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. ;-)
JBrowse - http://jbrowse.org
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