Description:

cstagcli 1.0.0

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
Using PyPI:
pip install cstag-cli

Using Bioconda:
conda install -c bioconda cstag-cli

💡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.


Note: The SAM/BAM file must contain an MD tag.


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

License

For personal and professional use. You cannot resell or redistribute these repositories in their original state.

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