[REVIEW]: covtobed: a simple and fast tool to extract coverage tracks from BAM files

[whedon]

Submitting author: @telatin (Andrea Telatin)
Repository: https://github.com/telatin/covtobed/
Version: v1.1.0
Editor: @will-rowe
Reviewer: @jdeligt, @brentp
Archive: 10.5281/zenodo.3695204

Status

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Markdown: [![status](https://joss.theoj.org/papers/0ed74df9f40a58a852bf3fff512acd2b/status.svg)](https://joss.theoj.org/papers/0ed74df9f40a58a852bf3fff512acd2b)

Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@jdeligt & @brentp, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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✨ Please try and complete your review in the next two weeks ✨

Review checklist for @jdeligt

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 repository url?
• 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 (@telatin) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• 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?

Review checklist for @brentp

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 repository url?
• 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 (@telatin) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• 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?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @jdeligt, @brentp it looks like you're currently assigned to review this paper 🎉.

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If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

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@whedon generate pdf

[whedon]

Reference check summary:

OK DOIs

- 10.1093/bioinformatics/btq033 is OK
- 10.1093/bioinformatics/btx699 is OK
- 10.1038/nrg3642 is OK
- 10.1093/bioinformatics/btp352 is OK
- 10.1093/bioinformatics/btr174 is OK
- 10.1016/j.hrthm.2018.11.015 is OK
- 10.5281/zenodo.3643386 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

👉 Check article proof 📄 👈

[brentp]

@whedon generate pdf

[whedon]

👉 Check article proof 📄 👈

[jdeligt]

Hi @telatin,

Overall looking good, please consider the integrity and performance check marks in;
telatin/covtobed#6

And please update example usage as specified in;
telatin/covtobed#5

Best regards,
Joep

[brentp]

LGTM

[telatin]

Dear @brentp and @jdeligt,
thank you very much for your quick and thorough review, we really feel that your input allowed us to improve the package quality.

Summarizing:

• paper updated clarifying some sentences
• automated tests have been expanded and documented
• the wiki documentation has been expanded, specifically including information on the coverage calculation and stressing the peculiar usage of "covtobed" (physical-coverage, strand-specific analysis, streaming)
• the benchmark section has been expanded to include a test with a whole human genome and its description extended
• released 1.0.1 with support for coverage > 2**16, initially naively excluded

See: https://github.com/telatin/covtobed/issues?utf8=%E2%9C%93&q=is%3Aissue+label%3Ajoss+ for the issues opened in the repo

[jdeligt]

Hi @telatin ,

Thank you for the quick responses and the additions made to the repo.
I added one last comment to issue#5 but this is a nice to have but should not hold up publication.
The clarifactions will help users better determine what the software does and is a nice intro into some of the vageries of coverage depth calculations.

@will-rowe, looks like @brentp is happy with it as well so I think we'll hand it back to you.

[will-rowe]

Perfect - thanks for your speedy and excellent reviews @jdeligt and @brentp!

This is looking really nice @telatin - I'll just give it a finally read through

[will-rowe]

@whedon generate pdf

[whedon]

👉 Check article proof 📄 👈

[will-rowe]

@whedon check references

[whedon]

Reference check summary:

OK DOIs

- 10.1093/bioinformatics/btq033 is OK
- 10.1093/bioinformatics/btx699 is OK
- 10.1038/nrg3642 is OK
- 10.1093/bioinformatics/btp352 is OK
- 10.1093/bioinformatics/btr174 is OK
- 10.1016/j.hrthm.2018.11.015 is OK
- 10.5281/zenodo.3643386 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[will-rowe]

Okay I think we can move toward acceptance here!

@telatin - I need you to tag a new release and archive it. Then can you get back to me with the version number and the archive DOI.

[telatin]

Thanks to you all for your great work!

• Archived release
  https://github.com/telatin/covtobed/releases/tag/v1.1.0

• Zeonodo
  Birolo, Giovanni, & Telatin, Andrea. (2020, March 3). covtobed - a simple and fast tool to convert the coverage track from a BAM file into a BED file (Version 1.1.0). Zenodo. http://doi.org/10.5281/zenodo.3695204

[will-rowe]

@whedon set 10.5281/zenodo.3695204 as archive

[whedon]

OK. 10.5281/zenodo.3695204 is the archive.

[will-rowe]

@whedon set v1.1.0 as version

[whedon]

OK. v1.1.0 is the version.

[will-rowe]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

Reference check summary:

OK DOIs

- 10.1093/bioinformatics/btq033 is OK
- 10.1093/bioinformatics/btx699 is OK
- 10.1038/nrg3642 is OK
- 10.1093/bioinformatics/btp352 is OK
- 10.1093/bioinformatics/btr174 is OK
- 10.1016/j.hrthm.2018.11.015 is OK
- 10.5281/zenodo.3643386 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

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

. Check final proof 👉 openjournals/joss-papers#1351

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1351, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[Kevin-Mattheus-Moerman]

I've read the paper and it looks good

[Kevin-Mattheus-Moerman]

@whedon accept deposit=true

[whedon]

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

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

🚨🚨🚨 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.02119 joss-papers#1356
1. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02119
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...

[arfon]

Dear authors and reviewers

We wanted to notify you that in light of the current COVID-19 pandemic, JOSS has decided to suspend submission of new manuscripts and to handle existing manuscripts (such as this one) on a "best efforts basis". We understand that you may need to attend to more pressing issues than completing a review or updating a repository in response to a review. If this is the case, a quick note indicating that you need to put a "pause" on your involvement with a review would be appreciated but is not required.

Thanks in advance for your understanding.

Arfon Smith, Editor in Chief, on behalf of the JOSS editorial team.

[will-rowe]

Pinging @openjournals/jose-eics - I think this can be closed now?

[whedon]

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[arfon]

Pinging @openjournals/jose-eics - I think this can be closed now?

Just a heads up @will-rowe that you mentioned the wrong EiC group here :-)