GitLab

-description for drosophila-specific file added

Uniprot/SPTREMBL and added support for tetraodon. For what it's worth.

changes to make elegans xrefs work

some changes from the old api which needed introducing here

overridden by command line options or configuration file) and
environment variables removed (since the old valus are now the default
values of exonerate anyway).

Writing to /dev/tty was bad.
(change doesn't affect -d usage)

ryo-string.

KornShell script (which will go away shortly).  I still need to add a
'-d' flag to read a configuration file...

(later today).

maps2db script to work with exonerate mapping, will replace maps2db as soon as we use it for production
handles cigar lines and match location on the 17th schema

  we're going to keep (speed improvment).
* Default score threshold set to 99% (only the top 1% of the alignments
  for a query is kept).  Default minimum percentage of identity is still
  25% for both query and target.
* Changed an array into a hash to catch query-target pairs that has
  already been seen (the alignment with the best score is kept if this
  occurs).

Ability to read [properly formatted] exonerate output instead of
running exonerate.
Smarter Perl.

(100/100==1), nothing major.

Modified error messages.

percent identity, score etc. that at a later stage is supposed to go
into the identity xref table.  The calculation of the percent identity
and the reformatting of cigar lines is carried out by a simple Perl
snippet.