JBrowse 1

JBrowse 1.10.10 maintenance release

November 21, 2013

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.

(Download disabled. Please download the[ 1.10.12 release](https://jbrowse.org/jbrowse-1-10-12/) "JBrowse 1.10.12 maintenance release") or later instead.)

Minor improvements

  • Spacing between tracks is now configurable by setting view.trackPadding in the configuration. Thanks to Chenchen Zhu for suggesting this (issue #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).

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).

  • 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).

  • 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.

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