@gmod/jbrowse/website/blog/2018-03-28-jbrowse-1-13-1-maintenance-release-index.md

JBrowse - client-side genome browser

---
layout: post
title: JBrowse 1.13.1 maintenance release
date: 2018-03-28
tags: ["Development","News","Software releases"]
---

JBrowse 1.13.1 has been released!

## Files for download

*   [JBrowse-1.13.1.zip](https://github.com/GMOD/jbrowse/releases/download/1.13.1-release/JBrowse-1.13.1.zip "download JBrowse-1.13.1.zip") - 2.7M
file SHA1 a22df76b7e970af9c7c6bda36ebdc4181344dbfd 
*   [JBrowse-1.13.1-dev.zip](https://github.com/GMOD/jbrowse/releases/download/1.13.1-release/JBrowse-1.13.1-dev.zip "download JBrowse-1.13.1-dev.zip") - 6.4M
file SHA1 686d04a3e0a07c70b62b8cd3ebe0741853971b03 

## Minor improvements

*   Gene, ProcessedTranscript, and Segments glyphs can now render third-level subfeatures
(such as `stop_codon_read_through` features) as simple boxes that draw on top of the
main segment glyph. Thanks to [@mpoelchau](https://github.com/mpoelchau) for pointing out the need for this!
([issue #584](https://github.com/gmod/jbrowse/issues/584), [@rbuels](https://github.com/rbuels))

*   CanvasFeatures tracks, when guessing which glyph to show for a feature in a track
that does not specify glyphs in its configuration, will now use a Segments glyph
instead of a Box glyph if the feature in question has subfeatures, and is not
otherwise recognized as a gene or processed transcript. [@rbuels](https://github.com/rbuels)

*   Added a check in the `setup.sh` script for NodeJS >= 6 and NPM >= 3.
([issue #1026](https://github.com/gmod/jbrowse/issues/1026), [@rbuels](https://github.com/rbuels))

*   Plugins that don't need CSS can now set `jbrowsePlugin.css` to `false` in their
package.json files to prevent JBrowse trying to load their css/main.css file,
if they don't use any CSS. ([@rbuels](https://github.com/rbuels))

*   Add ability for the CanvasFeatures feature labels to stay visible on the screen.
([issue #390](https://github.com/gmod/jbrowse/issues/390), [issue #971](https://github.com/gmod/jbrowse/pull/971), [@cmdcolin](https://github.com/cmdcolin), [@rbuels](https://github.com/rbuels))

*   Improve VCF tracks support for GVCF generated by GATK, and fix a number of related
VCF details display bugs. ([issue #991](https://github.com/gmod/jbrowse/pull/991), [@cmdcolin](https://github.com/cmdcolin))

*   `generate-names.pl` now supports indexing GFF3 files, enabling better use of
GFF3Tabix tracks. Thanks to [@billzt](https://github.com/billzt) for the initial implementation!
([issue #780](https://github.com/gmod/jbrowse/issues/780), [issue #900](https://github.com/gmod/jbrowse/pull/900), [@rbuels](https://github.com/rbuels))

*   CanvasFeatures `ProcessedTranscript` and `Gene` glyphs now support a "style→utrHeightPercent" configuration variable that sets the percentage of the overall feature's height that UTRs have. This was previously hardcoded to 65, now it is customizable, defaulting to its old value of 65. [@rbuels](https://github.com/rbuels)

## Bug fixes

*   Updated `NeatCanvasFeatures` and `NeatHTMLFeatures` plugins to support a `gradient`
configuration variable, fix rendering of outrons, restore their default
gradient-drawing behavior, disable gradients by default on Alignments and
Alignments2 track types, and clean up their documentation. ([issue #931](https://github.com/gmod/jbrowse/issues/931), [issue #982](https://github.com/gmod/jbrowse/issues/982),
[issue #985](https://github.com/gmod/jbrowse/issues/985), [issue #931](https://github.com/gmod/jbrowse/issues/931), [issue #992](https://github.com/gmod/jbrowse/issues/992), [issue #1011](https://github.com/gmod/jbrowse/pull/1011), [@enuggetry](https://github.com/enuggetry))

*   Fixed a bug with plugin loading that was preventing some plugins from working
correctly. ([issue #1025](https://github.com/gmod/jbrowse/issues/1025), [@rbuels](https://github.com/rbuels))

*   `flatfile-to-json.pl` will now refuse to format a track if the trackLabel
contains a '/' character. Thanks to [@dytk2134](https://github.com/dytk2134) for pointing this out, and [@cmdcolin](https://github.com/cmdcolin)
for the fix! ([issue #1023](https://github.com/gmod/jbrowse/issues/1023), [@cmdcolin](https://github.com/cmdcolin))

*   Fixed a bug in which the viewing location would not be preserved across page reloads
if `generate-names.pl` had not been run, or a names store had not otherwise
been defined. Thanks to [@cmdcolin](https://github.com/cmdcolin) for the bug report. ([issue #1016](https://github.com/gmod/jbrowse/issues/1016), [@rbuels](https://github.com/rbuels))