[Gmod-ajax] JBrowse 1.16.10 maintenance release

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

Hi all,
I'm pleased to announce a new update for JBrowse. This release contains
changes that fixes a bug rendering SNPs from reads with multiple CIGAR
skips, e.g. Iso-Seq. It also includes a modest speedup for long reads,
automatic generation of MD tags for BAM, and more. Please see the changelog
below!


   - JBrowse-1.16.10.zip
   <https://github.com/GMOD/jbrowse/releases/download/1.16.10-release/JBrowse-1.16.10.zip>
-
   minified release
   - JBrowse-1.16.10-dev.zip
   <https://github.com/GMOD/jbrowse/archive/1.16.10-release.zip> - use this
   if you modify jbrowse source code or use plugins
   - JBrowse-1.16.10-desktop-win32-x64.zip
   <https://github.com/GMOD/jbrowse/releases/download/1.16.10-release/JBrowse-1.16.10-desktop-win32-x64.zip>
   - JBrowse-1.16.10-desktop-linux-x64.zip
   <https://github.com/GMOD/jbrowse/releases/download/1.16.10-release/JBrowse-1.16.10-desktop-linux-x64.zip>
   - JBrowse-1.16.10-desktop-darwin-x64.zip
   <https://github.com/GMOD/jbrowse/releases/download/1.16.10-release/JBrowse-1.16.10-desktop-darwin-x64.zip>


Blog post https://jbrowse.org/blog/2020/09/24/jbrowse-1-16-10.html

Let us know if you have any questions, and stay safe out there :)
Minor improvements

   -

   Added an optimization for BAM that helps for long reads especially (
   @cmdcolin <https://github.com/cmdcolin>)
   -

   Added generation of the MD tag if none is specified in BAM (issue #1022,
   @cmdcolin <https://github.com/cmdcolin>)
   -

   Added customRefRename and replaceRefRename global configs for extending
   and replacing ref renaming functionality respectively. Ref renaming helps
   things like chrM and chrMT to be loaded onto the same chromosome in jbrowse
   (@cmdcolin <https://github.com/cmdcolin>, issue #1506
   <https://github.com/gmod/jbrowse/pull/1506>)
   -

   Added support for a -f option for setup.sh. This option causes setup to
   skip installing perl prerequisites and setting up sample data. It is
   primarily intended to support faster builds in a Docker context. (
   @scottcain <https://github.com/scottcain>)

<https://jbrowse.org/blog/2020/09/24/jbrowse-1-16-10.html#bug-fixes>Bug
fixes

   -

   Fix the display of mismatches from hard clipped BAM sequences (issue
   #1513 <https://github.com/gmod/jbrowse/pull/1513>)
   -

   Fix ability to use tracks from Open track dialog in combination tracks.
   Thanks to Sonny Arora for the repo (issue #1536
   <https://github.com/gmod/jbrowse/pull/1536>)
   -

   Fix mismatch/SNP calculation for reads with multiple skips, e.g. Iso-Seq
   (@cmdcolin <https://github.com/cmdcolin>)