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Commits on Jan 15, 2017
  1. Merge pull request #59 from GMOD/scotts-minor-fixes

    lstein committed Jan 15, 2017
    addition of CGI::multi_param to silence warnings when running tests--…
Commits on Jan 6, 2017
  1. addition of CGI::multi_param to silence warnings when running tests--…

    scottcain committed Jan 6, 2017
    …not sure if this is the right thing to do from a security perspective though (for example, should some of these calls be in a scalar context instead?)
Commits on Dec 29, 2016
Commits on Dec 27, 2016
Commits on Oct 28, 2014
  1. Merge pull request #32 from keiranmraine/master

    lstein committed Oct 28, 2014
    Makes pre-loading of datasources under fastcgi a configurable option
  2. Merge pull request #45 from nathanweeks/issue/regionsearch-features-s…

    lstein committed Oct 28, 2014
    …ame-location
    
    Search results return only one feature with the same type, start, and end
  3. Merge pull request #46 from nathanweeks/issue/karyotype-feature-highl…

    lstein committed Oct 28, 2014
    …ighting
    
    Improve feature visibility in karyotype display
Commits on Oct 23, 2014
Commits on Oct 21, 2014
  1. Merge pull request #42 from nathanweeks/issue/primerdesigner_without_…

    scottcain committed Oct 21, 2014
    …mod_perl
    
    Quell intermittent PrimerDesigner errors when run under mod_fcgid instead of mod_perl.  Makes sense to me!
  2. Merge pull request #38 from nathanweeks/issue/search_whitespace

    scottcain committed Oct 21, 2014
    Trim leading & trailing spaces from the search term.  Thanks Nathan!
Commits on Oct 1, 2014
  1. Restore the behavior whereby small features are displayed in the

    nathanweeks committed Oct 1, 2014
    karyotype display using the diamond glyph, greatly improving their visibility,
    and larger features are displayed using the generic glyph. This functionality
    appears to have been inadvertently disabled by commit
    68e13af.
    
    In the karyotype display, highlight features in a dark blue color to increase
    contrast.
Commits on Sep 26, 2014
  1. Fix issue where Bio::Graphics::Browser2::RegionSearch::search_features

    nathanweeks committed Sep 26, 2014
    "uniqueifies" results where the type and start & end locations are the same,
    despite a comment stating that name & type should be uniqueifying criteria,
    by adding display_name to the mix.
Commits on Aug 18, 2014
Commits on Aug 7, 2014
Commits on Jul 31, 2014
Commits on Jul 30, 2014
  1. add missing load helper file

    lstein committed Jul 30, 2014
  2. remove foobar file

    lstein committed Jul 30, 2014
Commits on Jul 29, 2014
Commits on Jul 24, 2014
  1. Allow user to select dna/rna query & specify minimum percent identity.

    nathanweeks committed Jul 24, 2014
    Remove unused check_seq() subroutine.
Commits on Jun 11, 2014
Commits on May 16, 2014
  1. BLAT hits are not necessarily reported in best-to-worst order. Read all

    nathanweeks committed May 16, 2014
    blat hits and sort by calculated score (percent query coverage).
    
    Add 1 to start coordinates, as Start coordinates in BLAT PSL output are
    0-based, not 1-based.
    
    Strand needs to be +1/-1 (rather than "+" or "-") in order for
    Bio::SeqFeature::Lite (base class of Bio::Graphics::Feature) to
    correctly interpret them (though there is a pull request to fix this:
        bioperl/bioperl-live#71
Commits on May 2, 2014
  1. Fixed syntax error

    mckays630 committed May 2, 2014
Commits on Apr 29, 2014
Commits on Apr 25, 2014
  1. Quell the following intermittent errors that were occasionally displa…

    nathanweeks committed Apr 25, 2014
    …yed in
    
    the browser:
        Undefined subroutine CGI::Pretty::delete_all
        at /opt/gbrowse/conf/plugins/PrimerDesigner.pm line 106
    The comment above the END code block indicates that this code was for
    mod_perl. The errors were observed under FastCGI.
Commits on Feb 26, 2014
Commits on Dec 11, 2013
  1. Merge pull request #37 from srobb1/master

    scottcain committed Dec 11, 2013
    added region_label to pass region name on in url--thanks Sofia!