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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-1.11.5 maintenance release date: 2014-09-04 tags: ["News","Software releases"] --- A new JBrowse release has arrived! JBrowse 1.11.5 incorporates many valuable contributions and feedback from the community which has been overwhelmingly positive. Some notable bugs have been fixed, including a long-standing VCF file parsing bug, a scrolling bug that affected popup boxes for variants on JBrowse 1.11.4, and a patch for setup.sh build errors. There are also some new configuration options for the tracklist and dialog boxes, and the ability to use tablet and touch-screen devices has been fixed! * [JBrowse-1.11.5.zip](http://jbrowse.org/releases/JBrowse-1.11.5.zip) - 4.9M file SHA1 480a9363c1799713666bed56d6a134af69982c9e * [JBrowse-1.11.5-dev.zip](http://jbrowse.org/releases/JBrowse-1.11.5-dev.zip) - 26M file SHA1 8b0040bda792b70a7a100a0f3fc19dcc829819c4 ## Minor improvements * Added the ability to disable sorting on the Hierarchical track selector using the sortHierarchical flag. Thanks to Chris Childers for the suggestion and Colin Diesh for the implementation ([issue #477](https://github.com/gmod/jbrowse/issues/477)). * Added saving of the display mode setting on the CanvasFeature based tracks. Thanks to Jon Hinton for the idea and Colin Diesh for the fix ([issue #469](https://github.com/gmod/jbrowse/issues/469)). * Added configurable click event handlers for Wiggle type tracks. Thanks to Richard Hayes for implementing this feature ([issue #489](https://github.com/gmod/jbrowse/issues/489)). * Added more configuration options for 'View details' popups as well as the ability to customize the 'About track' popups. Thanks to Colin Diesh for the idea and implementation ([issue #494](https://github.com/gmod/jbrowse/issues/494)). * Added the ability to load the category attribute from trackMetaData files to be used for the Hierarchical track selector. * Added the ability to specify initially collapsed categories in the Hierarchical track selector ([issue #507](https://github.com/gmod/jbrowse/issues/507)). * Added beta touch-screen and tablet support by fixing a related bug. Thanks to Paul Hale and Kieran Raine for reporting bugs and to Emily Greenfest-Allen for the suggested fix ([issue #505](https://github.com/gmod/jbrowse/issues/505)). ## Bug fixes * Fixed a bug with VCF tabix file parsing that caused unnecessary chunkSizeLimit errors. Thanks to Richard Hayes for finding and debugging this issue ([issue #486](https://github.com/gmod/jbrowse/issues/486))! * Fixed a bug where the Variant popup boxes would not display complete genotype information in previous 1.11.* versions. Thanks to Nando for reporting the bug and Colin Diesh for the bugfix ([issue #488](https://github.com/gmod/jbrowse/issues/488)). * Fixed a small error that occured when using variant type tracks with the REST API. * Added a bugfix that caused problems scrolling in dialog boxes for variant type tracks in 1.11.4 ([issue #492](https://github.com/gmod/jbrowse/issues/492)). * Fixed the use of the --refs flag on prepare-refseqs.pl. Thanks to Audrey for finding & fixing this bug ([issue #497](https://github.com/gmod/jbrowse/issues/497)). * Added missing template length flag to the Alignments popup dialogs. Thanks to Kieran Raine for the suggestion and Colin Diesh for the fix ([issue #471](https://github.com/gmod/jbrowse/issues/471)). * Fixed the functionality of the --incremental flag in the generate-names.pl script. Thanks to Richard Hayes and Colin Diesh fixing the issue ([issue #478](https://github.com/gmod/jbrowse/issues/478)). * Fixed legacy bam-to-json.pl support when running setup.sh due to samtools build modifications ([issue #501](https://github.com/gmod/jbrowse/issues/501)).