Revision history for Perl extension Bio::Grep.

0.10.5  Sat Jul  26 13:00:00 2008
    - META.yml broken 
    - small cleanup in Vmatch back-end
    - RE backend: switched to $+ and $- to retrieve the positions. 

0.10.4  Fri Jul  25 17:53:00 2008
    - New Perl::Critic passes
    - added Bio:Perl dependencies
    - Bugfix: -blanks in dirnames allowed (thanks Jamie)

0.10.3  Sun Apr  17 12:01:00 2008
    - code cleanup:
        * perlcritic severity 1
    - Bugfix: RNA databases allowed
        
0.10.2  Sun Sep  23 16:08:00 2007
    - code cleanup:
        * renamed test data files
        * perlcritic
        * renamed FilterI->reset to FilterI->reset_filter
          because reset is a buildin function
        * renamed SearchSettings->set to SearchSettings->set_attributes
          cause set is an ambigious name
    - more tests:
        * features.updownstream (more or less moved from guugle/RE specific
          tests)
    - New Features:
        * upstream / downstream in SearchResult
        * reverse_complement in SearchResult
    - Bugfixes:
        * Vmatch: $res->sequence undef when available downstream region
                  to small

0.10.1  Mon Sep  10 11:54:00 2007
    - Minor POD improvements
    - Benchmarks: 
       * generated with Template::Toolkit
       * added vmatch -online
       * ./Build dist asks whether benchmarks should be created

0.10.0  Tue Aug  21 17:00:00 2007
    - POD improvements:
        * methods now grouped in CONSTRUCTOR, ACCESSORS/MUTATORS, PACKAGE
          METHODS, INTERNAL METHODS, ABSTRACT METHODS
        * notes now under IMPORTANT NOTES, not DESCRIPTION  
    - code cleanup:
        * standard testfile "header" now in BioGrepTest, requires ToolSet
    - more tests:
        * features.alignments
    - New Features:
        * Bio::Seq objects as query 
    - Bugfixes:
        - bgrep not installed witch Build.PL
        - Added Bioperl dependency (ticket #28881, thanks siddhartha)
        - $res->query, $res->alignments not equal in back-ends
          now, '(reverse complement)' is added to $query->desc  

0.9.2  Fri Aug  17 12:33:00 2007
    - POD improvements
    - huge performance improvements (RE, Agrep)
    - support for TRE agrep
    - skip EMBOSS alignment calculation when hits can't have gaps
    - idsonly option in bgrep
    - better exception texts
    - sequence description in RE results
    - benchmarks
    
0.9.1  Tue Aug  15 16:10:00 2007
    - POD improvements
    - current directory default datapath (thanks Rick)
    - removed index from *.map files
      (you need to rebuild Agrep/RE dbs!)
    - add -pl option in generate_database (prefix_length)
    - skipping databases generation when database with that
      name already exists 
    - code cleanup: 
         - SearchResult->new wants a hashref as argument
         - RE.pm
         - perltidy
    - tests check warnings
    - more tests (especially GUUGle and RE)
    - maxhits for RE
    - Bugfixes
        - RE pretended to have mismatches feature
    
0.9.0  Mon Aug  08 18:05:00 2007
    - POD improvements
    - generate_database now wants a hashref as argument,
      symlinks fasta file per default, not copies (closes ticket #28691,
      thanks Rick),
      in theory, not only fasta files supported
      Vmatch: non-verbose call of mkvtree. Closes ticket #28720 (thanks Rick)   
    - $sbe->results now throws an deprecated warning 
    - removed HyPa back-end. seems to be a dead project and vmatch covered
      most features
    - Bugfixes
        - tests did not rm temporary directories

0.8.5  Mon Aug  06 13:41:00 2007
    - POD improvements 
    - Bugfixes:
       - SYNOPSIS test failed when Vmatch binary not in path. Closes ticket
         #28656 (thanks Malcolm)
       - arrays not possible with SearchSettings->set (and therefore also not in
         $sbe->search)

0.8.4  Fri Aug  03 14:37:00 2007
    - POD improvements 
    - code cleanup
    - RE back-end much faster

0.8.3  Thu Aug  02 20:00:00 2007
    - POD improvements 
    - dynamically loaded back-ends
    - check arguments of $sbe->get_sequences
    - more tests
    - Bio::Grep now returns a back-end object.
    - Bugfixes:
        - GUUGle back-end confused when sequence description missing
          with up-/downstream regions

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
