@gmod/jbrowse/website/blog/2018-10-05-jbrowse-1-15-4.md

JBrowse - client-side genome browser

---
layout: post
title: JBrowse 1.15.4 maintenance release
date: 2018-10-05
tags: ["News","Software releases"]
---

JBrowse 1.15.4 has been released! This release allows you to use bgzip indexed FASTA, adds a new `categoryOrder` config for sorting the Hierarchical track selector, and more!
Thanks to everyone for their feature requests and bug reports, and enjoy!

*   [JBrowse-1.15.4.zip](https://github.com/GMOD/jbrowse/releases/download/1.15.4-release/JBrowse-1.15.4.zip) - minified release
*   [JBrowse-1.15.4-dev.zip](https://github.com/GMOD/jbrowse/archive/1.15.4-release.zip) - use this if you modify jbrowse source code or use plugins
*   [JBrowse-1.15.4-desktop-win32-x64.zip](https://github.com/GMOD/jbrowse/releases/download/1.15.4-release/JBrowse-1.15.4-desktop-win32-x64.zip)
*   [JBrowse-1.15.4-desktop-linux-x64.zip](https://github.com/GMOD/jbrowse/releases/download/1.15.4-release/JBrowse-1.15.4-desktop-linux-x64.zip)
*   [JBrowse-1.15.4-desktop-darwin-x64.zip](https://github.com/GMOD/jbrowse/releases/download/1.15.4-release/JBrowse-1.15.4-desktop-darwin-x64.zip)




## Minor improvements

 * Added support for bgzipped indexed FASTA. To use, bgzip your FASTA with
   `bgzip -i file.fa`, which generates file.fa.gz and file.fa.gzi and then use
   `samtools faidx file.fa.gz`. If you specify the .fa.gz in the track config e.g.
   `"urlTemplate": "file.fa.gz"` and have all three files in your data directory,
   then they will automatically be detected (<a href="https://github.com/gmod/jbrowse/issues/1152">issue #1152</a>, <a href="https://github.com/gmod/jbrowse/pull/1200">issue #1200</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>)

 * Allow fna and mfa file extensions for FASTA to be recognized by default in
   the Open sequence dialog (<a href="https://github.com/gmod/jbrowse/issues/1205">issue #1205</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>)

 * Improve the layout slightly for dense features (<a href="https://github.com/gmod/jbrowse/issues/1210">issue #1210</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>)

 * Added a `topLevelFeaturesPercent` configuration variable that can be used to
   correct feature statistics estimates when `topLevelFeatures` is being used for
   a track, or when it contains deeply-nested features. This configuration variable
   is currently only used by BAM, BEDTabix, GFF3Tabix, and VCFTabix stores.
   (<a href="https://github.com/gmod/jbrowse/issues/1147">issue #1147</a>, <a href="https://github.com/gmod/jbrowse/pull/1209">issue #1209</a>, <a href="https://github.com/rbuels">@rbuels</a>)

 * Tabix-based data stores use a new storage backend based on the `@gmod/tabix` npm
   module. Users should see some modest performance improvements for Tabix-based
   tracks. (<a href="https://github.com/gmod/jbrowse/issues/1195">issue #1195</a>, <a href="https://github.com/gmod/jbrowse/pull/1209">issue #1209</a>, <a href="https://github.com/rbuels">@rbuels</a>)

 * Added `hideSequenceBox` config to allow hiding the FASTA boxes in the View details
   popups. Thanks to <a href="https://github.com/andreamini">@andreamini</a> for reporting (<a href="https://github.com/gmod/jbrowse/issues/1211">issue #1211</a>, <a href="https://github.com/gmod/jbrowse/pull/1219">issue #1219</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>)

 * Added `categoryOrder` config to allow sorting the categories in the Hierarchical
   track selector. For example, `categoryOrder=VCF,Quantitative/Density,BAM`. Note
   that we specify a lowest level subcategory e.g. Quantitative/Density to sort the
   parent category Quantitative to a position (<a href="https://github.com/gmod/jbrowse/issues/1203">issue #1203</a>, <a href="https://github.com/gmod/jbrowse/pull/1208">issue #1208</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>)

## Bug fixes

 * Fixed a bug in which feature labels would sometimes be repeated across the view,
   in the wrong locations. (<a href="https://github.com/rbuels">@rbuels</a>)

 * Fixed error where a chunk size limit error during histogram display would not be
   displayed (<a href="https://github.com/cmdcolin">@cmdcolin</a>)

 * Fixed issue where Open sequence dialog will open up the default "data" directory
   instead of a blank instance (<a href="https://github.com/gmod/jbrowse/issues/1207">issue #1207</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>)

 * Added check for PCR duplicates for CRAM features (<a href="https://github.com/cmdcolin">@cmdcolin</a>)

 * Fixed issue where editing the track names and types in the "Open track" dialog box
   was not working when editing multiple tracks (<a href="https://github.com/gmod/jbrowse/issues/1217">issue #1217</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>)

 * Fixed issue in which large VCF headers were not always correctly parsed by JBrowse
   (<a href="https://github.com/gmod/jbrowse/issues/1139">issue #1139</a>, <a href="https://github.com/gmod/jbrowse/pull/1209">issue #1209</a>, <a href="https://github.com/rbuels">@rbuels</a>)

 * Fixed issue where the histogram Y-scale bar would appear over features (issue
   #1214, <a href="https://github.com/gmod/jbrowse/pull/1218">issue #1218</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>)