[Debian-med-packaging] Comments regarding samblaster_0.1.24-1_amd64.changes

[Thorsten Alteholz]

Hi Steffen,

I marked your package for accept and don't want to withhold the comment from our FTP trainee.

  Thorsten



ACCEPT

samblaster was nicely Debianized with modern Debian practice.
The C++ program is written entirely by Greg Faust the upstream author
with very minor changes from other contributors for things like
macOS support.

Looks good to me!

Some nitpickings:

1. MIT vs Expat

I recall reading somewhere that it is preferable to use "Expat"
rather than "MIT" as the name of the license if it indeeds matches
the Expat variant of the MIT license in debian/copyright.
That appears to be the case here, so, maybe call it "Expat" instead?
:-)


2. License and authorship of of SAMBLASTER_Supplemental.pdf

The PDF file seems to be a supplement of the main journal paper
which Gregory G. Faust and Dr. Ira M. Hall co-wrote
(see https://academic.oup.com/bioinformatics/article/30/17/2503/2748175)
I suppose it is the case where G.G. Faust did the bulk of the work while
I.M. Hall provided supervision and guidance.

Indeed, in the supplemental material, the authors uses "we" for
self-reference, and, in the footnote:

  ©The Author(s) 2014.  This is the authors' un-refereed supplemental
  material for the following publication: Faust, G.G. and Hall, I.M.,
  SAMBLASTER: fast duplicate marking and structural variant read
  extraction. _Bioinformatics_ Sept. 2014; 30(17): 2503-2505.

No license was explicitly mentioned in the PDF file, but then,
it was the upstream author Gregory Faust's decision to place
SAMBLASTER_Supplemental.pdf alongside the LICENSE.txt file
citing the MIT License, so I think it is safe to say that the PDF file
is also placed under the MIT/Expat License.

The PDF file was printed/generated from Microsoft Word file
SAMBLASTER_SupplementalV5.docx whose author is "gf4ea", which is
Greg Faust's handle at the University of Virginia (gf4ea at virginia.edu).

So, while the PDF might have been written entirely by Greg Faust,
it is recommended to list Ira M. Hall is its co-author too, so perhaps
it would be better to add these lines to debian/copyright?

    Files: SAMBLASTER_Supplemental.pdf
    Copyright: 2014 Gregory G. Faust <gf4ea at virginia.edu>
               2014 Ira M. Hall <imh4y at virginia.edu>
    License: Expat

Of course, a clarification from Greg Faust would be helpful too.

And, if the license for the PDF file is clear, then I personally would
list it in debian/samblaster.docs too, even though it does take up 107kB
of space.  ;-)

Cheers,

Anthony Fok (Debian FTP Trainee)