updated release notes for all issues and pulls in the 1.12.4 milestone

release-notes.txt

@@ -4,36 +4,39 @@
 
   * Fixed SEVERE performance regression that basically made flatfile-to-json.pl
     unusable on Perl 5.18 and higher. Huge thanks to Colin Diesh for tracking
-    this down. (issue #470, @cmdcolin)
+    this down. (issue #470, pull #912, @cmdcolin)
 
   * setup.sh now uses npm instead of Bower (which is deprecated) to install
     dependencies. @enuggetry
 
   * Removed legacy `wig-to-json.pl` and `bam-to-json.pl` scripts.  @rbuels
 
   * Added a `--trackConfig` option to `prepare-refseqs.pl` to allow injecting
-    refseq configuration variables at format time.  @erasche
+    refseq configuration variables at format time. (pull #884, @erasche)
 
   * Added trackLabels: "no-block" config feature.  Moves track labels/menus
     above the features so as not to obscure the features. (issue #901, #490)
 
-  * Make jbrowse npm installable. thanks to @cmdcolin & @enuggetry.
+  * Added a `--category` option to `add-bw-track.pl` and `add-bam-track.pl` to
+    set the new track's category. Thanks to @loraine-gueguen for the implementation!
+    (pull #911, @loraine-gueguen)
 
-  * Change "Length on ref" to "Seq length on ref" in Alignments feature detail boxes,
-    so that the length on the reference appears next to the sequence length. Thanks to
-    @colindaven for the suggestion!
+  * Made jbrowse installable using `npm`. @cmdcolin and @enuggetry.
 
-  * implement express server for jbrowse for quick launch (jb_run.js).  @enuggetry.
+  * Implemented a built-in node.js Express server `jb_run.js` for quick JBrowse launching.
+    @enuggetry
 
-  * jb_setup.js @enuggetry.
+  * Added an `--unsorted` option to `prepare-refseqs.pl` that formats reference sequences
+    in the same order in which they appear in the input sequence file.  Thanks to
+    @dsenalik for the suggestion and implementation! (pull #924, @dsenalik)
 
   * Allows for dot-notation instead of JSON (pull #952) for addTracks, addBookmarks,
     and addStores. https://github.com/GMOD/jbrowse/pull/952. Address security concerns
     adding JSON to GET (https://nvd.nist.gov/vuln/detail/CVE-2016-6816) @nathandunn.
 
   * If a track has no `key` set in its track configuration, JBrowse will now look for
     a `key` in its track metadata, and use that if it is present. Thanks to Loraine
-    Guéguen for the idea (issue #957). @rbuels
+    Guéguen for the idea (issue #957, pull #958). @rbuels
 
   * Suppress execution of biodb-to-json.pl on sample data while running setup.sh
     on MacOS High Sierra with stock Perl due to an issue with the stock Perl having
@@ -58,6 +61,42 @@
 
   * Upgraded to use new Google Analytics API for usage reporting. (@rdhayes)
 
+  * Fixed bug in which start/stop codons were sometimes not displayed in the sequence
+    track at certain zoom levels (issue #858, pull req #859, @cmdcolin)
+
+  * Fixed a regression in which the `defaultTracks` configuration variable was no longer
+    respected when set to a comma-separated list. (issue #892, pull #896, @rdhayes)
+
+  * Made a cosmetic change to Alignments track detail popups, changing "Length on ref" to
+    be displayed as "Seq length on ref", so that it is displayed more usefully next to
+    "Seq length".  Thanks to @colindaven for the suggestion and implementation!
+    (pull #939, @colindaven)
+
+  * Improved the error messages displayed when a JBrowse glyph class fails to load. Thanks
+    to @scottcain and @cmdcolin for tracking down the issue and improving the error
+    handling! (issue #968, @cmdcolin)
+
+  * Added support for an `addFeatures` URL query parameter that can inject features from
+    the URL query string. (issue #976, @nathandunn)
+
+  * Changed the project's `git` workflow to utilize a `dev` branch that is separate from
+    `master`, with `master` only being updated when a new release of JBrowse is published.
+    (issue #975, @enuggetry)
+
+  * Implemented automated deployment of JBrowse releases to GitHub releases and `npm`.
+    Thanks to @abretaud, @nathandunn, @erasche, and @cmdcolin for valuable discussions.
+    (issue #822, pull #979, pull #984, @rbuels)
+
+  * Added a `--bigwigCoverage` option to `add-bam-track.pl` to support configuring pregenerated
+    coverage histograms from the command line.  Thanks to @loraine-gueguen for the suggestion
+    and implementation! (pull #972, @loraine-gueguen)
+
+  * Improved documentation of the `CategoryURL` plugin. (pull #985, @enuggetry)
+
+  * Re-enabled and improved documentation and configurability of the gradient colors in the
+    `NeatCanvasFeatures` plugin. (issue #982, pull #985, @enuggetry)
+
+
 # Release 1.12.3     2017-05-02 19:20:01 America/Los_Angeles
 
 ## Minor improvements