[Gmod-ajax] JBrowse 1.16.5 released

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

Hello all,
This is the real release announcement for the latest jbrowse version, 1.16.5

It contains a number of nice bugfixes contributed by the community. Please
see the release notes below

Enjoy browsing!


   - JBrowse-1.16.5.zip
   <https://github.com/GMOD/jbrowse/releases/download/1.16.5-release/JBrowse-1.16.5.zip>
-
   minified release
   - JBrowse-1.16.5-dev.zip
   <https://github.com/GMOD/jbrowse/archive/1.16.5-release.zip> - use this
   if you modify jbrowse source code or use plugins
   - JBrowse-1.16.5-desktop-win32-x64.zip
   <https://github.com/GMOD/jbrowse/releases/download/1.16.5-release/JBrowse-1.16.5-desktop-win32-x64.zip>
   - JBrowse-1.16.5-desktop-linux-x64.zip
   <https://github.com/GMOD/jbrowse/releases/download/1.16.5-release/JBrowse-1.16.5-desktop-linux-x64.zip>
   - JBrowse-1.16.5-desktop-darwin-x64.zip
   <https://github.com/GMOD/jbrowse/releases/download/1.16.5-release/JBrowse-1.16.5-desktop-darwin-x64.zip>

<http://jbrowse.org/blog/#minor-improvements>Minor improvements

   -

   Added better error reporting if there is a BAI file for a genome that is
   longer than 2^29 and requires a CSI index
   -

   Added default dontRedispatch=chromosome,region which avoids long
   GFF3Tabix redispatching for common gff3 types that don't need it.
   -

   Added a hideIframeDialogUrl option to hide the iframe url in a
   iframeDialog popup. Thanks to @mictadlo <https://github.com/mictadlo> for
   the suggestion (issue #1365)
   -

   Updated @gmod <https://github.com/gmod>/tabix and @gmod
   <https://github.com/gmod>/bam to unzip bgzf chunks as they are received
   instead of performing chunk merges. This also allows actual fileOffset to
   be used as a feature ID instead of CRC32 hash (@cmdcolin
   <https://github.com/cmdcolin>)
   -

   Added regularization of chromosome names using roman numerals, common in
   both S. cerevisiae and C. elegans genome communities. Thanks to
   @scottcain <https://github.com/scottcain> for assistance (issue #1376
   <https://github.com/gmod/jbrowse/pull/1376>, @cmdcolin
   <https://github.com/cmdcolin>)
   -

   Added ability for vertical scroll events to bubble out of the jbrowse
   div or iframe, which can be more intuitive in embedded jbrowse's.
   Otherwise, the GenomeView stopped all vertical scroll events in it's area.
   If you need the old behavior use alwaysStopScrollBubble. (@cmdcolin
   <https://github.com/cmdcolin>, issue #1373
   <https://github.com/gmod/jbrowse/pull/1373>)

<http://jbrowse.org/blog/#bug-fixes>Bug fixes

   -

   Fixed a long standing issue with BigWig files not accessing the lowest
   summary zoom level (e.g. the first one after unzoomed). (@cmdcolin
   <https://github.com/cmdcolin>, issue #1359
   <https://github.com/gmod/jbrowse/issues/1359>)
   -

   Fixed a bug with using the scoreType: maxScore configuration on Wiggle
   tracks failing at non-summary zoom levels. Thanks to @patrickcng90
   <https://github.com/patrickcng90> for reporting
   -

   Fixed a bug with name regularizing that particularly affected CRAM on
   mitochondrial chromosomes. Thanks to @sachalau
   <https://github.com/sachalau> for patience and sample data for debugging
   this issue! (issue #1367 <https://github.com/gmod/jbrowse/issues/1367>,
   @cmdcolin <https://github.com/cmdcolin>)
   -

   Fixed issue with GFF3/Tabix types colliding their attribute names with
   the field e.g. if start=0 was in column 9. Thanks to @loraine-gueguen
   <https://github.com/loraine-gueguen> for reporting (issue #1364
   <https://github.com/gmod/jbrowse/issues/1364>).
   -

   Fixed an issue with NeatHTMLFeatures when zoomed out. Thanks to @abretaud
   <https://github.com/abretaud> for the implementation and fix (issue #1368
   <https://github.com/gmod/jbrowse/pull/1368>).
   -

   Restored ability to access widest zoom level from bigwig. Thanks to
   @lukaw3d <https://github.com/lukaw3d> for noticing and debugging (issue
   #1375 <https://github.com/gmod/jbrowse/issues/1375>, @cmdcolin
   <https://github.com/cmdcolin>)
   -

   Fixed some minor parsing of 'b' type data series in CRAM files, which
   happens when CRAM is not using reference based compression so it is
   uncommon (@cmdcolin <https://github.com/cmdcolin>)
   -

   Added some more checks for track types for combination tracks (issue
   #1361)