Jesse Connell

Thanks a lot for pulling together that summary, Louis. I came across [this paper](https://doi.org/10.1186/s13059-022-02625-x) today, "Sustained software development, not number of citations or journal choice, is indicative of accurate bioinformatic...

Just managed to take a look now-- that looks pretty useful! It looks like the flagstats feature was added in samtools 1.10, so it would need a version bump in...

Oh, even better, then. And I see it now, I didn't realize that it takes either the command "flagstats" or "flagstat" in 1.10 but only "flagstat" in 1.9. Thanks. But,...

Yeah, maybe best to just stick with `flagstat` since then there's no need to touch the package versioning.

@seonyeong00 @adefewings sorry for the delayed response on this. I think this is the result of an outdated test in the test suite and should be fixed in the latest...

Oh yeah, good point, those columns are technically not from the SRA itself so they don't come along with that file. So maybe I've never gotten the biosample info this...

Sounds good, thanks! From SRA folks: If we just append `&retmode=xml` to that same URL, the XML version includes the additional information. But then you'd have to get into the...

Yep, just what I ended up doing. Thanks! As far as the documentation goes I realized what's in the [docstring for 1.79](https://github.com/biopython/biopython/blob/biopython-179/Bio/Align/__init__.py#L968) in the code itself actually *is* correct for...

Not that I've touched any Sunbeam code in a long long while, but for what it's worth, I think dynamically calling or not calling `temp()` on relevant outputs when defining...

No problem, I wasn't even going to bother making an issue at first until I realized the non-ORF matches got missed if there's an ORF one in front. I also...