[Debian-med-packaging] Bug#601568: bwa: Bug in scoring matrix incurs errors in indel calling.

[Charles Plessy]

Package: bwa
Version: 0.5.8a-1
Severity: important

As discussed in the upstream mailing list, bwa 0.5.8a has a scoring
matrix that produces some scientifically wrong results. This impairs
some uses of the program, but not all.

http://sourceforge.net/mailarchive/forum.php?thread_name=alpine.DEB.1.10.1006151606060.21551%40deskpro19670.dynamic.sanger.ac.uk&forum_name=bio-bwa-help

The scoring matrix has been corrected in version 0.5.8c, that I will
upload shortly. This version contains a couple of other changes:

 ChangeLog           |   43 ++++
 INSTALL             |    9 +
 Makefile.am         |   13 +
 autogen.sh          |    2 
 bwa.1               |    2 
 bwa.txt             |  452 ----------------------------------------------------
 bwape.c             |    2 
 bwt_gen/Makefile.am |    4 
 cleanup.sh          |    1 
 config.h.in         |  157 ++++++++++++++++++
 configure.in        |   49 +++++
 debian/changelog    |   12 +
 debian/control      |    2 
 debian/copyright    |  115 +++++++------
 m4/acx_pthread.m4   |  271 +++++++++++++++++++++++++++++++
 main.c              |    2 
 sracsfq2fq.pl       |   14 +
 stdaln.c            |   10 -
 18 files changed, 649 insertions(+), 511 deletions(-)

(debdiff attached).

As a scientist, I do not feel like distributing bwa 0.5.8a in
Squeeze. Likewise, I would not feel like backporting the correction of
the scoring matrix to 0.5.8a, because the changelog metions other bug
fixes, and I do not want to take the responsibility to distribute a
modified version from which these corrections would be excluded.

If it is not possible to replace 0.5.8a by 0.5.8c (which is completely
understandable and accepted in advance), then I would recommend to
simply remove it, especially that we do not distribute bwa in Lenny.


Have a nice day,

-- 
Charles Plessy
Debian Med packaging team
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan
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