[update docs] release 1.16.5

package.json

@@ -1,7 +1,7 @@
 {
   "name": "@gmod/jbrowse",
   "main": "browser/main.js",
-  "version": "1.16.5-alpha.0",
+  "version": "1.16.5",
   "description": "JBrowse - client-side genome browser",
   "repository": "https://github.com/GMOD/jbrowse.git",
   "scripts": {

release-notes.md

@@ -1,4 +1,4 @@
-{{$NEXT}}
+# Release 1.16.5     2019-06-12 16:57:19 UTC
 
 ## Minor improvements
 

src/JBrowse/package.json

@@ -1,6 +1,6 @@
 {
     "name": "JBrowse",
-    "version": "1.16.5-alpha.0",
+    "version": "1.16.5",
     "copyright":"© 2007-2017 The Evolutionary Software Foundation",
     "main": "main",
     "dependencies": {

website/blog/2019-06-12-jbrowse-1-16-5.md

@@ -0,0 +1,76 @@
+---
+layout: post
+title: JBrowse 1.16.5 maintenance release
+date: 2019-06-12
+tags: ["News","Software releases"]
+---
+
+I am pleased to announce the release of JBrowse 1.16.5. This includes some name regularization fixes (e.g. when you have chr1 and 1 it tries to map to the same thing), some bigwig fixes, a small speedup for BAM data, and more. Please read the release notes!
+
+*   [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)
+
+
+
+
+## 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 <a href="https://github.com/mictadlo">@mictadlo</a> for the suggestion (issue
+   #1365)
+
+ * Updated <a href="https://github.com/gmod">@gmod</a>/tabix and <a href="https://github.com/gmod">@gmod</a>/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
+   (<a href="https://github.com/cmdcolin">@cmdcolin</a>)
+
+ * Added regularization of chromosome names using roman numerals,
+   common in both S. cerevisiae and C. elegans genome communities.
+   Thanks to <a href="https://github.com/scottcain">@scottcain</a> for assistance (<a href="https://github.com/gmod/jbrowse/pull/1376">issue #1376</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>)
+
+ * 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`.
+   (<a href="https://github.com/cmdcolin">@cmdcolin</a>, <a href="https://github.com/gmod/jbrowse/pull/1373">issue #1373</a>)
+
+## Bug fixes
+
+ * Fixed a long standing issue with BigWig files not accessing the
+   lowest summary zoom level (e.g. the first one after unzoomed).
+   (<a href="https://github.com/cmdcolin">@cmdcolin</a>, <a href="https://github.com/gmod/jbrowse/issues/1359">issue #1359</a>)
+
+ * Fixed a bug with using the scoreType: maxScore configuration on
+   Wiggle tracks failing at non-summary zoom levels. Thanks to
+   <a href="https://github.com/patrickcng90">@patrickcng90</a> for reporting
+
+ * Fixed a bug with name regularizing that particularly affected CRAM
+   on mitochondrial chromosomes. Thanks to <a href="https://github.com/sachalau">@sachalau</a> for patience and
+   sample data for debugging this issue! (<a href="https://github.com/gmod/jbrowse/issues/1367">issue #1367</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>)
+
+ * Fixed issue with GFF3/Tabix types colliding their attribute names
+   with the field e.g. if start=0 was in column 9. Thanks to
+   <a href="https://github.com/loraine-gueguen">@loraine-gueguen</a> for reporting (<a href="https://github.com/gmod/jbrowse/issues/1364">issue #1364</a>).
+
+ * Fixed an issue with NeatHTMLFeatures when zoomed out. Thanks to
+   <a href="https://github.com/abretaud">@abretaud</a> for the implementation and fix (<a href="https://github.com/gmod/jbrowse/pull/1368">issue #1368</a>).
+
+ * Restored ability to access widest zoom level from bigwig. Thanks
+   to <a href="https://github.com/lukaw3d">@lukaw3d</a> for noticing and debugging (<a href="https://github.com/gmod/jbrowse/issues/1375">issue #1375</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>)
+
+ * 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 (<a href="https://github.com/cmdcolin">@cmdcolin</a>)
+
+ * Added some more checks for track types for combination tracks (issue
+   #1361)
+

website/siteConfig.js

@@ -27,7 +27,7 @@ const createVariableInjectionPlugin = variables => {
 };
 
 const v = {
-  "version": "1.16.4"
+  "version": "1.16.5"
 };
 const siteVariables = {
   version: v.version,