semvec/pypi-packages huggingface dataset:
cstag-cli 1.0.0
Command line interface of cstag to manipulate the minimap2's CS tag
License: MIT
Requires Python: >=3.7,<4.0

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# cstag-cli

`cstag-cli` is a command-line tool of [`cstag`](https://github.com/akikuno/cstag) for manipulating [minimap2's CS tags](https://github.com/lh3/minimap2#the-cs-optional-tag).

## 🌟Features

- `cstag append`: Appends CS tags to a SAM/BAM file

## 🛠 Installation

Using [PyPI](https://pypi.org/project/cstag-cli/):

```bash
pip install cstag-cli
```

Using [Bioconda](https://anaconda.org/bioconda/cstag-cli):

```bash
conda install -c bioconda cstag-cli
```

## 💡Usage

### Appending CS Tags to a SAM/BAM File

```bash
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:
```bash
cstag append tests/append/data/example.bam > example_cs_short.sam
```

- Appending CS tags in long format:
```bash
cstag append tests/append/data/example.bam --long > example_cs_long.sam
```
- Reading data from standard input:

```bash
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](https://github.com/akikuno/cstag-cli/issues) for all reporting purposes.  


Please note that this project is released with a [Contributor Code of Conduct](https://github.com/akikuno/cstag-cli/blob/main/CODE_OF_CONDUCT.md).  
By participating in this project you agree to abide by its terms.