Re: [PATCH] gnu: Add seqtk.

[Ben Woodcroft <b.woodcroft@uq.edu.au>]

On 09/09/16 22:37, Marius Bakke wrote:
> Ben Woodcroft <donttrustben@gmail.com> writes:
>
>> Well, despite the lightness of my touch, it seems the licensing is in now in
>> order.  I've updated the package, here's an updated patch.  Better?
> I don't think this was intended to be a commit message? :)

No indeed, I was responding to a thread so old I suspect it was before 
your time.

> The program seems to bundle {khash,kseq}.h from htslib. Could you try
> replacing them with the files directly from htslib? There are quite a
> few examples of doing this already in bioinformatics.scm.

I see your point, though I'm not sure that htslib is really the home of 
those files, and anyway our htslib doesn't provide them as an output 
since they are not a shared library (I believe).

I've always been a bit fuzzy on what the official policy is, to what 
extent we should remove bundled code, so I'm happy to be corrected. In 
this case since there is clear precedent I don't think we should bother 
removing the bundled files.

> I also think the original description from github is better:
> "Toolkit for processing sequences in FASTA/Q formats".
How about "Toolkit for processing biological sequences in FASTA/Q 
format"? I wanted to make it understandable in a more general context.

I'll push in the next day or two unless there are further comments.
Thanks for the review.
ben