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.
>
>
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