🚀 go-pugleaf

All,

Late.....but finally here...the Feb. newsletter.

Ed
-- 
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| Ed Griffiths, Acedb development, Informatics Group,                    |
|        Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus,  |
|               Hinxton, Cambridge CB10 1SA, UK                          |
|                                                                        |
| email: edgrif@sanger.ac.uk  Tel: +44-1223-494780  Fax: +44-1223-494919 |
 ------------------------------------------------------------------------


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  ACEDB User Group Newsletter - February 2004
  ###########################################

If you want to have this newsletter mailed to you *_or_* you want to
make comments/suggestions about the format/content then send an email to
acedb@sanger.ac.uk <mailto:acedb@sanger.ac.uk>.

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A month of mostly bug fixes.

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    New Features
    ************


      AceDB compiles on RedHat 9
      ++++++++++++++++++++++++++

We now have AceDB compiling on the RedHat 9 version of Linux which uses
the newer versions of Glib and the GTK toolkit. You need to get the
latest monthly release and set the ACEDB_MACHINE environment variable to
"LINUX_4_RH9" to compile on RedHat 9.

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    Bugs Fixed
    **********


      Embl dumping bugs
      +++++++++++++++++

Embl dumping was broken for one release because in fixing a problem with
checking that #EMBL_dump_info is specified correctly I forgot to ensure
that I jumped back out of the #EMBL_dump_info submodel before checking
for further tags, pathetic.

Also, for worm group, I have disabled the accession number output
because they have changed their model completely and the existing code
simply won't work. They now put in the accession number via an external
script.


      Blixem crash
      ++++++++++++

blixem was crashing with some sequences/homologies and it turns out that
this is because some gaps array mappings were not being clipped properly
resulting in blixem attempting to access non-existent sequence data.
This is now fixed.


      Confirmed introns crash
      +++++++++++++++++++++++

Sometimes confirmed_introns caused acedb to crash, it turns out this was
caused by the transition from fmap working at the "whole clone" level,
i.e. bringing in all of any clones required to make up an fmap, to fmap
clipping adjacent clones.

In this case it meant that confirmed introns of an adjoining clone were
not getting mapped, this was fine until we had the situation where we
had a confirmed intron being confirmed from 2 different sources. This is
effectively two introns with the same coords but different
confirmations. The first one did not get mapped correctly but because
the second one had the same coords the code assumed it had been mapped
and so tried to process the second intron as though everything was ok.
Now when introns have the same coords we check to see if the previous
intron was actually mapped.


      Composite class bug
      +++++++++++++++++++

Fix bug in pickRegisterClassMasks(), code assumed that a bsFlatten array
only has 4 byte fields in it but this is not true on the Alpha as one of
the union members is a pointer which is 8 bytes. This bug prevented
acedb from initialising on the Alphas if composite classes were declared
in subclasses.wrm.


      Blixem sort bug
      +++++++++++++++

Fix bug which meant that only the sequences passed in from acedb got
sorted initially, the sequences obtained from another source (e.g.
pfetch) did not get sorted until user selected a sort method. Now all
sequences are sorted from the start.

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    Developers Corner
    *****************


      xacez target
      ++++++++++++

As part of the ZMap development it is our intention to add a "ZMap"
display type to acedb and to facilitate development Rob has created a
new target called xacez.

This target is not compileable at the moment but will become so as we
develop the ZMap display.


      More on the Blixem crash
      ++++++++++++++++++++++++

The main cause of this problem is two fold: the homology conversion
routine was not recording any clipping of the main homology start/end
coordinates by the SMapMap() call. More seriously, sMapLocalMap() does
not take any notice of the start/end coords that are passed to it and
does not return a mapping status to indicate any clipping.

Currently this is fixed by mapping each gap separately so we can detect
if it gets mapped correctly. The better fix is to sort out
sMapLocalMap() and this will be done in the next month or so.

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    Feb monthly build now available.
    ********************************

You can pick up the monthly builds from:

*Sanger users*
    ~acedb/RELEASE.DEVELOPMENT
*External users*
    http://www.acedb.org/Software/Downloads/monthly.shtml
    <http://www.acedb.org/Software/Downloads/monthly.shtml>

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Ed Griffiths <edgrif@sanger.ac.uk> <mailto:edgrif@sanger.ac.uk>

Last modified: Tue Apr 13 17:30:49 BST 2004