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Bio-Grep-v0.9.1
River stage zero No dependents

Changes for version 0.9.1 - 2007-08-15

  • 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

Documentation

Bio::Grep::Cookbook
Bio::Grep Cookbook
bgrep
Wrapper for several suffix array tools

Modules

Bio::Grep
Perl extension for searching in Fasta files
Bio::Grep::Backend::Agrep
Agrep back-end
Bio::Grep::Backend::BackendI
Superclass for all back-ends
Bio::Grep::Backend::GUUGle
GUUGle back-end
Bio::Grep::Backend::RE
Perl Regular Expression back-end
Bio::Grep::Backend::Vmatch
Vmatch back-end
Bio::Grep::Filter::FilterI
Superclass for all filter modules
Bio::Grep::Filter::FilterRemoveDuplicates
Example Filter
Bio::Grep::Root
Superclass for all Bio::Grep* packages
Bio::Grep::SearchResult
Data structure for a back-end search hit
Bio::Grep::SearchSettings
Data structure for all search settings

Other files