cstag-cli

cstag-cli is a command-line tool of cstag for manipulating minimap2's cs tags.

🌟Features

• cstag append: Appends cs tags to a SAM/BAM file

🛠 Installation

Prerequisites

• Python 3.11 or later
• Unix-like environment (Linux, macOS, WSL, etc.)

Installation

Using Bioconda (Recommended):

conda create -n env-cstag -c conda-forge -c bioconda python=3.11 cstag-cli -y
conda activate env-cstag

Using PyPI:

pip install cstag-cli

[!CAUTION] If you encounter any issues during the installation, please refer to the Troubleshooting Guide

Development

python -m pip install -e . --group dev
ruff format --check .
ruff check .
mypy
python -m pytest tests -W error
sh tests/append/tests.sh
sh tests/test_version.sh
python -m build

💡Usage

Appending cs tags to a SAM/BAM File

cstag append <file> [-l/--long]

• <file>: Path to the SAM/BAM file. If omitted, the program reads from standard input.

[!IMPORTANT] The SAM/BAM file must contain an MD tag.
if the SAM/BAM files do not have MD tags, use samtools calmd.

• -l/--long: Generates cs tags in long format

Examples

• Appending cs tags in short format:

cstag append tests/append/data/example.bam > example_cs_short.sam

• Appending cs tags in long format:

cstag append tests/append/data/example.bam --long > example_cs_long.sam

• Reading data from standard input:

cat tests/append/data/example.bam | cstag append > example_cs_short.sam

📣Feedback and Support

For questions, bug reports, or other forms of feedback, we'd love to hear from you!
Please use GitHub Issues for all reporting purposes.

Please refer to CONTRIBUTING for how to contribute and how to verify your contributions.

🤝 Code of Conduct

Please note that this project is released with a Contributor Code of Conduct.
By participating in this project you agree to abide by its terms.

📄 Citation

• Kuno, A., (2024). cstag and cstag-cli: tools for manipulating and visualizing cs tags. Journal of Open Source Software, 9(93), 6066, https://doi.org/10.21105/joss.06066