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2012-10-29	Florent Angly	PrimarySeq::length() speedup	commit \| commitdiff \| tree
2012-10-10	Florent Angly	Better 0-length sequence support for Bio::DB::Qual...	commit \| commitdiff \| tree
2012-10-10	Florent Angly	Better support for 0-length sequences	commit \| commitdiff \| tree
2012-09-24	Florent Angly	Merge branch 'master' of github.com:bioperl/bioperl...	commit \| commitdiff \| tree
2012-09-24	Florent Angly	Fixed an untested regression in Bio::DB::Fasta	commit \| commitdiff \| tree
2012-09-10	Florent Angly	Regexp to match RNA on request only	commit \| commitdiff \| tree
2012-09-10	Florent Angly	Fixed indentation	commit \| commitdiff \| tree
2012-09-10	Florent Angly	Reversed problematic commit 8334d175ffba095a9447038d421cac0d...	commit \| commitdiff \| tree
2012-09-10	Florent Angly	Merge branch 'amplicons'	commit \| commitdiff \| tree
2012-09-10	Florent Angly	Merge branch 'master' of github.com:bioperl/bioperl...	commit \| commitdiff \| tree
2012-09-10	Florent Angly	Removed some comments	commit \| commitdiff \| tree
2012-09-10	Florent Angly	Compound ID can now includ the strand	commit \| commitdiff \| tree
2012-09-10	Florent Angly	Bio::DB::IndexedBase compliance with Bio::DB:SeqI and...	commit \| commitdiff \| tree
2012-09-10	Florent Angly	Fixed typo	commit \| commitdiff \| tree
2012-09-10	Florent Angly	Fixed silly error	commit \| commitdiff \| tree
2012-09-10	Florent Angly	Updated Bio::DB::SeqI POD according to info in Bio...	commit \| commitdiff \| tree
2012-09-10	Florent Angly	Updated Changes file	commit \| commitdiff \| tree
2012-09-10	Florent Angly	Explicit variable name instead of Bio/DB/Qual.pm	commit \| commitdiff \| tree
2012-09-10	Florent Angly	Handle RNA and IUPAC characters in Bio::DB::Fasta	commit \| commitdiff \| tree
2012-09-10	Florent Angly	Updated Changes file	commit \| commitdiff \| tree
2012-09-10	Florent Angly	Better alphabet detection method that honors IUPAC...	commit \| commitdiff \| tree
2012-09-10	Florent Angly	Fasta and Qual only use the IndexedBase base	commit \| commitdiff \| tree
2012-09-10	Florent Angly	POD update	commit \| commitdiff \| tree
2012-09-09	Florent Angly	POD update	commit \| commitdiff \| tree
2012-09-09	Florent Angly	Fixed bug introduced in recent commit	commit \| commitdiff \| tree
2012-09-09	Florent Angly	makeid logic in IndexedBase	commit \| commitdiff \| tree
2012-09-09	Florent Angly	Added error checks on Fasta into Qual	commit \| commitdiff \| tree
2012-09-09	Florent Angly	Small simplificatiosn	commit \| commitdiff \| tree
2012-09-09	Florent Angly	Test -makeid option	commit \| commitdiff \| tree
2012-09-09	Florent Angly	More streamlining	commit \| commitdiff \| tree
2012-09-09	Florent Angly	Support for specifying sequence strand	commit \| commitdiff \| tree
2012-09-09	Florent Angly	Using the _parse_compound_id() method	commit \| commitdiff \| tree
2012-09-09	Florent Angly	Removed a test because method length() does not take...	commit \| commitdiff \| tree
2012-09-09	Florent Angly	Storing number of residues in index file	commit \| commitdiff \| tree
2012-09-09	Florent Angly	Fix to avoid a warning	commit \| commitdiff \| tree
2012-09-09	Florent Angly	Variable name changes	commit \| commitdiff \| tree
2012-09-09	Florent Angly	Small changes	commit \| commitdiff \| tree
2012-09-09	Florent Angly	Renamed function more appropriately	commit \| commitdiff \| tree
2012-09-09	Florent Angly	More methods in IndexedBase	commit \| commitdiff \| tree
2012-09-09	Florent Angly	Misleading variable name	commit \| commitdiff \| tree
2012-09-09	Florent Angly	Cosmetic changes	commit \| commitdiff \| tree
2012-09-09	Florent Angly	Small changes	commit \| commitdiff \| tree
2012-09-09	Florent Angly	Fixed a couple of typos and worked on consistent indentaion	commit \| commitdiff \| tree
2012-09-09	Florent Angly	Sub to parse compound IDs	commit \| commitdiff \| tree
2012-09-08	Florent Angly	Fixed bug affecting Bio::DB::SeqFeature	commit \| commitdiff \| tree
2012-09-08	Florent Angly	Fixing some failing tests	commit \| commitdiff \| tree
2012-09-08	Florent Angly	Renamed test files for consistency	commit \| commitdiff \| tree
2012-09-08	Florent Angly	POD reorganization	commit \| commitdiff \| tree
2012-09-08	Florent Angly	Fixed test	commit \| commitdiff \| tree
2012-09-08	Florent Angly	POD update	commit \| commitdiff \| tree
2012-09-08	Florent Angly	Test header()	commit \| commitdiff \| tree
2012-09-08	Florent Angly	fh() moved to _fh() in IndexedBase	commit \| commitdiff \| tree
2012-09-08	Florent Angly	POD update	commit \| commitdiff \| tree
2012-09-08	Florent Angly	POD update	commit \| commitdiff \| tree
2012-09-08	Florent Angly	POD update	commit \| commitdiff \| tree
2012-09-08	Florent Angly	Improved tests	commit \| commitdiff \| tree
2012-09-07	Florent Angly	POD update	commit \| commitdiff \| tree
2012-09-07	Florent Angly	Big POD update	commit \| commitdiff \| tree
2012-09-07	Florent Angly	New option to remove index file when done	commit \| commitdiff \| tree
2012-09-07	Florent Angly	More improvements	commit \| commitdiff \| tree
2012-09-07	Florent Angly	Some more streamlining	commit \| commitdiff \| tree
2012-09-07	Florent Angly	Moved get_seq_stream to IndexedBase	commit \| commitdiff \| tree
2012-09-07	Florent Angly	Migrating more code to IndexedBase	commit \| commitdiff \| tree
2012-09-07	Florent Angly	Code simplification	commit \| commitdiff \| tree
2012-09-07	Florent Angly	Small POD change	commit \| commitdiff \| tree
2012-09-07	Florent Angly	Misc changes	commit \| commitdiff \| tree
2012-09-07	Florent Angly	User can supply an arbitrary name for the index file	commit \| commitdiff \| tree
2012-09-06	Florent Angly	Support indexing an arbitrary set of files	commit \| commitdiff \| tree
2012-09-06	Florent Angly	Better error checking	commit \| commitdiff \| tree
2012-09-06	Florent Angly	Slight code rearrangement	commit \| commitdiff \| tree
2012-09-06	Florent Angly	Support for indexing multiple files	commit \| commitdiff \| tree
2012-09-06	Florent Angly	More modularity and code reuse	commit \| commitdiff \| tree
2012-09-06	Florent Angly	Removed some temporary code	commit \| commitdiff \| tree
2012-09-06	Florent Angly	Small changes	commit \| commitdiff \| tree
2012-09-06	Florent Angly	Removed unneeded pragmas	commit \| commitdiff \| tree
2012-09-06	Florent Angly	More IndexedBase work	commit \| commitdiff \| tree
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
2012-08-21	Florent Angly	Merge branch 'master' into amplicons	commit \| commitdiff \| tree
2012-08-18	Florent Angly	IUPAC matches RNA sequences too	commit \| commitdiff \| tree
2012-08-18	Florent Angly	Typo fixes	commit \| commitdiff \| tree
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