JBrowse 1

JBrowse 1.10.11 maintenance release

December 3, 2013

JBrowse 1.10.11 has been released, with many bug fixes and better support for spliced alignments in SNPCoverage tracks.

(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

  • Made the sequence track's "zoom in to see sequence" placeholder take up less vertical space. Thanks to Scott Cain for pointing out that making it be the same height as it will eventually be when zoomed in to base level is silly.

  • By default highlighting features after searching for them by name is now turned off. Set the highlightSearchedRegions top-level conf variable to true to turn this back on. Turns out, most people seem not to like this behavior. Thanks to Gregg Helt and Cris Lawrence for pointing this out.

  • SNPCoverage tracks now correctly display "skipped" regions in alignments, such as those produced by TopHat. Thanks to Josh Orvis, Gustavo Cerquiera, and others for reminders that this was still an issue.

  • SNPCoverage tracks now provide per-strand counts of "reference" reads at each position, like they already were providing for reads with mismatches.

  • SNPCoverage tracks now accept a mismatchScale configuration variable that sets the viewing scale (i.e. zoom level, pixels per bp) above which base-level mismatches will be drawn. Defaults to 1/10. Making this value larger can speed up SNPCoverage tracks for high-coverage data at the cost of needing to zoom in further to see mismatches.

  • setup.sh now uses curl for downloading things instead of wget, since curl is more widely available. Thanks to Keiran Raine for suggesting and implementing this (issue #393).

Bug fixes

  • Fixed a bug in which generate-names.pl would sometimes report the incorrect number of hashing bits in verbose output, and would sometimes use the number of hashing bits for an existing index even if that index was being regenerated. Thanks to Richard Hayes for pointing out the incorrect log output.

  • Fix generate-names.pl crashing on some older versions of Perl with an error like Bareword "POSIX::O_RDONLY" not allowed while "strict subs" in use. Thanks to Chris Childers for pointing this out.

  • Fix setup.sh failing on some older versions of Perl. It now runs generate-names.pl with the --safeMode flag.

  • Fixed a bug where the value display in SNPCoverage tracks would sometimes report "NaN%" for the reference when no reads cover a region.

  • Fixed a bug in which activating rubberband zooming using the SHIFT key while in highlighting mode would cause all the tracks to be dragged when attempting to highlight a region afterward. Thanks to Erik Derohanian for pointing out and fixing this (issue #387).

  • Fixed the location of the dojo/nls directory in release zipfiles. Was erroneously in src/nls, supposed to be src/dojo/nls. Thanks to Matt Bomhoff for pointing this out.

  • The in-memory GFF3 parser now copes with a missing newline at the end of a GFF3 file. Previously, the last line was ignored if it did not end with a newline character. Thanks to Colin Davenport for pointing this out (issue #394).

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