[Gmod-ajax] JBrowse 1.16.7 maintenance release

[Colin <col...@gm...>]

Hello everyone! I'm pleased to announce a new jbrowse maintenance version.

This includes a number of features and bugfixes suggested by the community.

Please see the release notes below for details.

   - JBrowse-1.16.7.zip
   <https://github.com/GMOD/jbrowse/releases/download/1.16.7-release/JBrowse-1.16.7.zip>
-
   minified release
   - JBrowse-1.16.7-dev.zip
   <https://github.com/GMOD/jbrowse/archive/1.16.7-release.zip> - use this
   if you modify jbrowse source code or use plugins
   - JBrowse-1.16.7-desktop-win32-x64.zip
   <https://github.com/GMOD/jbrowse/releases/download/1.16.7-release/JBrowse-1.16.7-desktop-win32-x64.zip>
   - JBrowse-1.16.7-desktop-linux-x64.zip
   <https://github.com/GMOD/jbrowse/releases/download/1.16.7-release/JBrowse-1.16.7-desktop-linux-x64.zip>
   - JBrowse-1.16.7-desktop-darwin-x64.zip
   <https://github.com/GMOD/jbrowse/releases/download/1.16.7-release/JBrowse-1.16.7-desktop-darwin-x64.zip>


Blog post http://jbrowse.org/blog/2020/01/24/jbrowse-1-16-7.html

PS: the JBrowse team had a really great time presenting our new work on
JBrowse 2 at PSB 2020 and PAG 2020 recently and meeting everyone. Look
forward to new announcements about JBrowse 2 in the upcoming months!
Minor improvements

   -

   Add name regularization for refseqs named MtDNA (issue #1408
   <https://github.com/gmod/jbrowse/pull/1408>, @scottcain
   <https://github.com/scottcain>, @cmdcolin <https://github.com/cmdcolin>)
   -

   Improved performance of startup time with large tracklists (issue #1412
   <https://github.com/gmod/jbrowse/pull/1412>, @cmdcolin
   <https://github.com/cmdcolin>)
   -

   Improve consistency of scrolling behavior across browsers using
   normalize-wheel npm package (@cmdcolin <https://github.com/cmdcolin>,
   @scottcain <https://github.com/scottcain>, issue #1429
   <https://github.com/gmod/jbrowse/pull/1429>)
   -

   Add trackMetadata->sortFacets boolean flag which can be set to false to
   disable sorting the facet categories in the left hand column of the faceted
   track selector. Thanks to Val Wood for championing this issue for pombase! (
   @cmdcolin <https://github.com/cmdcolin>)
   -

   Add relativeUrl to trackMetadata config so that URLs relative to the
   data directory can be specified (the standard url config is relative to
   the jbrowse root). Thanks to @loraine-gueguen
   <https://github.com/loraine-gueguen> for the report (issue #1457
   <https://github.com/gmod/jbrowse/issues/1457>)

<http://jbrowse.org/blog/2020/01/24/jbrowse-1-16-7.html#bug-fixes>Bug fixes

   -

   Fix bug that has existed since 1.16.0 (since the introduction of @gmod
   <https://github.com/gmod>/bam) that caused some BAM tags to be missed in
   feature details under some conditions.
   -

   Added a fix for a performance regularization for large tracklists that
   contain a lot of data. Thanks to @scottcain
   <https://github.com/scottcain> for reporting (#issue #1412
   <https://github.com/gmod/jbrowse/pull/1412>, @cmdcolin
   <https://github.com/cmdcolin>)
   -

   Fixed ability to access remote data directories in desktop app (issue
   #1413 <https://github.com/gmod/jbrowse/issues/1413>)
   -

   Fixed ability to open FASTA files with the .fasta extension in the
   desktop app. Thanks to @iankorf <https://github.com/iankorf> for
   reporting (issue #1415 <https://github.com/gmod/jbrowse/issues/1415>, issue
   #1426 <https://github.com/gmod/jbrowse/pull/1426>, @cmdcolin
   <https://github.com/cmdcolin>)
   -

   Fixed generate-names.pl to not overwrite the name store class (@Bjoernsen
   <https://github.com/Bjoernsen>, issue #1297
   <https://github.com/gmod/jbrowse/issues/1297>, issue #1423
   <https://github.com/gmod/jbrowse/pull/1423>)
   -

   Fixed some documentation for Content-Range CORs headers and
   renderAlignment configs (@cmdcolin <https://github.com/cmdcolin>)
   -

   Fixed rendering of CRAM hard clipping, which would display mismatches
   incorrectly (@cmdcolin <https://github.com/cmdcolin>, issue #1440
   <https://github.com/gmod/jbrowse/pull/1440>, issue #1438
   <https://github.com/gmod/jbrowse/issues/1438>)
   -

   Fixed issue where some BAM features were given the incorrect feature ID
   across blocks (@cmdcolin <https://github.com/cmdcolin>,
   https://github.com/GMOD/bam-js/pull/36)
   -

   Removed monkey patching from the dropdown refseq box, thanks to @lukaw3d
   <https://github.com/lukaw3d> for finding and fixing (@lukaw3d
   <https://github.com/lukaw3d>, issue #1439
   <https://github.com/gmod/jbrowse/pull/1439>)
   -

   Added fix for bigbed files with large headers, e.g. large autoSql schema
   (@cmdcolin <https://github.com/cmdcolin>)
   -

   Make VCF based features have distinct file IDs for similar overlapping
   features with same ID, ALT, REF, etc. Thanks @scottcain
   <https://github.com/scottcain> for the report (@cmdcolin
   <https://github.com/cmdcolin>)