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Bug#439996: marked as done (ITP: ngila -- global pairwise alignments with logarithmic and affine gap costs)

Your message dated Mon, 01 Sep 2008 11:59:32 -0600
with message-id <E1KaDga-0003f0-9a@merkel.debian.org>
and subject line WNPP bug closing
has caused the Debian Bug report #439996,
regarding ITP: ngila -- global pairwise alignments with logarithmic and affine gap costs
to be marked as done.

This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.

(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact owner@bugs.debian.org
immediately.)


-- 
439996: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=439996
Debian Bug Tracking System
Contact owner@bugs.debian.org with problems
--- Begin Message --- 
Package: wnpp
Severity: wishlist
Owner: Charles Plessy <charles-debian-nospam@plessy.org>

  Package name    : ngila
  Version         : 1.2.1
  Upstream Author : Reed A. Cartwright <reed@scit.us> or <racartwr@ncsu.edu>
  URL             : http://scit.us/projects/ngila/
  License         : GPL v3 or later
  Programming Lang: C++
  Description     : global pairwise alignments with logarithmic and affine gap costs

 Ngila is an application that will find the best alignment of a pair
 of sequences using log-affine gap costs, which are the most
 biologically realistic gap costs.
 .
 Ngila implements the Miller and Myers (1988) algorithm in order to
 find a least costly global alignment of two sequences given homology
 costs and a gap cost. Two versions of the algorithm are
 included: holistic and divide-and-conquer. The former is faster but
 the latter utilizes less memory. Ngila starts with the
 divide-and-conquer method but switches to the holistic method for
 subsequences smaller than a user-established threshold. This improves
 its speed without substantially increasing memory requirements. Ngila
 also allows users to assign costs to end gaps that are smaller than
 costs for internal gaps. This is important for aligning using the
 free-end-gap method.
 .
 Ngila is published in Cartwright RA Bioinformatics 2007
 23(11):1427-1428; doi:10.1093/bioinformatics/btm095
 .
  Homepage: http://scit.us/projects/ngila/

-- 
Charles Plessy
Debian-Med packaging team
Wako, Saitama, Japan

--- End Message ---
--- Begin Message --- 
Hello,

This is an automatic mail sent to close the ITP you have reported or 
are involved with.

Your ITP wnpp bug is being closed because of the following reasons:
- It is, as of today, older than 365 days.
- It hasn't had any activity recently.

As this is an automatic procedure, it could of course have something
wrong and probably it would be closing some bugs that are not 
intended by owners and submitters (like you) to be closed, for
example if the ITP is still of your interest, or there has been 
some kind of activity around it. In that case, please reopen the
bug, do it, DO IT NOW! (I don't want to be blamed because of
mass closing and not let people know that they can easily reopen
their bugs ;-).

To re-open it, you simply have to mail control@bugs.debian.org
with a body text like this:

 reopen 439996
 stop

Further comments on the work done in the bug sent to
439996@bugs.debian.org would be truly welcomed.
Anyway, if you have any kind of problems when dealing with
the BTS, feel free to contact me and I'd be more than happy to help
you on this: <damog@debian.org>.

A similar process is being applied to other kind of wnpp bugs.

Thanks for your cooperation,

 -- David Moreno Garza <damog@debian.org>.

--- End Message ---
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