@gmod/jbrowse/website/blog/2013-04-25-jbrowse-1-9-1-index.md

JBrowse - client-side genome browser

---
layout: post
title: JBrowse 1.9.1 maintenance release
date: 2013-04-25
tags: ["Software releases"]
---

JBrowse 1.9.1 has been released, with performance improvements in both BAM and VCF tracks, and lots of smaller fixes and improvements.

Files for download:

*   [JBrowse-1.9.1.zip](/wordpress/wp-content/plugins/download-monitor/download.php?id=45 "download JBrowse-1.9.1.zip") - 5.0M
file SHA1 1dc089e42e626da5312a8091dbcd1972a1cfb0fd
*   [JBrowse-1.9.1-dev.zip](http://jbrowse.org/wordpress/wp-content/plugins/download-monitor/download.php?id=46 "download JBrowse-1.9.1-dev.zip") - 28.6M
file SHA1 bc5bb43ad8b71a9190e8c2a400d7db2364882e09
Changes in this release:

*   Significant speed and memory optimizations in BAM data backend
(issue #242).
*   Significant speed and memory optimizations in VCF data backend.
*   JBrowse now attempts to smooth over mismatches in the naming of
reference sequences between various datasets. For instance, if a
BAM file contains reference sequences named like "chrom1", and the
canonical reference sequences used in a JBrowse installation are
named like "chr1", JBrowse will recognize these two names as
equivalent for the purposes of displaying the BAM data. This
behavior can be disabled by setting the global configuration
variable `exactReferenceSequenceNames` to `true`. (issue #239).
*   Removed support for track `blockDisplayTimeout` configuration
variable. It never worked very well, and the problem it was meant
to address (delays caused by large data) are better mitigated by
`maxHeight` and the faster rendering offered by canvas-based track
types.
*   Fixed a bug that prevented displaying some VCF files. Thanks to
Steffi Geisen for pointing this out.
*   Reduced the default value of `maxHeight` for canvas-based feature
tracks (like Alignments2) from 1000 to 600.
*   Fixed a bug in the `Alignments` track type where BAM features with
missing mate pairs that are not drawn due to their position above
the track's `maxHeight` caused the track rendering to crash.
Thanks to Tristan Lubinski for reporting this.
*   If no global `refSeqOrder` is specified in the configuration, the
reference sequences are now not sorted. Currently, this means that
they will appear in the same order as loaded by
`prepare-refseqs.pl`. Users with a very large number of (more than
10,000) reference sequences may wish to avoid specifying a
`refSeqOrder`, since sorting the reference sequences is done at
JBrowse startup time. Thanks to Tristan Lubinski for reporting
this.
*   Fixed bug preventing display of quantitative data from files loaded
with flatfile-to-json.pl. Thanks to Gwendoline Andres for pointing
this out.
*   Instead of quantitative (wiggle) tracks throwing an error when they
cannot choose a min and max for the display scale, they now just
make a guess. While probably wrong, this at least has the track
displaying something, and users can then look up how to fix the
display scale.
*   Added support for a `chunkSizeLimit` configuration variable for BAM
and VCF-based tracks, which defaults to 5MB for BAM and 15MB for
VCF. When fetching data, if a given region requires fetching a
file chunk that is larger than this limit, a 'Too much data'
message is displayed. This helps prevent speed and memory problems
when displaying deep-coverage BAM tracks and large VCF tracks
(issue #242). Thanks to Gustavo Cerquiera (GitHub user cerca11)
for pushing for progress on this.
*   Fixed a regression in which callbacks and interpolations were not
evaluated in left-click and right-click menu configurations.
*   Fixed incorrect display of negative values in log-scale wiggle
tracks. Thanks to GitHub user drusch for pointing this out
(issue #244).
*   Fixed more minor errors when running under IE 7.
*   Fixed "Max height reached" message sometimes being drawn under
instead of over HTML-based features.