cstag-cli 1.0.0

Command line interface of cstag to manipulate the minimap2's CS tag

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.