JBrowse 1

JBrowse 1.6.5 bugfix release

October 26, 2012

I'm pleased to announce the release of JBrowse 1.6.5, containing some small new features, plus fixes for some issues in the 1.6.4 release.

Files for download:

  • JBrowse-1.6.5-min.zip - 2.8M

  • JBrowse-1.6.5-full.zip - 27.3M Changes in this release:

  • The location box now shows the length of the currently visible ** region** in parentheses. For example: ctgB:1244..3566 (2.32 Kb). Thanks to Karsten Hokamp for the suggestion!

  • The arrow keys on the keyboard can now be used to pan and scroll around the genome view.

  • Wiggle track mouseover cursors now display the score with only 6 significant digits, avoiding confusion over approximations introduced by scores being converted to IEEE floating-point numbers (as for BigWig files) and back to text.

  • The faceted track selector now renders any HTML that may be present in the track metadata by default. To turn this off, it now accepts an escapeHTMLInData option that, if set to true or 1, will not render the HTML, but will instead display the raw code (issue #145).

  • Upgraded to a more recent version of jszlib, which contains some important bugfixes (issue #157).

  • Fixed bug dealing with very large regions with the same value in canvas-based Wiggle tracks (also issue #157).

  • prepare-refseqs.pl now by default uses a more scalable directory ** structure for storing sequences**. This fixes problems some users were experiencing with large numbers of reference sequences (issue #139).

  • ucsc-to-json.pl now supports a --primaryName option allowing the users to alter which UCSC data field is displayed by JBrowse as ** the primary name** of the features in a track. Also, ucsc-to-json.pl now treats as indexable names all UCSC data columns called "name", "alias", or "id" followed by zero or more digits. Thanks to Steffi Geisen for this suggestion.

  • Fixed "Duplicate specification" warnings coming from flatfile-to-json.pl and remove-track.pl.

  • Fixed bugs in which both the first few and the last few bases of a reference sequence were not displaying correctly in a DNA track.

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