[Debian-med-packaging] How are bed files created? (Was: trinculo_0.96+dfsg-1_amd64.changes REJECTED)

[Liubov Chuprikova]

Hi Andreas and Pranav,

On Thu, 9 Apr 2020 at 10:06, Andreas Tille <andreas at an3as.eu> wrote:

> Hi folks,
>
> could anybody who works with sequences comment on this?
>

I have just checked the file and as Michael said during the Jitsi meeting,
Plink (in Debian) uses such a format. I just tried quickly and it's
possible to convert the file back to flat format:

plink1 --bfile examples/genotypes --recode --tab --out genotypes --noweb

and back to binary, here three files will be created: *.bed, *.fam, *.bim
(those are in examples folder):

plink1 --file genotypes --make-bed --out genotypes --noweb

So, the binary can be excluded and replaced by a flat version of the file.

Regards,
Liubov

In the worst case we would need to remove the bed file from the source
> archive and as I learned recently fetch it in autopkgtest from remote.
>
> Kind regards
>
>      Andreas.
>
> On Wed, Apr 08, 2020 at 09:00:10PM +0000, Scott Kitterman wrote:
> >
> > In debian/README.test it says:
> >
> > Notes on how this package can be tested.
> >
> > This package can be tested by running the provided test:
> >
> >     sh run-unit-test
> >
> > in order to confirm its integrity.
> >
> > This file is not included, so README.test should be removed.
> >
> > How is the file examples/genotypes.bed generated?  If it's in its
> > preferred form of modification, then that should be documented, since it
> is
> > not clearly so.  If it's not, the source and the tools need to be in
> Debian
> > and that should be documented.
> >
> > Please fix/remove the above and re-upload.
> >
> > Scott K
> >
> >
> >
> >
> > ===
> >
> > Please feel free to respond to this email if you don't understand why
> > your files were rejected, or if you upload new files which address our
> > concerns.
> >
> >
> > _______________________________________________
> > Debian-med-packaging mailing list
> > Debian-med-packaging at alioth-lists.debian.net
> >
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>
> --
> http://fam-tille.de
>
>
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