JBrowse 1.10.11 released

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JBrowse 1.10.11 released

Robert Buels-2
Hi all,

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

It can be downloaded from http://jbrowse.org/jbrowse-1-10-11.

# Release 1.10.11     2013-12-03 17:21:20 EST5EDT

## 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

  * 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

  * 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).

Happy browsing.  ;-)

Robert Buels
Lead Developer
JBrowse - http://jbrowse.org