@gmod/jbrowse/website/blog/2013-09-04-jbrowse-1-10-3-index.md

JBrowse - client-side genome browser

---
layout: post
title: JBrowse 1.10.3 maintenance release
date: 2013-09-04
tags: ["Software releases"]
---

JBrowse 1.10.3 has been released, with a lot of small enhancements and important bugfixes.

Files for download:

*   [JBrowse-1.10.3.zip](/wordpress/wp-content/plugins/download-monitor/download.php?id=67 "download JBrowse-1.10.3.zip") - 4.8M
file SHA1 3be482df63ce10a9211483bc760d3b4137a2e77f
*   [JBrowse-1.10.3-dev.zip](http://jbrowse.org/wordpress/wp-content/plugins/download-monitor/download.php?id=68 "download JBrowse-1.10.3-dev.zip") - 26M
file SHA1 825093524bbf09f0f724f80332342b99f8e50734
<span style="color: #000000; font-size: 1.8em; line-height: 1.5em;">Minor improvements</span>

*   Added options to Alignments, Alignments2, and SNPCoverage tracks to
allow hiding reads that are duplicates, fail vendor QC, have
missing mate pairs, are secondary alignments, and/or are
supplementary alignments. Thanks to Kieran Raine and Andrew Uzilov
for pointing out the need for this, and for their input on its
design (issue #332).
*   Added support for a `variables` configuration for SPARQL data
stores that can be used to specify additional variables for
interpolating into a SPARQL query. Thanks to Toshiaki Katayama for
suggesting this.
*   Added the ability for Sequence tracks to display a 6- or 3-frame
translation of the reference sequence. Thanks to Daniel Kasenberg
for implementing this (issue #221).
*   Added checkboxes in the track menu of Sequence tracks that allow
users to toggle the display of the forward strand, reverse strand,
and 6-frame translation.
*   Added support for an `addStores` variable in the query string of the
URL used to start JBrowse. This variable accepts store
configurations (which are a way to specify data sources separately
from track configurations, so multiple tracks can use the same data
source) in JSON format. For example, to add a store called
"urlbam" that points to a BAM file, you could use the JSON:`{ "urlbam": { "type": "JBrowse/Store/SeqFeature/BAM", "urlTemplate": "/path/to/my/bamfile.bam" }}`

which, when URI-escaped and put in the query string, looks like:

`addStores=%7B%20%22urlbam%22%3A%20%7B%20%22type%22%3A%20%22JBrowse%2FStore%2FSeqFeature%2FBAM%22%2C%20%22urlTemplate%22%3A%20%22%2Fpath%2Fto%2Fmy%2Fbamfile.bam%22%20%7D%7D`
*   Slightly improved performance of generate-names.pl in cases where
--completionLimit is zero. Also improved the POD documentation of
the --completionLimit parameter for generate-names.pl. Thanks to
Richard Hayes for his continued patience.

## Bug fixes

*   Fixed some bugs that prevented proper display of BigWig files
larger than 4GB. Thanks to Keiran Raine for pointing this out.
*   Fixed a major performance bug that unnecessarily slowed down
display of large BigWig files with Wiggle tracks when `autoscale`
is set to "local".
*   Fixed a bug that prevented display of BAM reads that had MD tags
but no associated CIGAR string. Thanks to Keiran Raine for point
this out (issue #330).
*   Fixed a bug in which FixedImage tracks (e.g. legacy image-based
Wiggle tracks) never take down the "Loading" message when
displaying on a reference sequence for which no image data has been
provided.
*   Fixed a bug that prevented rendering of mismatches, insertions, and
deletions in a BAM read that occurred after a skip. Thanks to Gregg
Helt for noticing this and fixing it (issue #325).
*   Fixed a bug in which the SNP frequencies calculated by SNPCoverage
tracks were sometimes incorrect. Thanks to Matthew Conte for
pointing this out (issue #335).
*   Fixed a bug in which reference sequences with a start coordinate
other than zero would cause the overview scale track to not be
drawn correctly. Thanks to Gregg Helt for noticing this and
working on an initial fix (issue #324).
*   Fixed a bug in which the most recent location visited on a given
reference sequence was not properly being restored from the saved
cookie. Thanks to Gregg Helt for the initial fix for this
(issue #321).
*   Fixed a bug in which event handlers and blocks in CanvasFeatures
tracks were not being properly cleaned up. The most prominent
visible consequences of this were duplicate dialog boxes being
opened when clicking on a canvas feature. Thanks to Keiran Raine
for noticing this and making sure it was fixed (issue #329).
*   Fixed a bug with flatfile-to-json.pl parsing of GenBank locations.
Thanks to Steve Marshall for pointing this out (issue #323).
*   Fixed a bug in which SNPCoverage tracks would not always properly
display error messages when something goes wrong, particularly
under IE 9.