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Branch: master
Commits on May 30, 2015
  1. @cjfields

    Merge pull request #101 from christiam/master

    cjfields authored
    Expand RemoteBlast synopsis sample code.  Merge seems like it should be fine (travis fails may be unrelated)
  2. @cjfields

    Merge pull request #104 from douglasgscofield/master

    cjfields authored
    Open Bio::DB::Taxonomy flatfile indices read-only
Commits on Apr 10, 2015
  1. @cjfields

    Merge pull request #111 from adsj/master

    cjfields authored
    Accept space after equal sign in qualifiers when reading EMBL.
  2. @adsj

    Accept space after equal sign in qualifiers when reading EMBL.

    adsj authored
    This makes /product= "some long ... value" read as if the space
    after the '=' was not there; this formatting has been observed
    in the wild.
Commits on Apr 9, 2015
  1. @douglasgscofield

    merge upstream

    douglasgscofield authored
Commits on Mar 29, 2015
  1. @cjfields
  2. @cjfields
  3. @cjfields

    add readthedocs badge; will gradually start migrating docs to that si…

    cjfields authored
    …te (including HOWTOs, installation etc)
Commits on Mar 25, 2015
  1. @cjfields

    even better DOI

    cjfields authored
  2. @cjfields

    add DOI badge from Zenodo

    cjfields authored
Commits on Mar 19, 2015
  1. @fjossandon

    Merge pull request #106 from lairdm/master

    fjossandon authored
    Add Bio::Seq::RichSeq to trunc() for not using clone()
  2. @lairdm

    A test to ensure Bio::PrimarySeqI->trunc() doesn't use clone() for a …

    lairdm authored
    …Bio::Seq::RichSeq type object
  3. @lairdm

    Darn you, emacs, putting tab characters in. Sorry, didn't realize I h…

    lairdm authored
    …adn't changed my configs after reinstalling my laptop last month.
    
    - Changed line in trunc testing if an object is a Bio::Seq::RichSeq so it uses spaces for indentation rather than a tab character.
  4. @lairdm
  5. @lairdm

    Added Bio::Seq::RichSeq as a seq object type that will cause Bio::Pri…

    lairdm authored
    …marySeqI->trunc() not to do a clone of the original object first. The clone was cloning features of the rich sequence object outside the requested range in trunc()
  6. @majensen

    Remove cruft (soz)

    majensen authored
  7. @majensen

    Merge branch 'topic_105'

    majensen authored
  8. @majensen

    fix #105 - find the real "first orf"

    majensen authored
    Update Bio::PrimarySeqI::_find_orfs_nucleotide so that
    translate(-orf => 1) performs as advertised when there
    are multiple overlapping ORFs. Add relevant tests to
    t/Seq/PrimarySeq.t.
Commits on Mar 16, 2015
  1. @douglasgscofield
Commits on Mar 5, 2015
  1. @cjfields
  2. @cjfields
  3. @cjfields

    remove test file

    cjfields authored
  4. @majensen
  5. @majensen

    Fix #103

    majensen authored
Commits on Mar 2, 2015
  1. @cjfields
  2. @cjfields
  3. @cjfields

    bit more docs on todo items

    cjfields authored
Commits on Mar 1, 2015
  1. @cjfields
  2. @cjfields

    all but two tests passing

    cjfields authored
  3. @cjfields
  4. @cjfields

    remove pasto

    cjfields authored
  5. @cjfields

    vent

    cjfields authored
  6. @cjfields
  7. @cjfields

    start testing Bio::Taxon

    cjfields authored
  8. @cjfields

    implement get_taxids()

    cjfields authored
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