[REVIEW]: Bam-readcount - rapid generation of basepair-resolution sequence metrics

[whedon]

Submitting author: @chrisamiller (Christopher A. Miller)
Repository: https://github.com/genome/bam-readcount
Version: v1.0.1
Editor: @lpantano
Reviewers: @friedue, @bebatut
Archive: 10.5281/zenodo.5879149

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Markdown: [![status](https://joss.theoj.org/papers/1bcbb483ff8b512cc4598e44807ce8a2/status.svg)](https://joss.theoj.org/papers/1bcbb483ff8b512cc4598e44807ce8a2)

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.)

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@friedue, 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 start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Review checklist for @friedue

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 (@chrisamiller) made major contributions to the software? Does the full list of paper authors seem appropriate and complete? #3731
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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 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 @bebatut

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 (@chrisamiller) made major contributions to the software? Does the full list of paper authors seem appropriate and complete? #3731
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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 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. @friedue it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

⭐ Important ⭐

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 😿

To fix this do the following two things:

1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

2. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

For a list of things I can do to help you, just type:

@whedon commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.06 s (870.7 files/s, 81442.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
CMake                           20            210            404            960
Python                           5            112            223            914
C++                              8            140            111            846
Markdown                         5            100              0            169
C/C++ Header                     5             29              0            128
XSLT                             1              5              0            112
Perl                             2             24              0             96
Dockerfile                       1              9              6             27
YAML                             1              0              0             21
diff                             1              4             16             10
Bourne Shell                     1              0              0              1
-------------------------------------------------------------------------------
SUM:                            50            633            760           3284
-------------------------------------------------------------------------------


Statistical information for the repository '04f8f3c9ee7bd25d0aa32333' was
gathered on 2021/09/13.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Ajay Khanna                      9           110             47            2.84
Chris Miller                     2             9              1            0.18
Dave Larson                     57          1358            866           40.30
Morgan Taschuk                   1             1              1            0.04
Sam Brightman                    1             4              4            0.14
Travis Abbott                   16          1133            986           38.39
dlarson                          7           973             26           18.10

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Ajay Khanna                  92           83.6         13.3               16.30
Chris Miller                  7           77.8         78.8                0.00
Dave Larson                 865           63.7         83.8                6.47
Morgan Taschuk                1          100.0         72.7                0.00
Sam Brightman                 4          100.0         58.8                0.00
Travis Abbott               546           48.2        102.9                9.89

[whedon]

PDF failed to compile for issue #3722 with the following error:

 Can't find any papers to compile :-(

[apldx]

@whedon generate pdf from branch joss-paper

[whedon]

Attempting PDF compilation from custom branch joss-paper. Reticulating splines etc...

[whedon]

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

[friedue]

I've opened a couple of issues in the repo, most of them dealing with relatively minor issues. The main issue IMO is the installation/docker use and the lack of a proper use-case.

genome/bam-readcount#79, genome/bam-readcount#80, genome/bam-readcount#81, genome/bam-readcount#82

[lpantano]

@whedon add @bebatut as reviewer

[whedon]

OK, @bebatut is now a reviewer

[bebatut]

I agree with @friedue about the major issues. I added some comments in the already existing issues and also create new ones:

• Functionality documentation: [JOSS REVIEW] Any functionality documentation? genome/bam-readcount#84
• Community contribution guidelines: [JOSS REVIEW] Missing the community contribution guidelines genome/bam-readcount#83

A last comment: is the data used to generate the graphs in the paper available somewhere?

[chrisamiller]

Thanks, both of you, for the feedback. We'll get cracking on this and report back soon!

[whedon]

👋 @friedue, please update us on how your review is going (this is an automated reminder).

[bebatut]

Sorry for the delay (some health issues). Everything looks good now on my side. It seems ready to go 🚀

[chrisamiller]

Appreciated, all! Just let us know what the next steps are from our side!

[lpantano]

@chrisamiller, At this point could you:

• Make a tagged release of your software, and list the version tag of the archived version here.
• Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
• Check the archival deposit (e.g., in Zenodo) has the correct metadata. This includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it). You may also add the authors' ORCID.
• Please list the DOI of the archived version here.

I can then move forward with accepting the submission.

[chrisamiller]

• Release is v1.0.1
• It has been archived in Zenodo I am unclear on how to make the title match the paper - we have Github/Zenodo set up to auto-archive every tagged version, and it auto-generates that title. Would including the paper title in the description of the repository be sufficient?
• Metadata all matches up
• Zenodo DOI: 10.5281/zenodo.5879149

Thanks!

[lpantano]

@whedon set v1.0.1 as version

[whedon]

OK. v1.0.1 is the version.

[chrisamiller]

Just checking in - is there anything else we need to do here? @lpantano Thanks!

[lpantano]

sorry, got into some other tasks. I asked, and it seems it is ok not to have the title match.

[lpantano]

@whedon set 10.5281/zenodo.5879149 as archive

[whedon]

OK. 10.5281/zenodo.5879149 is the archive.

[lpantano]

@whedon recommend-accept t

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

PDF failed to compile for issue #3722 with the following error:

 Can't find any papers to compile :-(

[chrisamiller]

Thanks! Think it'll need to be pointed to branch joss-paper

[arfon]

@whedon recommend-accept from branch joss-paper

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.1093/gigascience/giab007 is OK
- 10.1038/nm.3733 is OK
- 10.1111/gcb.15291 is OK
- 10.1186/s12920-019-0508-5 is OK
- 10.1371/journal.pcbi.1004274 is OK
- 10.1093/bioinformatics/btw536 is OK
- 10.1038/s41375-018-0193-y is OK
- 10.1001/jamaoncol.2016.0494 is OK
- 10.1016/j.cels.2015.08.015 is OK
- 10.1182/blood-2017-03-735654 is OK
- 10.1093/infdis/jiy358 is OK
- 10.1002/0471250953.bi1504s44 is OK
- 10.3390/v12121414 is OK
- 10.1101/2021.05.06.21256753 is OK
- 10.1056/NEJMoa1301689 is OK
- 10.1038/s41598-020-64708-8 is OK
- 10.1093/bioinformatics/bty518 is OK
- 10.1101/mcs.a002444 is OK
- 10.1038/s41588-018-0257-y is OK
- 10.1093/bioinformatics/bty316 is OK
- 10.1093/bioinformatics/bty316 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#2914

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2914, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true from branch joss-paper 

[arfon]

@whedon accept deposit=true from branch joss-paper

[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.03722 joss-papers#2915
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03722
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]

@friedue, @bebatut – many thanks for your reviews here and to @lpantano for editing this submission! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you ✨

@chrisamiller – your paper is now accepted and published in JOSS ⚡🚀💥

[whedon]

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

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.03722/status.svg)](https://doi.org/10.21105/joss.03722)

HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.03722/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03722/status.svg
   :target: https://doi.org/10.21105/joss.03722

This is how it will look in your documentation:

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