JBrowse 1.10.5 released

classic Classic list List threaded Threaded
1 message Options
Reply | Threaded
Open this post in threaded view
|

JBrowse 1.10.5 released

Robert Buels-2
Hi all,

JBrowse 1.10.5 has been released, with some important bug fixes and more
performance improvements for data formatting scripts.

It can be downloaded from http://jbrowse.org/jbrowse-1-10-5

# Release 1.10.5     2013-10-03 10:21:37 EST5EDT

## Minor improvements

  * Greatly improved the speed and reduced the memory footprint when
    running `prepare-refseqs.pl` with the --fasta and --gff options.

  * Added an `impliedUTRs` option to the ProcessedTranscript and Gene
    glyphs for CanvasFeatures tracks.  Thanks to Ben Booth for pointing
    out the need for this (issue #348).

  * Upgraded flatfile-to-json.pl to use a new version of
    Bio::GFF3::LowLevel::Parser for GFF3 parser, which has a lookback
    buffer limit that makes it easier to parse large GFF3 files that do
    not contain enough '###' directives.

  * Further improved the memory footprint and speed of
    generate-names.pl. Thanks to Richard Hayes for his continued help
    with testing improvements and reporting problems.

  * Removed explicit dependency on GD::Image, which is only used by the
    old tiled-image generation demo code.  This will make dependency
    installation easier for many people, at a (very) small cost to
    backward compatibility.

## Bug fixes

  * Fixed a bad bug that prevented combination tracks from working.
    Thanks to Harry Yoo for pointing this out (issue #351).

  * Fixed a bug in which one of the temporary files used by
    generate-names.pl was not being created in the correct location.
    Thanks to Richard Hayes for testing this.

  * Fixed a bug in which `generate-names.pl` could sometimes crash when
    run with the -v (verbose) switch, or in setup.sh.

  * Fixed odd behavior when entering coordinate ranges in the location
    box under Safari.  Thanks to Keiran Raine for pointing this out
    (issue #341).


Happy browsing.  ;-)

Robert Buels
Lead Developer
JBrowse - http://jbrowse.org