Revision history for Perl extension Bio::Grep.

0.10.6 Thu Nov 12 18:00:00 2009

• Perl::Tidy 20090616 passes
• Added Test::NoWarnings to tests
• Build dist benchmarks more automated, support for new Sys::Info
• Agrep back-end: check if agrep is TRE in search(), not new()
• use autodie instead of Fatal
• Bugfixes: Fix Warning with Bioperl 1.6.1 (thanks Jeremy)

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