0
Description-Content-Type: text/markdown

# qualrepair

[![PyPI Release](https://badge.fury.io/py/qualrepair.svg)](https://badge.fury.io/py/qualrepair)
[![CI](https://github.com/clintval/qualrepair/actions/workflows/python_package.yml/badge.svg?branch=main)](https://github.com/clintval/qualrepair/actions/workflows/python_package.yml?query=branch%3Amain)
[![Python Versions](https://img.shields.io/badge/python-3.11_|_3.12_|_3.13-blue)](https://github.com/clintval/qualrepair)
[![MyPy Checked](http://www.mypy-lang.org/static/mypy_badge.svg)](http://mypy-lang.org/)
[![uv](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/uv/main/assets/badge/v0.json)](https://github.com/astral-sh/uv)
[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://docs.astral.sh/ruff/)

Update the FASTQ quality scores from a subsequence FASTQ.

```console
pip install qualrepair
```

## Example

Repair the qualities in a sub-sequence FASTQ file from its original FASTQ file.

```bash
❯ qualrepair --in-source "r1.fastq.gz" --in-subseq "r1.subseq.fastq.gz"
```

This tool is primarily used to mitigate an unsolved issue in the [`splitcode`](https://github.com/pachterlab/splitcode/issues/18) tool.

## Development and Testing

See the [contributing guide](./CONTRIBUTING.md) for more information.
