From 8a041eb63122860adb138fe3f89f4922c3fbdd64 Mon Sep 17 00:00:00 2001 From: Colin Date: Wed, 12 Jun 2019 12:57:19 -0400 Subject: [PATCH] [update docs] release 1.16.5 --- package.json | 2 +- release-notes.md | 2 +- src/JBrowse/package.json | 2 +- website/blog/2019-06-12-jbrowse-1-16-5.md | 76 +++++++++++++++++++++++ website/siteConfig.js | 2 +- 5 files changed, 80 insertions(+), 4 deletions(-) create mode 100644 website/blog/2019-06-12-jbrowse-1-16-5.md diff --git a/package.json b/package.json index df04009539..d24ab973a9 100644 --- a/package.json +++ b/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": { diff --git a/release-notes.md b/release-notes.md index cd31585451..85d977183a 100644 --- a/release-notes.md +++ b/release-notes.md @@ -1,4 +1,4 @@ -{{$NEXT}} +# Release 1.16.5 2019-06-12 16:57:19 UTC ## Minor improvements diff --git a/src/JBrowse/package.json b/src/JBrowse/package.json index bbb6d280ae..f90e6bb267 100644 --- a/src/JBrowse/package.json +++ b/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": { diff --git a/website/blog/2019-06-12-jbrowse-1-16-5.md b/website/blog/2019-06-12-jbrowse-1-16-5.md new file mode 100644 index 0000000000..33a6365ac5 --- /dev/null +++ b/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 @mictadlo for the suggestion (issue + #1365) + + * Updated @gmod/tabix and @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) + + * Added regularization of chromosome names using roman numerals, + common in both S. cerevisiae and C. elegans genome communities. + Thanks to @scottcain for assistance (issue #1376, @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, issue #1373) + +## 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, issue #1359) + + * Fixed a bug with using the scoreType: maxScore configuration on + Wiggle tracks failing at non-summary zoom levels. Thanks to + @patrickcng90 for reporting + + * Fixed a bug with name regularizing that particularly affected CRAM + on mitochondrial chromosomes. Thanks to @sachalau for patience and + sample data for debugging this issue! (issue #1367, @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 for reporting (issue #1364). + + * Fixed an issue with NeatHTMLFeatures when zoomed out. Thanks to + @abretaud for the implementation and fix (issue #1368). + + * Restored ability to access widest zoom level from bigwig. Thanks + to @lukaw3d for noticing and debugging (issue #1375, @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) + + * Added some more checks for track types for combination tracks (issue + #1361) + diff --git a/website/siteConfig.js b/website/siteConfig.js index b793a558e2..8791cd0f10 100644 --- a/website/siteConfig.js +++ b/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,