cstag-cli 0.1.1

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

Append CS tags to a SAM/BAM file

cstag append [-f/--file] [-l/--long]

• -f/--file: Specifies the path to a SAM/BAM file. If no file is provided, it reads from standard input. An MD tag is required in the SAM/BAM file.
• -l/--long: Outputs CS tags in the long format

Examples

• To append CS tags in the short format:

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

• To append CS tags in the long format:

cstag append -f tests/append/data/example.bam -l > 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 any other inquiries, feel free to reach out! Please use GitHub Issues for reporting.