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Bio-Grep-v0.9.0
River stage zero No dependents

Changes for version 0.9.0 - 2007-08-08

  • 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

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