JBrowse 1

JBrowse 1.11.1 maintenance release

January 7, 2014

JBrowse 1.11.1 has been released, with a number of bug fixes and some nice improvements to Alignments2 tracks. Most of the Alignments2 improvements were thought up by Keiran Raine at Sanger, thanks Keiran! Thanks also to Cris Lawrence and Richard Hayes, who were helpful in finding some other bugs and opportunities for improvements.

Files for download:

Minor improvements

  • Alignments2 tracks now include right-click menu items to view the location of an alignment's mate pair or next segment in a popup or a new tab. Thanks to Keiran Raine for suggesting this (issue #406).

  • Alignments2 tracks now draw gaps and deletions in reads regardless of zoom level, as long as the alignment is at least 3 pixels wide in the display. Thanks to Keiran Raine for pointing out the need for this (issue #403).

  • Added support for a histograms.max variable for CanvasFeatures-based tracks that can be used to manually set the max value of a histogram display. Thanks to Keiran Raine for pointing out the need for this.

  • Added support for drawing clip markers (with their color set by histograms.clip_marker_color) in CanvasFeatures-based tracks. Thanks to Keiran Raine for pointing out the need for this (issue #402).

  • Canvas-based feature tracks now try to draw histograms, if available, when the data backend throws a data-overflow error (like when the BAM backend exceeds the chunkSizeLimit). Thanks to Keiran Raine for motivating this (issue #405).

  • Make it easier to set JS loading baseUrl by moving it into the initial dojo configuration. Thanks to Jillian Rowe for pointing out the need for this.

  • Enhanced new text-based config syntax to support arrays of values in a list like:

    [trackMetadata]
sources =
  + data/mymeta.csv
  + data/more_meta.csv

Bug fixes

  • When a number is typed into the location box, JBrowse first checks if it is the name of a feature in the names index, and only interprets it as a coordinate if it is not found in the names index. Thanks to Richard Hayes for pointing this out (issue #407).

  • Fixed bug that caused client-side GFF3 tracks to appear as "Loading" forever if the GFF3 is malformed (like malformed GFF3 files that are opened with the File->Open tool).

  • Fixed bug in which no default value for maxFeatureSizeForUnderlyingRefSeq was being set, which made default feature detail popups try to fetch and display a feature's underlying reference sequence even if it is way too large, unless the variable was set explicitly in the configuration.

  • JBrowse now shows a more understandable error message when trying to open an uncompressed BAM file. Thanks to Keiran Raine for pointing this out (issue #404).

  • Fixed jbrowse.conf faceted track selector configuration examples not working as written. Thanks to Cris Lawrence for pointing this out.

  • Fixed a bug in which right-clicking on feature labels in an HTMLFeatures-based track did not bring up the right-click menu for a feature. Thanks to Cris Lawrence for pointing this out (issue #408).

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