Skip to content

HTTPS clone URL

Subversion checkout URL

You can clone with
or
.
Download ZIP
Fetching contributors…

Cannot retrieve contributors at this time

447 lines (335 sloc) 19.052 kB
{{$NEXT}}
* Added a default `menuTemplate` to all HTML-based features, so that
all HTML features now have a right-click menu by default.
* Add `css` configuration variable that allows users to specify
either strings or URLs containing CSS to add.
* Fixed feature-layout performance problem when zoomed very far in
on features that are much larger than the viewing window.
1.6.1 2012-08-28 16:50:41 America/New_York
* JBrowse now attempts to prevent feature labels being obscured by
track labels by keeping the feature labels a bit further away from
the left side of the view, if possible.
* Fixed bug in which welcome page was not shown when JBrowse has not
been configured yet (issue #130).
* Fixed bug in which passing `tracklist=0` (as when running the
browser in embedded mode) caused JBrowse to crash (issue #132).
* Added dependency on Bio::GFF3::LowLevel::Parser 1.4, which has an
important bugfix related to multi-location features (issue #109).
Thanks to Victor Poten for help in isolating this problem.
1.6.0 2012-08-25 18:04:44 America/New_York
* 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](http://www.mocklerlab.org/) 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.
1.5.0 2012-08-13 15:37:27 America/New_York
* Added a direct-access storage driver for BigWig data files, based
on code from the Dalliance Genome Explorer by Thomas Down. BigWig
file access is supported now by the current versions of all major
browsers except Internet Explorer (which is expected to work when
version 10 is released along with Windows 8).
* Added a `canvas`-based wiggle track implementation for quantitative
data that, when used with the new BigWig storage backend, removes
the need to pre-generate rendered images of wiggle data. Its
display is also highly configurable, with configuration options
modeled on the GBrowse `wiggle_xyplot` glyph type
(i.e. `Bio::Graphics::Glyph::wiggle_xyplot`).
* Added highly configurable behavior for left-clicking and
right-clicking features in HTML-based feature tracks. If a
`menuTemplate` option is specified in the track configuration,
right-clicking a feature brings up a context menu, the items in
which can be configured to do nearly anything, but that are easy to
configure for the very common use case of wanting to display
content from a certain URL. Feature left-clicks are also
configurable using the same mechanism. Thanks to Alexie
Papanicolaou and Temi Varghese for the initial implementation of
context menus.
* Improved the default HTML feature left-click dialog box. It is now
both prettier, and more comprehensive, displaying all available
data for the feature.
* Added the long-missing ability to render a second line of label
text for features containing their description, which is taken from
the feature's 'Note' or 'description' attribute, if present. The
description is only displayed if the track's `description`
configuration variable is set to a true value, which is the
default. There is also a style.maxDescriptionLength value, that
can be set to control how long a description can be before it is
truncated with ellipses. It defaults to 70 characters.
* Added a small helper script, `add-track-json.pl` that developers
and advanced users can use to programmatically add a block of track
configuration JSON to an existing JBrowse configuration file.
* Improved / fixed vertical alignment of sub-elements of HTML
features, including subfeatures and the arrowheads that show
strand. All elements in a feature are now vertically centered by
default.
1.4.2 2012-07-12 15:38:55 America/New_York
* Restore support for histScale, subfeatureScale, and labelScale in
--clientConfig and track configuration JSON. Thanks to Hernán
Bondino for pointing this out.
1.4.1 2012-07-10 14:58:34 America/New_York
* Made displayColumns option for the faceted track selector
case-insensitive, and interpret a column name of "Name" as meaning
the track's key.
* `bam-to-json.pl` now filters out alignments that are not at least
two nucleotides in length. Thanks to Tristan Lubinski for
assistance.
* Introduced limits on the sizes of cookies that can be set,
preventing '400 bad request' errors (issue #113).
1.4.0 2012-06-14 17:43:50 America/New_York
* Added a full-featured faceted track selector for users that have
many (hundreds or thousands) of tracks. This can be turned on by
setting the `trackSelectorType` config variable to "Faceted". See
the JBrowse wiki for more documentation on how to use faceted track
selection. (issue #95)
* Removed the dropdown selector for reference sequences in favor of
making the location box auto-complete reference sequence and
feature names. This makes JBrowse much more scalable to large
numbers of reference sequences. (fixes issues #3, #60, and #101)
* Added a vertical-scrolling marker on the right side of the track
pane, making it much easier to discern the vertical position of the
track display. (issue #93).
* biodb-to-json.pl and flatfile-to-json.pl now load all available
feature data: all attributes of features are now encoded in the
JSON and are available for use by feature callbacks. (issue #72)
* Feature labels now do not scroll off screen if any part of the
feature is still visible (fixes issue #62).
* Added jbrowse_conf.json, a default JSON-format configuration file,
to the JBrowse root directory. Makes it easier to get started
with more advanced JBrowse configuration.
* JBrowse instances now report usage statistics to the JBrowse
developers. This data is very important to the JBrowse project,
since it is used to make the case to grant agencies for continuing
to fund JBrowse development. No research data is transmitted, the
data collected is limited to standard Google Analytics, along with
a count of how many tracks the JBrowse instance has, how many
reference sequences are present, their average length, and what
types of tracks (wiggle, feature, etc) are present. Users can
disable usage statistics by setting "suppressUsageStatistics: true"
in the JBrowse configuration.
1.3.1 2012-04-19 17:55:44 America/New_York
* Fixed memory-management bug that caused way too much RAM to be used
by FeatureTrack loading (flatfile, bam, and biodb-to-json.pl) when
loading with very large numbers of reference sequences. Big thanks
to Tristan Lubinski for help in isolating this.
* Fixed some bugs in BAM support section of setup.sh autosetup
script, thanks to Tristan Lubinski for help in isolating this as
well.
* Added an example document with an iframe running JBrowse in
embedded mode in docs/examples/embedded_mode.html
* flatfile-to-json.pl now loads the 'score' attribute of features in the
JSON.
1.3.0 2012-04-13 17:04:30 America/New_York
* Added support for "rubberband" dynamic zooming, in which users can
click and drag to select a region to zoom to. Dragging on any
scale bar, or shift-dragging on the main track pane, triggers a
dynamic zoom.
* Correcting a long-standing oversight, wiggle data tracks and
feature histograms now have numerical y-axis scales that show the
numerical values of the data.
* Server-side data-formatting scripts now support a --compress option
to compress (gzip) feature and sequence data to conserve server
disk space. Using this option requires some web server
configuration. Under Apache, AllowOverride FileInfo (or
AllowOverride All) must be set for the JBrowse data directories in
order to use the included .htaccess files, and mod_headers and
mod_setenvif must be installed and enabled. Under nginx a
configuration snippet like the following should be included in the
configuration:
location ~* "\.(json|txt)z$" {
add_header Content-Encoding gzip;
gzip off;
types { application/json jsonz; }
}
* flatfile-to-json.pl: now much faster and more memory-efficient,
especially for GFF3 files. Remember that '###' directives are very
important to have in large GFF3 files! Also removed nonfunctional
--extraData switch.
* Added ability to turn off some JBrowse UI panels via URL arguments
to the default index.html, or via arguments to the Browser
constructor itself. Can dynamically turn off the navigation box,
the overview panel, and the track list, respectively. When all of
these are off, and if run in an iframe, JBrowse is running in an
"embedded mode" that looks similar to the output of GBrowse's
gbrowse_img script, with the exception that the view in this case
is a fully functioning, scrollable and zoomable JBrowse. See the
GMOD wiki (http://gmod.org/wiki/JBrowse) for more on how to set up
embedded mode. Thanks to Julie Moon, a co-op student working at
OICR, for this work!
* Improved graphical look and feel.
* Browser support for this release:
* Google Chrome 18 perfect
* Google Chrome 17 perfect
* Mozilla Firefox 11.0 perfect
* Mozilla Firefox 10.1 perfect
* Mozilla Firefox 10.0.2 perfect
* Mozilla Firefox 3.6.28 nonfunctional
* Apple Safari 5.1.5 (Lion) perfect
* Microsoft Internet Explorer 9 perfect
* Microsoft Internet Explorer 8 good
* Microsoft Internet Explorer 7 minor problems
* Microsoft Internet Explorer 6 not tested
* KDE Konqueror 4.7.4 nonfunctional
* KDE Konqueror 4.5.5 nonfunctional
* Opera (all versions) not tested
NOTE: Internet Explorer 6 is no longer supported by JBrowse.
* Added an automated-setup script, setup.sh, that tries to install
Perl prerequisites, format Volvox example data, and install Wiggle
and BAM support (fetching samtools from SVN if necessary)
automatically.
* Navigating to JBrowse with missing or malformed configuration or
data will now bring up an error page with useful messages and links
to help documentation, instead of a blank white page.
* JBrowse data directories now include an Apache .htaccess in their
root directory that, if mod_headers is installed and AllowOverride
FileInfo or AllowOverride All is enabled, will emit the proper HTTP
headers to allow cross-origin XHR requests for the data.
* A new "Help" link in the upper right, or pressing "?" on the
keyboard, brings up a "JBrowse Help" dialog box with basic usage
information and links to more help information.
* Arrowheads indicating strandedness are now drawn inside feature
boundaries.
* Clicking on the overview bar or the main scale bar now centers the
view at the clicked position. In addition, while holding down
shift, clicking in the main track panel will also center the view
at that position.
* Added bin/remove-track.pl, a script to remove a track from a
JBrowse data directory. Run bin/remove-track.pl -? to see its
documentation.
* Added build instrumentation to support a JSDoc-based system of
developer API documentation. This documentation is still far from
complete.
* Ian Davis contributed code to add a view of the reverse strand of
the sequence in the DNA track. Thanks Ian!
* Fixed bug in which, for some sequence chunk sizes, the DNA bases
would display incorrectly.
* Added minor gridlines to the main track view.
* Fixed a long-standing off-by-one bug where the window could not be
scrolled to view the last base in the reference sequence.
* Coordinates displayed in the user interface are now 1-based closed
coordinates, which are more familiar to most users. Previously,
the labels displayed interbase (i.e. 0-based half-open)
coordinates.
* NON-BACKWARDS-COMPATIBLE improvements to the JSON format used for
track configuration, feature data, and image data
- initial support for a new hook system for greater
administrator-configurability of feature display
- support for more than one level of subfeatures
* Miscellaneous improvements and refactoring of data-formatting Perl
code.
* More detailed POD-based help documentation on all scripts
* --tracklabel options to all scripts replaced with --trackLabel.
* New suite of integration tests, and some unit tests, for
server-side Perl code.
* Beginnings of a suite of Selenium-based integration tests for the
front-end JavaScript code.
* Support for Apple touch-based devices merged into normal
index.html, so that the same link can be used regardless of the
browsing platform.
* Bug fixed in which non-stranded features do not display properly
(a problem with the CSS styles).
========================================================
version 1.2.1, March 2011
Fixed bugs in release 1.2:
- problems with BED handling reported by Gregg Helt and Brenton Graveley
- performance regression reported by Chris Childers
- incorrect handling of names in ucsc-to-json.pl
- wig2png slowdown reported by Brenton Graveley
========================================================
version 1.2, Febrary 2011
These notes document changes since release 1.1 in September 2010.
Most of the work in this release went into making JBrowse handle large
amounts of feature data better. Before, the amount of memory used
when processing BAM files was more than 10 times the size of the file;
now, the amount of memory required is fixed.
Other new features in this release:
- Import of UCSC database dumps. A ucsc-to-json.pl script is now
provided for taking database dumps from UCSC and creating a JBrowse
instance using them. The "genePred" and "bed" track types are
currently supported; "psl" tracks are not yet supported.
- Touch. Juan Aguilar's code for using JBrowse on an iOS device
(iPhone, iPod touch, iPad) is now integrated. As of the current
release, users wanting to use JBrowse on those devices have to
navigate to a separate HTML page (touch.html) rather than the
default index.html; i.e. the code does not currently detect
touchscreen devices automatically.
- Bug fixes. A number of bugs have also been fixed, including one that
restricted the placement of the "data" directory, and a bug in
wiggle rendering that caused spurious peaks or troughs at tile
boundaries.
Known issues/limitations with this release:
- Some additional CPAN modules are now required:
PerlIO::gzip
Heap::Simple
Devel::Size
- No JSON-level backward compatibility. If you are upgrading from an
older version of JBrowse, you will have to regenerate all the JSON
files on your server. This means wiping your jbrowse/data directory
and re-running all server scripts (flatfile-to-json, biodb-to-json,
wig-to-json, etc.) to regenerate your data from the original
FASTA/GFF/BED/WIG files. We apologize for the inconvenience of this,
but it is inevitable sometimes; we do aim to minimize the number of
releases which are backwardly-incompatible in this way.
========================================================
version 1.1, September 2010.
These notes document JBrowse developments in the period from July 2009
(online publication of the first JBrowse paper in Genome Research, the
de facto "version 1.0") up to September 2010 (the first in a planned
series of quarterly releases).
New features in this release:
- Scalability. JBrowse can now handle very large data tracks,
including human EST/SNP tracks, or tracks of next-gen sequence
reads. Large datasets are broken into smaller chunks, so there is no
loading delay for big tracks.
- Extensibility. A Perl module (ImageTrackRenderer.pm) for creating
user-drawn image tracks is now available, based on the CPAN GD.pm
module. An example program is provided, draw-basepair-track.pl, that
uses this module to draw arcs over a sequence representing the
base-pairing interactions of RNA secondary structure.
- Bug fixes. Numerous display glitches have been fixed, including
issues with wide-screen monitors and long mostly-offscreen features.
Known issues/limitations with this release:
- No JSON-level backward compatibility. If you are upgrading from an
older version of JBrowse, you will have to regenerate all the JSON
files on your server. This means wiping your jbrowse/data directory
and re-running all server scripts (flatfile-to-json, biodb-to-json,
wig-to-json, etc.) to regenerate your data from the original
FASTA/GFF/BED/WIG files.
- Next-gen sequence display is currently restricted to the
co-ordinates of the outermost region to which a single read is
mapped. There is no support (yet) for displaying pairing between
reads, sequences of reads, alignment of read to reference sequence
(e.g. splicing), or mismatches between read and reference.
- Processing SAM/BAM next-gen sequence files takes a lot of memory
(about 500 megabytes per million features).
- Numerical (as opposed to comparative) readout of the data in Wiggle
tracks, e.g. via a y-axis label or mouseover popup, is still
unsupported.
Please visit the website for contact info
http://jbrowse.org/
Jump to Line
Something went wrong with that request. Please try again.