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https://github.com/akikuno/cstag-cli

CLI to manipulate minimap2's cs tag

https://github.com/akikuno/cstag-cli

Science Score: 23.0%

This score indicates how likely this project is to be science-related based on various indicators:

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    CITATION.cff file
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    codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 5 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: joss.theoj.org, zenodo.org
  • ○
    Academic email domains
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    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (14.0%) to scientific vocabulary

Keywords

bioinformatics cstag
Last synced: 10 months ago · JSON representation

Repository

CLI to manipulate minimap2's cs tag

Basic Info
  • Host: GitHub
  • Owner: akikuno
  • License: mit
  • Language: Python
  • Default Branch: main
  • Homepage:
  • Size: 278 KB
Statistics
  • Stars: 1
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 3
Topics
bioinformatics cstag
Created almost 3 years ago · Last pushed over 2 years ago
Metadata Files
Readme Contributing License Code of conduct

README.md

Licence Test Python PyPI Bioconda JOSS DOI

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

Prerequisites

  • Python 3.7 or later
  • Unix-like environment (Linux, macOS, WSL, etc.)

Installation

Using Bioconda (Recommended):

bash conda create -n env-cstag -c conda-forge -c bioconda python=3.10 cstag-cli -y conda activate env-cstag

[!NOTE] To Apple Silicon (ARM64) users:
Since the Bioconda channel does not yet support Apple Silicon, please use the following command to install cstag-cli through Rosetta. bash CONDA_SUBDIR=osx-64 conda create -n env-cstag -c conda-forge -c bioconda python=3.10 cstag-cli -y conda activate env-cstag conda config --env --set subdir osx-64

Using PyPI:

bash pip install cstag-cli

[!CAUTION] If you encounter any issues during the installation, please refer to the Troubleshooting Guide

💡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.

[!IMPORTANT] The SAM/BAM file must contain an MD tag.
if the SAM/BAM files do not have MD tags, use samtools calmd.

  • -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 and Support

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 refer to CONTRIBUTING for how to contribute and how to verify your contributions.

🤝 Code of Conduct

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.

📄 Citation

  • Kuno, A., (2024). cstag and cstag-cli: tools for manipulating and visualizing cs tags. Journal of Open Source Software, 9(93), 6066, https://doi.org/10.21105/joss.06066

Owner

  • Name: Akihiro Kuno
  • Login: akikuno
  • Kind: user
  • Location: Tsukuba, Ibaraki, Japan
  • Company: University of Tsukuba

Bioinformatician working at the Laboratory Animal Resource Center

GitHub Events

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Last Year

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 2
  • Total pull requests: 4
  • Average time to close issues: 10 days
  • Average time to close pull requests: 1 minute
  • Total issue authors: 1
  • Total pull request authors: 1
  • Average comments per issue: 6.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 4
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
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Top Authors
Issue Authors
  • betteridiot (2)
Pull Request Authors
  • akikuno (4)
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Packages

  • Total packages: 1
  • Total downloads:
    • pypi 17 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 3
  • Total maintainers: 1
pypi.org: cstag-cli

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

  • Versions: 3
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 17 Last month
Rankings
Dependent packages count: 7.5%
Average: 38.7%
Dependent repos count: 69.8%
Maintainers (1)
akikuno
Last synced: 10 months ago