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

[Charles Plessy]

Le Thu, Apr 09, 2020 at 06:21:17PM +0200, Liubov Chuprikova a écrit :
> 
> 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.

Hi all,

indeed, this "bed" file is in binary format; I just found its
description on the plink website:

http://zzz.bwh.harvard.edu/plink/binary.shtml

By the way, it is unfortunate that the ".bed" file extension for "binary
PED files" is also used by the – much more frequently encountered –
"Browser Extensible Data" files that describe features in coordinate
windows on reference DNA sequence files.  (I do not know which one came
first…)  But at the URL above there is a description of the magic number
to identify binary PED files.  Would there be anybody interested in
submitting an entry to the file or the sharedmimeinfo databases ?  That
might help us and the FTP team if such files appear again in new
packages.

Have a nice day,

Charles

-- 
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Akano, Uruma, Okinawa, Japan