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Bio-Grep-v0.0.4
River stage zero No dependents

Changes for version 0.0.4 - 2007-03-07

  • 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

Documentation

bgrep
Wrapper for several suffix array tools

Modules

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

Other files