Command line interface of cstag to manipulate the minimap2's CS tag
Project description
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 theshort 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.
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