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2012-09-06	Florent Angly	Packing methods inside IndexedBase	commit \| commitdiff \| tree
2012-09-06	Florent Angly	More IndexedBase work	commit \| commitdiff \| tree
2012-09-06	Florent Angly	More DB building code in IndexedBase	commit \| commitdiff \| tree
2012-09-06	Florent Angly	Tied hash interfact in IndexedBase module	commit \| commitdiff \| tree
2012-09-05	Florent Angly	IndexedBase module	commit \| commitdiff \| tree
2012-09-05	Florent Angly	Using Bio::DB::Indexed::Stream instead of Bio::DB:...	commit \| commitdiff \| tree
2012-09-05	Florent Angly	Using same packing for Qual as for Fasta	commit \| commitdiff \| tree
2012-09-05	Florent Angly	Handle empty sequences gracefully	commit \| commitdiff \| tree
2012-09-05	Florent Angly	Typo fix	commit \| commitdiff \| tree
2012-09-05	Florent Angly	Bio::DB::Fasta reports correct alphabet for files with...	commit \| commitdiff \| tree
2012-09-05	Florent Angly	More error checking and some reorganization	commit \| commitdiff \| tree
2012-09-05	Florent Angly	Test update for Bio::DB::Qual	commit \| commitdiff \| tree
2012-09-04	Florent Angly	Use File::Spec for portable file names	commit \| commitdiff \| tree
2012-09-04	Florent Angly	Fixed a typo in POD	commit \| commitdiff \| tree
2012-08-27	Florent Angly	Removed some undef warnings	commit \| commitdiff \| tree
2012-08-27	Florent Angly	Remove some temporary code	commit \| commitdiff \| tree
2012-08-27	Florent Angly	Prevent warning 'Subroutine path redefined'	commit \| commitdiff \| tree
2012-08-27	Florent Angly	Use File::Spec::catfile() for portable filenames	commit \| commitdiff \| tree
2012-08-27	Florent Angly	POD update, and return values for clarity	commit \| commitdiff \| tree
2012-08-27	Florent Angly	Formatting and consistent tabulation	commit \| commitdiff \| tree
2012-08-25	Florent Angly	Cannot recommend FClone::Fast over Clone because its...	commit \| commitdiff \| tree
2012-08-08	Florent Angly	Clone::Faster as a faster alternative to Clone. On...	commit \| commitdiff \| tree
2012-08-08	Florent Angly	Make Bio::Tools::Primer3 use the clone() method from...	commit \| commitdiff \| tree
2012-08-08	Florent Angly	Documented that Clone and Storable modules are used...	commit \| commitdiff \| tree
2012-08-04	Florent Angly	Changes file update	commit \| commitdiff \| tree
2012-08-02	Florent Angly	Merge branch 'master' of github.com:bioperl/bioperl...	commit \| commitdiff \| tree
2012-08-02	Florent Angly	Cosmetic changes	commit \| commitdiff \| tree
2012-08-02	Florent Angly	Fixed crash when feature does not have the requested tag	commit \| commitdiff \| tree
2012-08-02	Florent Angly	Using File::Spec->catfile for better platform compatibility	commit \| commitdiff \| tree
2012-08-02	Florent Angly	Indentation cleaning	commit \| commitdiff \| tree
2012-06-27	Florent Angly	Changes file update	commit \| commitdiff \| tree
2012-06-18	Florent Angly	Fixed POD syntax issue	commit \| commitdiff \| tree
2012-06-18	Florent Angly	Fixed some POD syntax problems and some typos	commit \| commitdiff \| tree
2012-06-09	Florent Angly	Merge branch 'master' of github.com:bioperl/bioperl...	commit \| commitdiff \| tree
2012-06-09	Florent Angly	Allow ID of 0 in trait files	commit \| commitdiff \| tree
2012-06-09	Florent Angly	Skip tree nodes without trait value	commit \| commitdiff \| tree
2012-05-21	Florent Angly	Option to ignore leaves with missing trait value when...	commit \| commitdiff \| tree
2012-05-21	Florent Angly	POD update and indentation cleaning	commit \| commitdiff \| tree
2012-05-21	Florent Angly	Return undef if column number is exceeded in add_trait()	commit \| commitdiff \| tree
2012-05-21	Florent Angly	POD update and minor changes to add_trait()	commit \| commitdiff \| tree
2012-05-17	Florent Angly	Merge branch 'master' of github.com:bioperl/bioperl...	commit \| commitdiff \| tree
2012-05-17	Florent Angly	New get_taxon() option to help with ambiguous taxon...	commit \| commitdiff \| tree
2012-05-10	Florent Angly	Added a help message, updated POD doc, misc small code...	commit \| commitdiff \| tree
2012-05-10	Florent Angly	Actually make sure that input is a valid file	commit \| commitdiff \| tree
2012-05-10	Florent Angly	Fixed bug where one could pass a directory instead...	commit \| commitdiff \| tree
2012-05-10	Florent Angly	Fixed POD typo, inconsistent indentation and 'variable...	commit \| commitdiff \| tree
2012-05-09	Florent Angly	Removed a rogue temporary test file	commit \| commitdiff \| tree
2012-05-08	Florent Angly	Fixed bug in Bio::DB::Taxonomy::list. One can now create...	commit \| commitdiff \| tree
2012-05-08	Florent Angly	Fixed mistake introduced in previous commit	commit \| commitdiff \| tree
2012-05-08	Florent Angly	Added a get_num_taxa() method to all Bio::DB::Taxonomy...	commit \| commitdiff \| tree
2012-05-08	Florent Angly	Fixed malformed POD in Bio::Tree::Tree method descriptions	commit \| commitdiff \| tree
2012-05-07	Florent Angly	Module for the Silva taxonomy	commit \| commitdiff \| tree
2012-05-07	Florent Angly	More optimizations	commit \| commitdiff \| tree
2012-05-07	Florent Angly	More code stramlining	commit \| commitdiff \| tree
2012-05-07	Florent Angly	To save memory, don't store rank information when no...	commit \| commitdiff \| tree
2012-05-07	Florent Angly	Misc changes	commit \| commitdiff \| tree
2012-05-07	Florent Angly	More small changes	commit \| commitdiff \| tree
2012-05-07	Florent Angly	More small changes	commit \| commitdiff \| tree
2012-05-07	Florent Angly	Small tweak	commit \| commitdiff \| tree
2012-05-07	Florent Angly	Speed improvements	commit \| commitdiff \| tree
2012-05-06	Florent Angly	Merge branch 'tree_bugfix'.	commit \| commitdiff \| tree
2012-05-06	Florent Angly	Greengenes is a local database	commit \| commitdiff \| tree
2012-05-06	Florent Angly	Fixed bug introduced by commit 3d1882a78c1c039461173b5b224d6...	commit \| commitdiff \| tree
2012-05-06	Florent Angly	POD doc update	commit \| commitdiff \| tree
2012-05-06	Florent Angly	POD doc clarifications	commit \| commitdiff \| tree
2012-05-06	Florent Angly	More SeqBuilder tests	commit \| commitdiff \| tree
2012-05-05	Florent Angly	Greengenes is a local database	commit \| commitdiff \| tree
2012-04-13	Florent Angly	New method, get_lineage_string in Bio::Tree::TreeFunctionsI	commit \| commitdiff \| tree
2012-04-13	Florent Angly	Removed another 'undef' warning	commit \| commitdiff \| tree
2012-04-13	Florent Angly	Removed some 'uninitialized' warnings	commit \| commitdiff \| tree
2012-04-13	Florent Angly	Taxonomy test updates	commit \| commitdiff \| tree
2012-04-13	Florent Angly	Small POD and code updates for Greengenes taxonomy	commit \| commitdiff \| tree
2012-04-12	Florent Angly	Fixed bug in list taxonomies: taxa with same name are...	commit \| commitdiff \| tree
2012-04-12	Florent Angly	Fixed 2 failing Entrez tests	commit \| commitdiff \| tree
2012-04-12	Florent Angly	Small optimizations in list taxonomies	commit \| commitdiff \| tree
2012-04-12	Florent Angly	Large speed improvements	commit \| commitdiff \| tree
2012-04-11	Florent Angly	Distinguish IDs from Bio::DB::Taxonomy::list and greengenes...	commit \| commitdiff \| tree
2012-04-11	Florent Angly	small test update	commit \| commitdiff \| tree
2012-04-11	Florent Angly	Basic Greengenes taxonomy support	commit \| commitdiff \| tree
2012-04-11	Florent Angly	More informative error messages	commit \| commitdiff \| tree
2012-04-11	Florent Angly	Removing extraneous code	commit \| commitdiff \| tree
2012-04-11	Florent Angly	Cross-platform filenames	commit \| commitdiff \| tree
2012-04-11	Florent Angly	Use a platform-independent temp directory, not /tmp	commit \| commitdiff \| tree
2012-03-23	Florent Angly	Preferring get_all_tags() and get_tag_values() over...	commit \| commitdiff \| tree
2012-03-07	Florent Angly	Sane deprecation	commit \| commitdiff \| tree
2012-03-07	Florent Angly	Bio::SimpleAlign compliance with Bio::FeatureHolderI	commit \| commitdiff \| tree
2012-03-07	Florent Angly	Bio::Seq compliance with Bio::FeatureHolderI	commit \| commitdiff \| tree
2012-03-07	Florent Angly	POD update: no mention of add_seqfeatures(@feats)	commit \| commitdiff \| tree
2012-03-07	Florent Angly	Removed tabs	commit \| commitdiff \| tree
2012-03-07	Florent Angly	Clarification on coordinate system	commit \| commitdiff \| tree
2012-03-06	Florent Angly	Better return non-compiled regexp so that it is easier...	commit \| commitdiff \| tree
2012-03-05	Florent Angly	Renamed test file for consistency	commit \| commitdiff \| tree
2012-03-05	Florent Angly	Formatting	commit \| commitdiff \| tree
2012-03-05	Florent Angly	Renamed test file for consistency	commit \| commitdiff \| tree
2012-03-05	Florent Angly	SeqFeature::Annotated tests	commit \| commitdiff \| tree
2012-03-05	Florent Angly	Gene gets its own test file too	commit \| commitdiff \| tree
2012-03-05	Florent Angly	FeaturePair gets its own test file	commit \| commitdiff \| tree
2012-03-05	Florent Angly	Updated method names to follow Bio::SeqFeature::Generic...	commit \| commitdiff \| tree
2012-03-05	Florent Angly	Separate test file for Bio::SeqFeature::Computation	commit \| commitdiff \| tree
2012-03-05	Florent Angly	For SeqFeatureI compliance, Bio::SeqFeature::Generic...	commit \| commitdiff \| tree
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