Re: Help needed: Bug#962292: ITP: flye -- de novo assembler for single molecule sequencing reads using repeat graphs
Hi Steffen,
On Sun, Jun 07, 2020 at 01:10:25AM +0200, Steffen Möller wrote:
> > > The suspicion that the minimap2 code copy in flye is patched. I have
> > > attached the diff between the Debian packaged minimap2 which actually
> > > introduces --secondary-seq.
> > >
> > > I wonder if there is some volunteer to talk to both upstreams to
> > > merge the patch.
> >
> > I'll do that.
>
> https://github.com/fenderglass/Flye/issues/275
Thanks a lot.
> We could adopt that patch, but this would open a can of worms - our
> patches preferably are only technical for Debian's peculiarities.
>From my reading the patch should not change the original behaviour.
I agree that we should be very carefully what patch to take over.
However, I've also patched bamtools for tiddit
https://salsa.debian.org/med-team/bamtools/-/blob/master/debian/patches/tiddit.patch
(I admit its always a bit scary for me if I do not get any input on
questions about this[1]) and we are currently adding a patch to add an
ocaml interface to mcl.
I'm not sure what might be the best option in the current case so
further opinions here are welcome and may be there is a quick response
to the issue you have opened.
Kind regards
Andreas.
[1] https://lists.debian.org/debian-med/2020/05/msg00202.html
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