From b8324df0033796b6d502696dc65c9ff888aae2f3 Mon Sep 17 00:00:00 2001 From: Colin Date: Thu, 24 Sep 2020 12:06:00 -0400 Subject: [PATCH] [update docs] release 1.16.10 --- package.json | 2 +- release-notes.md | 2 +- src/JBrowse/package.json | 2 +- website/blog/2020-09-24-jbrowse-1-16-10.md | 48 ++++++++++++++++++++++ website/siteConfig.js | 2 +- 5 files changed, 52 insertions(+), 4 deletions(-) create mode 100644 website/blog/2020-09-24-jbrowse-1-16-10.md diff --git a/package.json b/package.json index f6bda9d5d9..4c5555afd6 100644 --- a/package.json +++ b/package.json @@ -1,7 +1,7 @@ { "name": "@gmod/jbrowse", "main": "browser/main.js", - "version": "1.16.0-alpha.0", + "version": "1.16.10", "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 a63ada7e72..4d9a354acf 100644 --- a/release-notes.md +++ b/release-notes.md @@ -1,4 +1,4 @@ -{{$NEXT}} +# Release 1.16.10 2020-09-24 16:06:00 UTC ## Minor improvements diff --git a/src/JBrowse/package.json b/src/JBrowse/package.json index 09435d2165..3f45c3207d 100644 --- a/src/JBrowse/package.json +++ b/src/JBrowse/package.json @@ -1,6 +1,6 @@ { "name": "JBrowse", - "version": "1.16.0-alpha.0", + "version": "1.16.10", "copyright":"© 2007-2017 The Evolutionary Software Foundation", "main": "main", "dependencies": { diff --git a/website/blog/2020-09-24-jbrowse-1-16-10.md b/website/blog/2020-09-24-jbrowse-1-16-10.md new file mode 100644 index 0000000000..9cac4a470c --- /dev/null +++ b/website/blog/2020-09-24-jbrowse-1-16-10.md @@ -0,0 +1,48 @@ +--- +layout: post +title: JBrowse 1.16.10 maintenance release +date: 2020-09-24 +tags: ["News","Software releases"] +--- + +Hello all, + +This contains that helps long reads especially and a bugfix for rendering SNPs on iso-seq reads/reads with multiple CIGAR skips. There are also other small bugfixes and improvements. 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) + + + + +## Minor improvements + +- Added an optimization for BAM that helps for long reads especially + (@cmdcolin) + +- Added generation of the MD tag if none is specified in BAM (issue + #1022, @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, issue #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) + +## Bug fixes + +- Fix the display of mismatches from hard clipped BAM sequences (issue #1513) + +- Fix ability to use tracks from Open track dialog in combination tracks. + Thanks to Sonny Arora for the repo (issue #1536) + +- Fix mismatch/SNP calculation for reads with multiple skips, e.g. Iso-Seq + (@cmdcolin) + diff --git a/website/siteConfig.js b/website/siteConfig.js index 7302294fc8..67a5c98cd0 100644 --- a/website/siteConfig.js +++ b/website/siteConfig.js @@ -27,7 +27,7 @@ const createVariableInjectionPlugin = variables => { }; const v = { - "version": "1.16.9" + "version": "1.16.10" }; const siteVariables = { version: v.version,