JBrowse 1

JBrowse 1.6.0 released, includes feature descriptions and more!

August 25, 2012

I'm very pleased to announce the release of JBrowse 1.6.0! This release is not quite as major as the previous two releases, but there are still some nice things added.

As usual, this release comes in two flavors: the "minimal" release (JBrowse-1.6.0-min.zip) - 2.8M) that includes only the software and documentation necessary to format your own data and run the browser, and the "full" release (JBrowse-1.6.0-min.zip- 27.2M) that includes the developers' test suite, more sample data files, and developer documentation. Here is the full list of new improvements in 1.6.0:

  • Added description capabilities to HTML-based features, similar to GBrowse's descriptions. If zoomed in far enough (as defined by style.descriptionScale), adds a second line of text below the feature's label that shows the content's of the featur's Note or description attribute (issue #67).

  • Give prepare-refseqs.pl the capability to load reference sequences from embedded FASTA sections in GFF3 files (issue #128).

  • Configuration files can now recursively include eachother, and tracks sections are merged intelligently.

  • Made sequence tracks not disappear when zoomed out too far to see base pairs. Instead, sequence tracks simply display lines suggesting that DNA would be visible at higher magnification. (issue #124).

  • Double-clicking track labels in the simple track selector now turns the track on (issue #123).

  • Fixed bug in BigWig tracks that use the "scale": "log" option: did not render properly when the wiggle data included 0's. This was due to the fact that the origin was being mapped to Infinity. Thanks to the Mockler Lab for the fix! (issue #127).

  • Fixed bug in NCList binary search code in which zero-length features at node boundaries would not be found (fix by Ed Lee).

  • Fixed bug in which dragging the scroll bar on the simple track selector can sometimes cause a drag-and-drop to erroneously begin (issue #89).

  • Fixed some bugs in the layout of HTML-based features in which features in different blocks would overlap in some circumstances. Under the hood, replaced the contour-based layout engine with a simpler, not-much-slower implementation that is more correct in the general case (issue #122).

  • Fixed a bug with vertical centering of strand arrows and other sub-elements of HTML-based features.

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