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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 1.10.5 maintenance release date: 2013-10-03 tags: ["Software releases"] --- JBrowse 1.10.5 has been released, with some important bug fixes and more performance improvements for data formatting scripts. Files for download: * [JBrowse-1.10.5.zip](/wordpress/wp-content/plugins/download-monitor/download.php?id=71 "download JBrowse-1.10.5.zip") - 4.6M file SHA1 17a07058a98900d2cff5d1db441ab3d2b5a425a1 * [JBrowse-1.10.5-dev.zip](http://jbrowse.org/wordpress/wp-content/plugins/download-monitor/download.php?id=72 "download JBrowse-1.10.5-dev.zip") - 26M file SHA1 c060c487fcd361cc4b41075696cef6cfc005f150 ## Minor improvements * Greatly improved the speed and reduced the memory footprint when running `prepare-refseqs.pl` with the --fasta and --gff options. * Added an `impliedUTRs` option to the ProcessedTranscript and Gene glyphs for CanvasFeatures tracks. Thanks to Ben Booth for pointing out the need for this ([issue #348](https://github.com/gmod/jbrowse/issues/348)). * Upgraded flatfile-to-json.pl to use a new version of Bio::GFF3::LowLevel::Parser for GFF3 parser, which has a lookback buffer limit that makes it easier to parse large GFF3 files that do not contain enough '###' directives. * Further improved the memory footprint and speed of generate-names.pl. Thanks to Richard Hayes for his continued help with testing improvements and reporting problems. * Removed explicit dependency on GD::Image, which is only used by the old tiled-image generation demo code. This will make dependency installation easier for many people, at a (very) small cost to backward compatibility. ## Bug fixes * Fixed a bad bug that prevented combination tracks from working. Thanks to Harry Yoo for pointing this out ([issue #351](https://github.com/gmod/jbrowse/issues/351)). * Fixed a bug in which one of the temporary files used by generate-names.pl was not being created in the correct location. Thanks to Richard Hayes for testing this. * Fixed a bug in which `generate-names.pl` could sometimes crash when run with the -v (verbose) switch, or in setup.sh. * Fixed odd behavior when entering coordinate ranges in the location box under Safari. Thanks to Keiran Raine for pointing this out ([issue #341](https://github.com/gmod/jbrowse/issues/341)).