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

[Charles Plessy <plessy@debian.org>]

Le Fri, Apr 10, 2020 at 06:07:57AM +0200, Matthias Klumpp a écrit :
> 
> Hmm, if those bed files can easily converted into their textual
> representation (which presumably is their preferred form of
> modification) just adding a hint that this is possible is probably
> enough for Debian.

Hi Matthias and everybody,

for scientific data, the "preferred form of modification" is a rather
misleading concept.  The pedigree files in PLINK are telling which gene
variants are found in which person, and therefore modifying them does
not make much sense.

Also, in general, text representations are not necessarly the preferred
form for modification of scientific data, because it .  For instance,
with the "BAM" format, some tools can operate directly on binary
streams. Other example, some data (like DNA sequenes produced by Oxford
Nanopore sequencers) is in HDF5, which in theory might be serialised in
text format with third-party tools, but in practice will always be
handled in binary form.

I think that what was important to show here is that these files are
example data in a standard format, and not a deliberate obsfucation of
functional parts of the software (like binary blobs in the kernel,
minified Javascript, etc).

Have a nice day,

Charles

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