Revision history for Perl extension Bio::Grep.

0.8.2  Tue Jul  31 16:11:00 2007
    - POD improvements 
    - more tests
    - code cleanup (Bio::Grep::Root)
    
0.8.1  Tue Jul  31 16:11:00 2007
    - POD improvements 
    - code cleanup
    - Cookbook
    - removed directory Container (unnecessary and confusing)
    - Error messages more consistent
    - more tests
    
0.8.0  Mon Jul  30 19:20:00 2007
    - POD improvements
    - direct_and_rev_com
    - RE back-end
    - use Fatal qw(open close), removed own exception handling
    - replaced global dirhandle in BackendI with local dirhandle
    - more tests
    - renamed generate_database_out_of_fastafile() to
      generate_database()
    - renamed Backends/ to Backend  
    - Bugfixes:
        - GUUGle back-end confused when sequence description missing

0.7.0  Tue Jul  24 16:55:00 2007
    - POD improvements:
       * added section exception handling in Bio::Grep
       * removed exception handling in the back-ends
         SYNOPSIS
       * polishing 
    - Bugfixes:
       * Agrep back-end: called two times 

0.6.0  Tue Mar  27 14:09:10 2007
    - POD improvements
    - BackendI code cleanups 
    - renamed feature QUERYFILE to QUERY_FILE
    - did not throw an exception when query and query_file
      are set
    - more tests
    - removed $res->get_gene_id and $res->alignment_to_csv
    
0.5.0  Sat Mar  23 17:34:20 2007
    - POD improvements
    - different values for upstream and downstream in GUUGle
    - did not throw an exception when alphabet file was missing
    - database generation in bgrep broken
    - more tests

0.4.0  Fri Mar  23 15:59:00 2007
    - hxdrop, exdrop flags for vmatch
    - more tests
    - POD improvements
    - long queries in vmatch broken

0.3.0  Thu Mar  12 15:49:19 2007
    - POD improvements
    - Filter broken with GUUGle
    - more tests

0.2.0  Thu Mar  11 15:16:39 2007
    - POD improvements
    - small bgrep improvements
    - more tests
    - GUUGle: upstream/downstream with query_file broken

0.1.0  Thu Mar  09 18:58:09 2007
    - POD improvements
    - more tests
    - small bgrep improvements
    - upstream and downstream in GUUGle broken
    - maxhits in GUUGle broken
    - test searches for EMBOSS

0.0.4  Thu Mar  08 21:34:17 2007
    - forgot to include perlcritic test and 00.checkprereq
    - POD improvements
    - Cleanup: removed unnecessary use lines
    - switched to Data::Dumper for settings->to_string()
    - more tests
    - Vmatch did not calculate query_length if complete(0)
    - GUUGle: reverse_complement was switched (revcom(1) was revcom(0)
      and vice versa).
    - Agrep: did not store $res->query  
    
0.0.3  Wed Mar  07 15:13:26 2007
    - POD improvements
    - more tests (Devel::Cover)
    - Vmatch now throws an exception if showdesc + upstream instead of
      just a warning
    - skip tests if bioperl and/or bioperl-run is not found  
    
0.0.2  Thu Mar  06 01:03:43 2007
   - POD improvements
   - bgrep did not accept -man and -help
   
0.0.1  Thu Mar  05 15:26:11 2007
   first public release on cpan
   - renamed to Bio::Grep (from Weigel::Search)
   - added backend GUUGle
   - added bgrep
   - POD improvements
   - renamed querylength to query_length
   - added feature to specify settings in search call