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Apr 22, 2014

  1. Francisco J. Ossandon

    Standardized URL to ""

    instead of ""
    (since the first is the dominant form in the other hundreds files)
    authored April 22, 2014

Apr 21, 2014

  1. changes all issue tracking in preparation for switch to github issues

    authored April 20, 2014

Apr 08, 2014

  1. bosborne

    Minor edits

    authored April 08, 2014

Mar 29, 2014

  1. Dave Messina

    allowing lines with species label ($seq) without $rest, as comes with…

    … yn00
    reported by Volker Brendel
    authored March 28, 2014 Chris Fields committed March 28, 2014
  2. spellink

    authored March 28, 2014

Mar 27, 2014

  1. Francisco J. Ossandon

    Merge pull request #66 from nathanweeks/sqlite_collate_nocase

    Use COLLATE NOCASE instead of LOWER() for Bio::DB::SeqFeature::Store::DBI::SQLite
    authored March 26, 2014

Mar 18, 2014

  1. bosborne

    Used quoted strings in Bio::Species to avoid a 'Invalid [] range in r…

    …egex' error, Species.t and genbank.t pass
    authored March 18, 2014

Mar 15, 2014

  1. Francisco J. Ossandon

    SeqIO/ At 'next_seq' subroutine, added a little more

    flexibility to the ID field in the ID line, to allow custom IDs
    authored March 15, 2014

Mar 13, 2014

  1. Nathan T. Weeks

    Add the COLLATE NOCASE constraint to the,

    attribute.attribute_value, and typelist.tag; and remove the user of the
    LOWER() function; to allow the use of indexes instead of full-table
    scans. Add the COLLATE NOCASE opterator to affected queries for
    backwards compatibility with Bio::DB::SeqFeature::Store databases
    created without the COLLATE NOCASE constraints.
    authored March 13, 2014

Mar 07, 2014

  1. Francisco J. Ossandon

    SeqIO/Genbank: Complete elimination of the use of '$_',

    except inside map/grep blocks. Also extensive cleanup of tabs,
    parenthesis, indentation, etc. Test suite pass.
    authored March 07, 2014

Mar 06, 2014

  1. Francisco J. Ossandon

    Unflattener: Fix for Bug #3458. Incorporated Bastien Chevreux

    suggestions to improve error reports from "problem" subroutine
    by adding feature location and locus_tag. Also merged all
    tests from 'Unflattener2.t' into 'Unflattener.t' to have
    all tests in a single file.
    authored March 06, 2014
  2. Francisco J. Ossandon

    SeqIO/ Fixed an uninitialized value warning from

    "_get_writer" by changing '$Bio::SeqIO::tinyseq::VERSION' to
    '$Bio::Root::Version::VERSION'. Also cleaned tabs, indentation
    and trailing whitespace from both module and test file.
    authored March 06, 2014

Mar 04, 2014

  1. Francisco J. Ossandon

    SearchResultEventBuilder: Simplified calculation of 'HSP-query_length'

    and 'HSP-hit_length' in "end_hsp" subroutine. Also fixed an
    undefined value warning for $hit_bits in "_add_hit"
    authored March 04, 2014
  2. Francisco J. Ossandon

    Bio/Ontology/InterProTerm: Fixed an uninitialized warning in

    "to_string" method, and cleaned indentation and tabs from test file
    authored March 04, 2014
  3. Francisco J. Ossandon

    SeqFeatureDB Postgres: Changed the use of system("cp") command

    to the more portable File::Copy. Tested and works fine.
    authored March 04, 2014

Feb 28, 2014

  1. Francisco J. Ossandon

    Massive check of file open lines. Changed bareword filehandles

    to lexical with three-argument opens calls, added die/throw
    and reason of failure $! where missing, and made error messages
    more uniform and consistent with Florent Angly messages for Root
    (like quoting of filenames). Also deleted a few unused open
    filehandles and some unnecessary parenthesis. Tests pass.
    authored February 28, 2014

Feb 25, 2014

  1. Francisco J. Ossandon

    Merge pull request #65 from MartinMcGrath/master

    Add reason for failure of file IO
    authored February 25, 2014
  2. Florent Angly

    Fixed filename in test

    Should be ">$o_file" and not "> $o_file"
    Also did miscellaneous cleaning (tabs, parentheses)
    authored February 25, 2014
  3. Florent Angly

    Fixed bad filename

    Was "sample_dataset.tigr " instead of "sample_dataset.tigr" (no trailing space)
    Also made style more consistent
    authored February 25, 2014

Feb 19, 2014

  1. Florent Angly

    Plan update

    authored February 19, 2014
  2. Florent Angly

    Finished variable rename

    authored February 19, 2014
  3. Florent Angly

    Added autodetection of file format in Bio::SeqIO::MultiFile

    authored February 19, 2014
  4. Florent Angly

    Slight SeqIO::guess code flow change

    authored February 19, 2014
  5. Florent Angly

    Fixed missing detection of format in SeqIO when given a -string

    authored February 19, 2014
  6. Florent Angly

    Removed mentions the ARGV and STDIN features

    1/ their documentation was less than clear
    2/ they seem to have been broken for quite some time
    3/ tests disagree that STDIN should be used this way
    authored February 19, 2014
  7. Florent Angly

    More POD clarifications

    authored February 19, 2014
  8. Florent Angly

    Mention -string parameter in POD

    authored February 19, 2014
  9. Florent Angly

    Bio::SeqIO::new POD update

    authored February 19, 2014
  10. Florent Angly

    Fixed synopsis typo

    authored February 19, 2014
  11. Florent Angly

    Updated number of tests

    authored February 19, 2014
  12. Florent Angly

    Reorganized guess() method of GuessSeqFormat

    authored February 19, 2014
  13. Florent Angly

    Fixed a typo

    authored February 19, 2014
  14. Florent Angly

    Restored test file for AlignIO

    authored February 19, 2014
  15. Florent Angly

    Removed test data files that are not needed anymore

    authored February 19, 2014
  16. Florent Angly

    Checked that all testable formats are tested

    authored February 19, 2014
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