[PRE 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: v1.0.0 Editor: @will-rowe Reviewers: @jdeligt, @brentp

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Thanks for submitting your paper to JOSS @telatin. Currently, there isn't an JOSS editor assigned to your paper.

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[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.84  T=0.04 s (321.8 files/s, 43989.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
C++                              2             92             44            683
C/C++ Header                     2             87            184            369
Markdown                         4             51              0            145
TeX                              1              5              0            117
Bourne Shell                     3             17             12             70
YAML                             1              0              0             22
Dockerfile                       1              2              0             14
-------------------------------------------------------------------------------
SUM:                            14            254            240           1420
-------------------------------------------------------------------------------

Statistical information for the repository '2058' was gathered on 2020/02/01.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Andrea Telatin                  14          1533             70           95.36
gbirolo                          4            37             41            4.64

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
Andrea Telatin             1435           93.6          0.0               13.66
gbirolo                      24           64.9          0.0               29.17

[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

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[Kevin-Mattheus-Moerman]

@csoneson, @will-rowe, @majensen, @lpantano could one of you edit this submission? Also can you judge if this work is significant enough to pass our "minor-utility" check?

[Kevin-Mattheus-Moerman]

@telatin thanks for your submission. I recommend that you reformulate your readme to be a bit more suitable to somebody from outside of this domain (like myself). It contains 2 undefined acronyms for instance. Perhaps create a lay-persons summary at the top so it is clear what this software is for to new comers. Furthermore if this work is reviewed at a later stage our reviewers will demand clear contributing guidelines. I have not found these from quickly looking through the readme. Perhaps you can consider adding clear contributing guidelines at this point while we determine the suitability of this software for JOSS. Thanks.

[will-rowe]

Good morning. I've been looking at this submission this morning and I'm afraid we may class this as a minor-utility. Whilst I think this is a useful tool and one which I would use to save myself bedtools + awk scripting, I don't think there is enough functionality here to pass our submission requirements.

I'd appreciate it if either @lpantano, @majensen or @csoneson could take a quick look and confirm this.

Best,

Will

[lpantano]

It seems a nice tool, if it is actually super fast compare to others like bedtools or mosdepth, it could be a good improvement. Otherwise, I could agree is minor.

[telatin]

Thanks @will-rowe and @lpantano for your quick feedback!

We were aware of this possible limitation, yet we were also thinking that "covtobed" fits into a broad set of common tasks, and different bioinformatics applications this specificity was somehow desirable. So we focused on supporting streaming and speed to have a reliable brick for multiple pipelines. (I think it's faster than a regular samtools/bedtools pipeline, but to assess the improvement I'll make some tests)

UPDATE: Should you consider that the tool is worth, I found a potential reviewer: mpallocc (alias Matteo Pallocca, Rome)

[will-rowe]

Hi @telatin. Thanks for your reply. I've been playing with covtobed again this morning - it is a good utility and is very nicely packaged and documented.

Of course you and @lpantano are right in that the speed makes this appealing. I was testing against bedtools (bedtools genomecov -ibam a.bam -bg), which gives the same output to covtobed a.bam. covtobed was roughly twice as fast (note: there were some output inconsistencies but that seems to be due to just using defaults for both programs) and allows streaming (which bedtools doesn't for genomecov at the moment).

Maybe if you could add some benchmarking to your paper and that would satisfy our concerns that this is a minor utility?

I have an alternative (and somewhat cheeky suggestion). Adding some functionality to generate a coverage plot from the bed file would make this an indispensable tool to many bioinformaticians. Something along the lines of the image in your README would be fantastic. This is of course only a suggestion and I'd be happy to put this paper into review with only the benchmarking data added

[telatin]

@will-rowe I really appreciate the time you dedicated to this tool!

To be fair, both suggestions are valuable, and I'll be glad to try addressing one or both. This will probably take some time, is it better to close this issue and resubmit mentioning the issue later or is it possible to keep the issue open in the meantime?

[will-rowe]

You're welcome @telatin.

Let's keep this issue as it's easiest to keep track of the conversation history. I'm happy to assign myself as editor and you can ping this thread when you'd like me to take another look and we can take it from there?

[will-rowe]

@whedon assign @will-rowe as editor

[whedon]

OK, the editor is @will-rowe

[kthyng]

@will-rowe and @telatin Sounds great what you've planned. I will go ahead and add the "paused" label for now to indicate your decision. When ready to go again, it is easy to remove.

[telatin]

Hello! We tested our tool comparing its speed with bedtools and mosdepth. With either small genomes or large genomes having a small targets (e. g. Human gene panels), covtobed outperforms both tools (up to 60X faster). In whole exome sequencing covtobed is 3-5X slower than mosdepth but 2-4X faster than bedtools.

More details here: https://github.com/telatin/covtobed/tree/master/benchmark

We believe that this combined with peculiar features (covtobed is available for mac, allows to split the coverage by strand and works in pipes) makes the tool a useful addition in the bioinformatician's toolshed.

Hope you agree :)

[will-rowe]

Hi @telatin. Many thanks for the update. I think this sounds great and I'd be happy to put it out to review. Let me find some reviewers

[will-rowe]

@whedon assign @will-rowe as editor

[whedon]

OK, the editor is @will-rowe

[will-rowe]

Hi @brentp. Would you be interested in reviewing this submission for JOSS?

[will-rowe]

Hi @jdeligt - would you also be interested in reviewing this submission?

[jdeligt]

Sure, happy to help

On Tue, 25 Feb 2020, 4:10 am Will Rowe, notifications@github.com wrote:

Hi @jdeligt https://github.com/jdeligt - would you also be interested in reviewing this submission?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/2058?email_source=notifications&email_token=ABMUN75XWLPLERQN7TMWEEDREPPMPA5CNFSM4KORTCPKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEMYFDYQ#issuecomment-590369250, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABMUN77UCHIYZGTWHBABEIDREPPMPANCNFSM4KORTCPA .

[brentp]

yes

[will-rowe]

Brilliant. Thanks everyone. I'll start the review now and you'll shortly receive links to the new review issue - let me know if any of you need further instruction on the JOSS review process.

[will-rowe]

@whedon assign @jdeligt as reviewer

[whedon]

OK, @jdeligt is now a reviewer

[will-rowe]

@whedon add @brentp as reviewer

[whedon]

OK, @brentp is now a reviewer

[will-rowe]

@whedon start review

[whedon]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/2119.