[Gmod-ajax] JBrowse 1.15.4 released

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

Hello all,

I'm pleased to announce that JBrowse 1.15.4 has been released! This release
allows you to use bgzip indexed FASTA, adds a new categoryOrder config for
sorting the Hierarchical track selector, and more! Thanks to everyone for
their feature requests and bug reports, and enjoy!

   - JBrowse-1.15.4.zip
   <https://github.com/GMOD/jbrowse/releases/download/1.15.4-release/JBrowse-1.15.4.zip>
-
   minified release
   - JBrowse-1.15.4-dev.zip
   <https://github.com/GMOD/jbrowse/archive/1.15.4-release.zip> - use this
   if you modify jbrowse source code or use plugins
   - JBrowse-1.15.4-desktop-win32-x64.zip
   <https://github.com/GMOD/jbrowse/releases/download/1.15.4-release/JBrowse-1.15.4-desktop-win32-x64.zip>
   - JBrowse-1.15.4-desktop-linux-x64.zip
   <https://github.com/GMOD/jbrowse/releases/download/1.15.4-release/JBrowse-1.15.4-desktop-linux-x64.zip>
   - JBrowse-1.15.4-desktop-darwin-x64.zip
   <https://github.com/GMOD/jbrowse/releases/download/1.15.4-release/JBrowse-1.15.4-desktop-darwin-x64.zip>


Blog post http://jbrowse.org/blog/2018/10/05/jbrowse-1-15-4.html
<http://jbrowse.org/blog/#minor-improvements>Minor improvements

   -

   Added support for bgzipped indexed FASTA. To use, bgzip your FASTA
with bgzip
   -i file.fa, which generates file.fa.gz and file.fa.gzi and then usesamtools
   faidx file.fa.gz. If you specify the .fa.gz in the track config
e.g. "urlTemplate":
   "file.fa.gz" and have all three files in your data directory, then they
   will automatically be detected (issue #1152
   <https://github.com/gmod/jbrowse/issues/1152>, issue #1200
   <https://github.com/gmod/jbrowse/pull/1200>, @cmdcolin
   <https://github.com/cmdcolin>)
   -

   Allow fna and mfa file extensions for FASTA to be recognized by default
   in the Open sequence dialog (issue #1205
   <https://github.com/gmod/jbrowse/issues/1205>, @cmdcolin
   <https://github.com/cmdcolin>)
   -

   Improve the layout slightly for dense features (issue #1210
   <https://github.com/gmod/jbrowse/issues/1210>, @cmdcolin
   <https://github.com/cmdcolin>)
   -

   Added a topLevelFeaturesPercent configuration variable that can be used
   to correct feature statistics estimates when topLevelFeatures is being
   used for a track, or when it contains deeply-nested features. This
   configuration variable is currently only used by BAM, BEDTabix, GFF3Tabix,
   and VCFTabix stores. (issue #1147
   <https://github.com/gmod/jbrowse/issues/1147>, issue #1209
   <https://github.com/gmod/jbrowse/pull/1209>, @rbuels
   <https://github.com/rbuels>)
   -

   Tabix-based data stores use a new storage backend based on the
   @gmod/tabix npm module. Users should see some modest performance
   improvements for Tabix-based tracks. (issue #1195
   <https://github.com/gmod/jbrowse/issues/1195>, issue #1209
   <https://github.com/gmod/jbrowse/pull/1209>, @rbuels
   <https://github.com/rbuels>)
   -

   Added hideSequenceBox config to allow hiding the FASTA boxes in the View
   details popups. Thanks to @andreamini <https://github.com/andreamini> for
   reporting (issue #1211 <https://github.com/gmod/jbrowse/issues/1211>, issue
   #1219 <https://github.com/gmod/jbrowse/pull/1219>, @cmdcolin
   <https://github.com/cmdcolin>)
   -

   Added categoryOrder config to allow sorting the categories in the
   Hierarchical track selector. For example,
   categoryOrder=VCF,Quantitative/Density,BAM. Note that we specify a
   lowest level subcategory e.g. Quantitative/Density to sort the parent
   category Quantitative to a position (issue #1203
   <https://github.com/gmod/jbrowse/issues/1203>, issue #1208
   <https://github.com/gmod/jbrowse/pull/1208>, @cmdcolin
   <https://github.com/cmdcolin>)

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

   -

   Fixed a bug in which feature labels would sometimes be repeated across
   the view, in the wrong locations. (@rbuels <https://github.com/rbuels>)
   -

   Fixed error where a chunk size limit error during histogram display
   would not be displayed (@cmdcolin <https://github.com/cmdcolin>)
   -

   Fixed issue where Open sequence dialog will open up the default "data"
   directory instead of a blank instance (issue #1207
   <https://github.com/gmod/jbrowse/issues/1207>, @cmdcolin
   <https://github.com/cmdcolin>)
   -

   Added check for PCR duplicates for CRAM features (@cmdcolin
   <https://github.com/cmdcolin>)
   -

   Fixed issue where editing the track names and types in the "Open track"
   dialog box was not working when editing multiple tracks (issue #1217
   <https://github.com/gmod/jbrowse/issues/1217>, @cmdcolin
   <https://github.com/cmdcolin>)
   -

   Fixed issue in which large VCF headers were not always correctly parsed
   by JBrowse (issue #1139 <https://github.com/gmod/jbrowse/issues/1139>, issue
   #1209 <https://github.com/gmod/jbrowse/pull/1209>, @rbuels
   <https://github.com/rbuels>)
   -

   Fixed issue where the histogram Y-scale bar would appear over features
   (issue #1214, issue #1218 <https://github.com/gmod/jbrowse/pull/1218>,
   @cmdcolin <https://github.com/cmdcolin>)