[REVIEW]: 'cstag and cstag-cli: tools for manipulating and visualizing CS tags'

[editorialbot]

Submitting author: @akikuno (Akihiro Kuno)
Repository: https://github.com/akikuno/cstag
Branch with paper.md (empty if default branch): joss
Version: 1.0.5, 1.0.0
Editor: @jmschrei
Reviewers: @betteridiot, @jbloom
Archive: 10.5281/zenodo.10544838

Status

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Reviewers and authors:

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Checklists

📝 Checklist for @betteridiot

📝 Checklist for @jbloom

[editorialbot]

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Software report:

github.com/AlDanial/cloc v 1.88  T=0.04 s (869.9 files/s, 76735.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          24            442            428           1420
Markdown                         5            126              0            311
HTML                             4             51              0            288
TeX                              1             11              0            127
TOML                             1              2              0             23
YAML                             1              1              4             18
Bourne Shell                     1              3              4              5
-------------------------------------------------------------------------------
SUM:                            37            636            436           2192
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 792

[editorialbot]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- None

MISSING DOIs

- 10.1093/bioinformatics/bty191 may be a valid DOI for title: Minimap2: pairwise alignment for nucleotide sequences
- 10.1038/s41592-018-0046-7 may be a valid DOI for title: Bioconda: sustainable and comprehensive software distribution for the life sciences

INVALID DOIs

- None

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[jmschrei]

Howdy @betteridiot and @jbloom!

Thanks for agreeing to review this submission.

The process for conducting a review is outlined above. Please run the command shown above to have @editorialbot generate your checklist, which will give a step-by-step process for conducting your review. Please check the boxes during your review to keep track, as well as make comments in this thread or open issues in the repository itself to point out issues you encounter. Keep in mind that our aim is to improve the submission to the point where it is of high enough quality to be accepted, rather than to provide a yes/no decision, and so having a conversation with the authors is encouraged rather than providing a single review post at the end of the process.

Here are the review guidelines: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html
And here is a checklist, similar to above: https://joss.readthedocs.io/en/latest/review_checklist.html

Please let me know if you encounter any issues or need any help during the review process, and thanks for contributing your time to JOSS and the open source community!

[betteridiot]

Review checklist for @betteridiot

Conflict of interest

• I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the https://github.com/akikuno/cstag?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@akikuno) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

[jbloom]

Review checklist for @jbloom

Conflict of interest

• I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the https://github.com/akikuno/cstag?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@akikuno) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

[jbloom]

I have reviewed the cstag submission by @akikuno. I support publication. This is a straightforward and well-documented package that solves a useful question, namely how to add / manipulate cs tags. I could definitely see using this package in my own work at some point, and it is well enough documented that I can figure out how I would do that.

I have completed the reviewer checklist above.

I would add the following notes that could be addressed in a few minor revisions:

1. Could be helpful if it was a little bit more clearly indicated that cstag-cli is installed from a separate repo.
2. In author could consider citing alignparse, which provides some similar-ish functionality in its cs_tag module.
3. I have made the following feature request. Note that this request is optional and not required for me to recommend acceptance of the current package, but if some similar feature was added it would make cstag package more useful for our work.

[jmschrei]

Thanks for the quick review, @jbloom!

[betteridiot]

Here are my notes for the review. Very minor fixes throughout with a couple of larger issues that will be addressed via GitHub issues on author's issue tracker.

Please see complete notes of the review at betteridiot/joss_reviews/blob/master/cstag/joss_review.md

Documentation

1. Paper version references cstag v.1.0.4, but the current version available is v1.0.5
2. Documentation does not express statement of need. It only describes what the program does.

Statement of the field

1. Acknowledges 2passtools but does not address its internal cs tag functionality
2. I am curious about the author's "rebranding" of calcs, which appears to be a precursor to cstag-cli. Maybe add a deconfliction/redirect statement to one of the packages involved.
3. As addressed by @jbloom, the author should recognize alignparse in their state of the field.

References

• Missing DOIs for minimap2 and Bioconda

[betteridiot]

As of @akikuno's latest push to cstag-cli, the only notes left are with respect to the documentation (missing statement of need in documentation), and the paper itself:

1. Cites alignparse in the bibliography, but does not reference it in the paper
2. Acknowledge 2passtools cs tag functionality
3. (optional) deconflict calcs package by describing the "rebranding" in either the cstag-cli or on calcs
   • That is, let users know which package is the one that will continue to be maintained in case of dependencies.

[jmschrei]

@akikuno how are the revisions coming? Do you have any comments about the reviews?

[akikuno]

@jmschrei
Thank you very much for your careful coordination of the peer review process.

@betteridiot @jbloom
I deeply appreciate your excellent peer review comments.
Thanks to your support, the update of the source code is mostly complete (I will soon respond to @jbloom 's request at akikuno/cstag#24), and I now plan to revise the JOSS documentation.

Let me comment here on the parts that have been revised.

@jbloom

Could be helpful if it was a little bit more clearly indicated that cstag-cli is installed from a separate repo.

Thank you very much for your valuable comment.
In response, I have added a documentation to the Availability section of the main text that stated cstag and cstag-cli are managed in a separate repository and registered separately in PyPI and BioConda.
akikuno/cstag@14f4b48

Furthermore, in the README.md of cstag, I have incorporated a [NOTE] highlight as follows to indicate that cstag-cli is managed in a separate repository:

Note

To add cs tags to SAM/BAM files, check out cstag-cli.

https://github.com/akikuno/cstag#cstag

I would appreciate it if you could check this.

[jmschrei]

@akikuno how are the revisions coming? Do you need me to ping any of the reviewers to respond to your revisions?

[akikuno]

@jmschrei
Thank you very much for reaching out. I apologize for the delay in my response, as I have been preoccupied with university-related tasks. I am now proceeding with the revision of the main document and will contact you shortly.

[akikuno]

@betteridiot
Thank you very much for your careful confirmation.

(optional) deconflict calcs package by describing the "rebranding" in either the cstag-cli or on calcs
That is, let users know which package is the one that will continue to be maintained in case of dependencies.

As you pointed out, calcs is the predecessor of cstag-cli and has ceased development. While calcs differs from cstag-cli in that it can add cs tags to SAM files without MD tags, from a computational speed perspective, it is recommended to use samtools calmd to add MD tags before using cstag-cli.

Therefore, the README in the GitHub repository has been updated as follows:

• The deprecation of calcs has been clearly stated in its README.md.
  calcs is deprecated

• Additionally, the README.md of cstag-cli has been updated to recommend using samtools calmd for adding MD tags.
  cstag-cli README.md

Happy holidays!

[editorialbot]

Done! version is now 1.0.5

[jmschrei]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1093/bioinformatics/bty191 is OK
- 10.21105/joss.01915 is OK
- 10.1186/s13059-021-02296-0 is OK
- 10.1371/journal.pbio.3001507 is OK
- 10.1038/s41592-018-0046-7 is OK
- 10.1038/nbt.1754 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/bcm-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#4922, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[akikuno]

@jmschrei I have read through the proof, and all looks good to me.

[jmschrei]

Great. We just need one of the EiC's to step in.

[Kevin-Mattheus-Moerman]

@editorialbot set 1.0.5, 1.0.0 as version

[editorialbot]

Done! version is now 1.0.5, 1.0.0

[Kevin-Mattheus-Moerman]

@akikuno as the AEiC of this track I'll now help to process final steps. Since this review features two packages/repositories, and two version tags etc. Some changes are required:

• Please can you create a single ZENODO archive for the two software entities (matching the above tagged releases) and please report back here with that archive link.
• Ensure that all the metrics, like before, the title, the authors, the license matches. Next use 1.0.5, 1.0.0 as the version tag for the archive.

[Kevin-Mattheus-Moerman]

@jmschrei note you did a good job here. Handling submissions featuring multiple repositories isn't streamlined yet I think, and we may optimise/formalise this better in the future. (I'll propose having comma-seperated repo/arhive/version tags etc for such papers, but this is not supported yet).

[akikuno]

@Kevin-Mattheus-Moerman
I have created a ZENODO archive, using version 1.0.5, 1.0.0 and confirmed that the title, the authors, and the license match.
10.5281/zenodo.10544838

Thank you very much for your support.

[Kevin-Mattheus-Moerman]

@editorialbot set 10.5281/zenodo.10544838 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.10544838

[Kevin-Mattheus-Moerman]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1093/bioinformatics/bty191 is OK
- 10.21105/joss.01915 is OK
- 10.1186/s13059-021-02296-0 is OK
- 10.1371/journal.pbio.3001507 is OK
- 10.1038/s41592-018-0046-7 is OK
- 10.1038/nbt.1754 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/bcm-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#4935, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[Kevin-Mattheus-Moerman]

@editorialbot accept

[editorialbot]

Doing it live! Attempting automated processing of paper acceptance...

[editorialbot]

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Kuno
  given-names: Akihiro
  orcid: "https://orcid.org/0000-0002-4674-6882"
contact:
- family-names: Kuno
  given-names: Akihiro
  orcid: "https://orcid.org/0000-0002-4674-6882"
doi: 10.5281/zenodo.10544838
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Kuno
    given-names: Akihiro
    orcid: "https://orcid.org/0000-0002-4674-6882"
  date-published: 2024-01-22
  doi: 10.21105/joss.06066
  issn: 2475-9066
  issue: 93
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6066
  title: "cstag and cstag-cli: tools for manipulating and visualizing cs
    tags"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06066"
  volume: 9
title: "`cstag` and `cstag-cli`: tools for manipulating and visualizing
  cs tags"

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

[editorialbot]

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

[editorialbot]

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.06066 joss-papers#4936
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06066
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[akikuno]

Everything looks fantastic! Once again, I want to extend my heartfelt thanks to all of you for the assistance in the review process!

[Kevin-Mattheus-Moerman]

@akikuno congratulations on this JOSS publication!

Thanks for editing @jmschrei !

And a special thank you to the reviewers: @betteridiot, @jbloom !!!!

[editorialbot]

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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HTML:
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reStructuredText:
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