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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 1.10.10 maintenance release date: 2013-11-21 tags: ["Software releases"] --- JBrowse 1.10.10 has been released, with new compression support in `generate-names.pl`, configurable inter-track spacing, and quite a few bug fixes. <div style="padding: 2em 1em; margin: 1em; border: 1px solid #eee; background: #fcfcfc">(Download disabled. Please download the[ 1.10.12 release](http://jbrowse.org/jbrowse-1-10-12/ "JBrowse 1.10.12 maintenance release") or later instead.) </div> ## Minor improvements * Spacing between tracks is now configurable by setting `view.trackPadding` in the configuration. Thanks to Chenchen Zhu for suggesting this ([issue #377](https://github.com/gmod/jbrowse/issues/377)). * If reference sequences are defined, but no tracks are yet added, JBrowse will start normally instead of going to the "Congratulations, JBrowse is on the web" page. * `generate-names.pl` now supports a `--compress` option that compresses the name index files to save server disk space. Thanks to Richard Hayes for pointing out the need for this ([issue #378](https://github.com/gmod/jbrowse/issues/378)). ## Bug fixes * `generate-names.pl` now uses IO::Uncompress::Gunzip instead of PerlIO::gzip to read compressed VCF files. This fixes a bug in which only the first few hundred names in a VCF were indexed. Thanks to Cris Lawrence for pointing this out ([issue #380](https://github.com/gmod/jbrowse/issues/380)). * Fixed a bug in which `generate-names.pl` would crash if run with `--incremental` and no existing names index. Thanks to Richard Hayes for pointing this out ([issue #379](https://github.com/gmod/jbrowse/issues/379)). * Fixed a bug in which `generate-names.pl` would sometimes choose the wrong number of hash bits when performing incremental updates, leading to the old data being lost. Thanks to Richard Hayes for lots of help troubleshooting this. * Fixed bug where other tracks are visible underneath pinned tracks when the display is scrolled down. Thanks to Ed Lee for pointing this out. * Fixed a bug in which tooltip does not hide after the mouse leaves a Wiggle track in Safari 5 and 6. Thanks to Charles Girardot for pointing this out. * Fixed a bug in which the `main.css` file for plugins was not being correctly loaded in some installations. Thanks to Matt Bomhoff for pointing this out.