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@gmod/jbrowse

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JBrowse - client-side genome browser

jbrowse.org

GMOD/jbrowse

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--- layout: post title: JBrowse 1.10.8 maintenance release date: 2013-10-25 tags: ["Software releases"] --- JBrowse 1.10.8 has been released, with an important bugfix for generate-names.pl, better REST data store feature caching, and more. Files for download: * [JBrowse-1.10.8.zip](/wordpress/wp-content/plugins/download-monitor/download.php?id=77 "download JBrowse-1.10.8.zip") - 4.6M file SHA1 c6161ee7814dbc02878cdf642ab62b82bc61dbab * [JBrowse-1.10.8-dev.zip](http://jbrowse.org/wordpress/wp-content/plugins/download-monitor/download.php?id=78 "download JBrowse-1.10.8-dev.zip") - 26M file SHA1 0b288a98220159c5c97f6ea3bd8eb5b987cc4087 ## Minor improvements * Added a new `navigateTo` action usable for customizing feature left-clicks and right-click menus. Thanks to Scott Cain for requesting this. * Added a new `feature_range_cache` option for the REST data backend. If set to true, the REST backend will more aggressively cache ranges of feature data. Thanks to Daniel Troesser for pointing out the need for this ([issue #369](https://github.com/gmod/jbrowse/issues/369)). * `maker2jbrowse` now, by default, runs `generate-names.pl` to generate names indexes. Also added a `--no_names_index` option to turn this off. Thanks to Josie Reinhardt for making me notice this was missing. * Tweaked `generate-names.pl` default indexing parameters to emphasize indexing speed more. Now defaults to a smaller average file size for the on-disk JSON files it produces, which is much faster to generate and write (up to 8 or 10x faster). However, the on-disk index is about 2-2.5x larger overall. * Removed support for the `--refids` command-line argument to `prepare-refseqs.pl`, which has probably never really worked. * Improved `prepare-refseqs.pl` support for Bio::DB::Das::Chado database backends. Thanks to Gwendoline Andres for helping troubleshoot this. ## Bug fixes * Fixed generate-names.pl making incorrect name indexes when using 16 or more bits of hashing (when the number of index entries exceeds about 4 million). Thanks to Josie Reinhardt for helping troubleshoot this ([issue #370](https://github.com/gmod/jbrowse/issues/370)). * The faceted track selector no longer refuses to display track unique labels even if they are explicitly included in the `displayColumns` setting.