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biology/bamtools: API and toolkit for handling BAM files
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Authored by jwb on Mar 28 2018, 3:57 AM.

Details

Summary

biology/bamtools: API and toolkit for handling BAM files
Approved by jrm (mentor) or wen (mentor)
Differential to be added to commit message

Test Plan

Passed pkglint and stage-qa
Poudriere tested on {10.3,11.1}-{amd64,i386}

Diff Detail

Repository
rP FreeBSD ports repository
Lint
Automatic diff as part of commit; lint not applicable.
Unit
Automatic diff as part of commit; unit tests not applicable.

Event Timeline

Looks good.

biology/bamtools/Makefile
20 ↗(On Diff #40827)

Does this need to be +=?

biology/bamtools/pkg-descr
3 ↗(On Diff #40827)

Would an opening paragraph describing BAM be useful? (I was not able to put this above the first sentence.)

`BAM is the binary alternative to the sequence alignment/map (SAM) format
used for storing genetic sequence data. It uses BGZF block compression
implemented on top of the standard gzip file format to provide good
compression while allowing efficient random access for indexed queries.`

This revision is now accepted and ready to land.Mar 28 2018, 1:00 PM
This revision was automatically updated to reflect the committed changes.

Yes, I did overlook your comment.

I've developed a habit of using += for any sort of configure arguments, out of paranoia over clobbering those that ports injects on its own. I can change this one to '='.

Do you consider this worth another commit, or should it wait until the next upgrade?

In D14877#312912, @jwb wrote:

Do you consider this worth another commit, or should it wait until the next upgrade?

There were two comments. It's up to you. Committing now doesn't affect much (other than the change itself) if you don't have to bump PORTREVISION. If you decided to make a change to pkg-desc, that probably warrants a PORTREVISION bump though.

I'll leave it alone for now rather than add noise to the commit log.

I added the changes to wip/bamtools to make sure they'll be included in the next upgrade.

Thanks for the improved description. I would not have come up with that on my own, as I'm not a bioinformatician.