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release-notes.txt
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{{$NEXT}}
# Release 1.12.3 2017-05-02 19:20:01 America/Los_Angeles
## Minor improvements
* Upgraded build system to install dependencies with bower and
updated to dojo 1.9.8 (issue #718).
* Added the ability to load tabix indexed GFF and BED files.
Thanks to Colin Diesh and @zhjilin for contributing (issue #670).
* Added ability to open BED files in the "Open track" user interface
(issue #729).
* Added ability to access SPARQL and other jbrowse data stores via
CORS. Thanks to the WebApollo hackathon and Eric Rasche for
contributing (issue #679).
* Added extra coloring schemes for the Sequence track when using
protein residues. Thanks to Eric Rasche for the idea and
implementation (issue #673).
* Added ability to specify custom exporter classes for the "Save
track data" option, for example, adding exporter code in plugins
(issue #682).
* Added ability to specify custom name store classes via plugins,
which allows plugins to implement their own search functionality
(issue #732).
* Added a timeout for the track feature density calculations which
can aid problems like consistent chunkSizeLimit issues
(issue #540, issue #730).
* Added an option to specify multiple highlights, or bookmarks,
using the config file, a remote service, or the URL bar
(issue #668).
* Added support for parsing BAM files from IonTorrent (issue #782,
issue #568).
* Added support for native file access to .2bit files (issue #759).
* Added list of plugins in about box (issue #848).
* Added cacheMismatches option to improve performance when viewing
long-read alignments (issue #860).
* Added subfeatureDetailLevel config item to make View details box
only load subfeatures on demand (issue #861).
* Added ability to draw scatter plot from BigWig tracks. Thanks to
Keiran Raine for the contribution (issue #741).
* Added a fullviewlink option for the URL bar to disable "View full
link" attribute in embedded JBrowse. Thanks to Vivek Krishnakumar
for contributing (issue #813).
* Added URL parameter &tracklabels=0 and config parameter to hide
track labels (issue #869).
* Added renderAlignment option which creates a per-base alignment
view of the read versus the reference (issue #795).
* Added inferCdsParts option which creates CDS subfeatures from a
continuous CDS region for CanvasFeatures glyphs. Thanks to
Vivek Krishnakumar for the contribution (issue #872).
* Added events tracks/focus, tracks/unfocus, allowing for context
switching based on selected track.
## Bug fixes
* Made the menu bar widgets centered again (issue #680).
* Fixed error where the sequence track would not load after "Open
sequence file" (issue #831).
* Fixed problem with persistant "Error reading from name store"
message. Thanks to Anthony Bretaudeau for contributing the fix!
(issue #820).
* Reverted to standard eukaryotic codon set.
* Fixed issue where saving session in JBrowse Desktop where plugins
were not saved with session.
* Fixed an error if there were numerical values being used as label
or description for the CanvasFeatures type tracks. Thanks to
Eric Rasche for reporting (issue #673).
* Fixed some issues where the Gene glyph would not layout some
features correctly. Thanks to Eric Rasche for reporting
(issue #686).
* Fixed an issue with JBrowse Desktop where saving session would not
save the tracks that were not visible.
* Added fix when using indexed fasta from prepare-refseqs.pl.
Thanks to @billzt for the report (issue #719).
* Added a fix for an issue where editing the configuration of files
that were opened by a user didn't work. Thanks to @lpryszcz for
the report (issue #569).
* Fixed some inconsistencies where "Open sequence" on file with a
.fasta file extension failed (issue #696).
* Fixed issue where track labels would re-appear during scroll
(issue #793).
* Added handler for click scrolling in genome view. Thanks to
@exogenesys for fixing (issue #709).
* Fixed a rare error that only affected some versions of Chrome
(issue #758).
* Removed linear gradients from some NeatFeatures tracks
(issue #721).
* Fixed issue where saving GFF3 would fail if the source data
was in VCF format (issue #800).
* Fixed issue where there was a mix of plugin declarations
(issue #866).
# Release 1.12.2 2016-05-31 America/Los_Angeles
Special Release for Apollo
# Release 1.12.1 2016-03-01 03:47:38 America/Los_Angeles
## Minor improvements
* Update Dojo to 1.8.10
## Bug fixes
* Fix RegexSearch plugin and NeatCanvasFeatures plugin - search track
loading failure (issue #676)
* Fix compat_121.html to access /css directory
# Release 1.12.0 2015-12-18 17:40:39 America/Los_Angeles
## New features
* Added ability to open a new genome in FASTA format from the
browser. Also supports indexed FASTA. Thanks to Bradford Powell
for the original indexed FASTA contribution (issue #495,
issue #647).
* Support for inline reference sequence configurations.
* Created stand-alone desktop version of JBrowse using the Electron
platform for OSX, Windows, Linux (issue #647).
## New plugins
* NeatHTMLFeatures - Add the drawing of introns and gradient features
to HTML tracks.
* NeatCanvasFeatures - Add the drawing of introns and gradient
features to Canvas tracks.
* CategoryUrl - Implements a cat= URL option to display tracks for a
given category (issue #618).
* DebugEvents - a plugin to display global publish and milestone
events on the debug console.
* HideTrackLabels - Adds a toolbar button to toggle the display of
track labels on and off (issue #614).
## Minor improvements
* Added new menu format to support loading your own genome. The open
genome option can be hidden via `hideGenomeOption` in config, and
the classic menu style can be restored via `classicMenu` in config.
* Added ability to load custom histograms for tracks loaded from
flatfile-to-json.pl (i.e. override a pre-existing histogram store).
See (issue #612).
* Added these options to add-bw-track.pl --clip_marker_color <color>,
--bg_color <color>, --height <value> (issue #510).
* Added an option for Wiggle tracks, scoreType: 'avgValue', which
helps preserve continuity when zooming in on certain tracks like
GC-content. It complements the scoreType: 'maxValue' introduced in
1.11.6. Thanks to Han Lin for the pull request (issue #504).
* Clarify track filter box description and feature search box
"placeholder" text. (issue #611)
* Implement option to have a separate location box from search box
(issue #611, issue #652).
* Move CSS files into css folder.
* Added ability to specify the set of startCodons and stopCodons in
the config files. Thanks to Eric Rasche for the contribution (issue
#657)!
## Bug fixes
* Add Travis-CI and jshint linting to build (issue #628).
* Fixed a bug where the BAM popup boxes would display some incorrect
info due to byte packing. Thanks to Thomas Downs for contributing
the fix.
* Fixed a bug where grid lines wouldn't render at some particular
zoom levels (issue #514).
* Fixed a bug where the user's --workdir parameter would be deleted
which could have unintended side effects if the --workdir was
pointing to important data, but this is uncommon (issue #563).
* Allow falsey values to be used in browser.cookie.
* Fix minor issue where sometimes the length field of refSeqs.json
was missing.
* Fix some issues that occurred when a reference sequence was named
'0' (issue #662, issue #610).
# Release 1.11.6-a7ddd9c 2015-10-16 11:55:18 EST5EDT
# Release 1.11.6-a842094 2015-08-05 10:02:13 America/New_York
# Release 1.11.6-2141cde 2015-07-02 16:16:21 America/New_York
# Release 1.11.6-675d21c 2015-06-24 14:34:00 EST5EDT
# Release 1.11.6 2015-02-12 18:27:38 America/Chicago
## Minor improvements
* Added the ability to customize the contents of HTMLFeatures and
CanvasFeatures mouseover tooltips more extensively. Thanks to David
Muller for the original bug report and Colin Diesh for the fix
(issue #480).
* Added new options for BigWig files to use min/max summary values
when zoomed out using `scoreType`. Thanks to Scott Cain for
reporting the issue and to Colin Diesh for the fix (issue #518).
* Added a checkbox for wiggle type tracks to have log scale. Thanks
to Han Lin for the pull request (issue #502).
* Added the ability to display paired-end reads in the same direction
on Alignments2 tracks with the "Use reverse template" option.
Thanks to Tomaz Berisa and Colin Diesh for their contributions
(issue #485).
* Added the ability to specify a codon table (or partial codon table)
for the Sequence track.
* Added the ability to show or hide the main menu bar using the
configuration file.
## Bug fixes
* Fixed "boolean is not a function" error when using CanvasFeatures
tracks with the Segments glyph in some situations.
* Fixed a dialog box display issue for VCF variants with "no call"
specified (issue #513).
* Fixed loading files from certain filepaths with special characters.
Thanks to Ben Bimber for reporting and helping diagnose the bug
(issue #508).
* Fixed popup-dialog callbacks not being called on BAM Alignments
tracks in 1.11.5.
* Fixed systemwide installations of JBrowse perl modules when using
Module::Build.
* Fixed a bug when displaying SNPs on hard clipped reads. Thanks
to Thon de Boer for the bug report and to Colin Diesh for the fix
(issue #516).
* Fixed a bug when displaying SNPs on spliced alignments. Thanks
to GitHub user 09140930 for the bug report and to Colin Diesh for
the fix (issue #523).
* Fixed a bug that affected some VCF and GFF popup dialogs in some
browsers, particularly Chrome 38 (issue #522).
* Fixed a bug with the incremental indexing with generate-names
that associated the wrong track with the name store. Thanks to
Richard Hayes for reporting this issue and to Colin Diesh for the
fix (issue #526).
* Fixed the `--workdir` parameter in generate-names.pl (issue #506).
* Fixed the display of alternative alleles in the genotype for VCF
pop-ups (issue #533).
* Fixed an issue where some paired-end read data wouldn't display
properly if they had the same start position (issue #521).
* Output .htaccess file for generate-names.pl when using the compress
option. Thanks to Sebastien Carrere for reporting the bug
(issue #541).
* Fixed a small bug with being able to scroll past end of chromosome
when using the `--sizes` option to prepare-refseqs.pl (issue #535).
* Fixed a small internal code inconsistency with the positioning of
the vertical position line. Thanks to Anurag Priyam for the fix
(issue #545).
* Fixed a small bug with some stylesheets not being able to be used
for the CanvasFeatures coloring, for example, LESS stylesheets.
Thanks to Anurag Priyam for reporting the issue (issue #527).
* Fixed a small bug with mouseovers on Wiggle type tracks. Thanks
to Han Lin for finding and fixing this bug (issue #503).
* Removed XS tag from the strand calculation for alignments and made
it an optional rendering option for BAM files with the "Use XS"
option. Thanks to Kieran Raine and the pull request (issue #473).
* Added a bugfix that prevented viewing the details of haploid VCF
files. Thanks to Colin Diesh for finding and fixing this bug
(issue #536).
* Added a bugfix for an issue that made browsing very buggy when
using private browsing mode in Safari.
* Fixed the `shortDescription` option for the mouseover description
of tracks in the Hierarchical track list (issue #553).
* Re-added filter options that were missing for SNPCoverage tracks.
# Release 1.11.5 2014-09-04 16:03:22 America/Chicago
## Minor improvements
* Added the ability to disable sorting on the Hierarchical track
selector using the sortHierarchical flag. Thanks to Chris Childers
for the suggestion and Colin Diesh for the implementation
(issue #477).
* Added saving of the display mode setting on the CanvasFeature based
tracks. Thanks to Jon Hinton for the idea and Colin Diesh for the
fix (issue #469).
* Added configurable click event handlers for Wiggle type tracks.
Thanks to Richard Hayes for implementing this feature (issue #489).
* Added more configuration options for 'View details' popups as well
as the ability to customize the 'About track' popups. Thanks to
Colin Diesh for the idea and implementation (issue #494).
* Added the ability to load the category attribute from trackMetaData
files to be used for the Hierarchical track selector.
* Added the ability to specify initially collapsed categories in the
Hierarchical track selector (issue #507).
* Added beta touch-screen and tablet support by fixing a related bug.
Thanks to Paul Hale and Kieran Raine for reporting bugs and to
Emily Greenfest-Allen for the suggested fix (issue #505).
## Bug fixes
* Fixed a bug with VCF tabix file parsing that caused unnecessary
chunkSizeLimit errors. Thanks to Richard Hayes for finding and
debugging this issue (issue #486)!
* Fixed a bug where the Variant popup boxes would not display
complete genotype information in previous 1.11.* versions.
Thanks to Nando for reporting the bug and Colin Diesh for the
bugfix (issue #488).
* Fixed a small error that occured when using variant type tracks
with the REST API.
* Added a bugfix that caused problems scrolling in dialog boxes
for variant type tracks in 1.11.4 (issue #492).
* Fixed the use of the --refs flag on prepare-refseqs.pl. Thanks to
Audrey for finding & fixing this bug (issue #497).
* Added missing template length flag to the Alignments popup dialogs.
Thanks to Kieran Raine for the suggestion and Colin Diesh for the
fix (issue #471).
* Fixed the functionality of the --incremental flag in the
generate-names.pl script. Thanks to Richard Hayes and Colin Diesh
fixing the issue (issue #478).
* Fixed legacy bam-to-json.pl support when running setup.sh due to
samtools build modifications (issue #501).
# Release 1.11.4 2014-05-14 12:04:54 America/Chicago
## Minor improvements
* Added high-resolution rendering for CanvasFeatures, SNPCoverage,
BigWig tracks, and histograms. This allows rendering for canvas-
based tracks to look much sharper on high-resolution displays and
can even look sharper when zooming. The high-resolution rendering
is disabled by default to avoid conflicts with existing instances,
but feel free to test it out by setting "highResolutionMode" in
jbrowse.conf. Thanks to Colin Diesh for the idea and implementation
(issue #456)
* Added the ability to run jbrowse scripts outside of the JBrowse
root directory. Thanks to Chien-Chi Lo for the patch (issue #465).
* Added basic GTF parser that can open files from the File->Open
menu or by using the in-memory adaptor. Big thanks to Andrew Warren
for the contribution (issue #453).
* Added a change to the highlight button to allow the user to more
easily clear highlights. Thanks to Paul Hale for the suggestion
and Colin Diesh for the fix (issue #445).
## Bug fixes
* Fixed help page icons not loading since JBrowse 1.11.2. Thanks to
Colin Diesh for catching the bug and fixing it (issue #460).
* Fixed updating of the y-axis scale when using the resize
quantitative tracks feature. Thanks again to Evan Briones for the
original implementation and Colin Diesh for the fix (issue #461).
* Changed the CanvasFeatures 'View details' pages to display the name
and description of features in the dialog box. Thanks to Colin
Diesh for the fix (issue #463).
* Added a bugfix for non-compliant servers that add a trailing slash
to the URL. Thanks to Colin Diesh for the fix (issue #462).
* Fixed a broken link in the documentation for biodb-to-json.
* Updated setup.sh to maintain compatibility with the latest BioPerl.
Thanks to Thomas Sibley and Scott Cain for helping with this issue
(issue #468).
* Fixed a long standing bug with the coloring of nucleotides on the
SNPCoverage/Alignments2 track. Thanks to Long Le for reporting this
on the mailing list.
* Fixed a long standing bug with the scrollbar in the dialog box on
Chrome and Safari browsers. Thanks to the #dojo irc channel and
and Colin Diesh for helping fix this problem (issue #386).
* Fix a small rendering problem that causes one pixel gap to appear
on Safari due to subpixel rendering issues. Thanks to Colin Diesh
for the preliminary fix (issue #341).
* Fix a bug with CanvasFeatures based tracks loading huge amounts
of data to generate histograms instead of using pre-generated
histograms. Also lowered the maxScreenFeatureDensity default on
the CanvasFeatures tracks so that histograms can be displayed more
readily. Thanks to Daniel Troesser for reporting this issue on the
mailing list and Colin Diesh for the fix (issue #475).
# Release 1.11.3 2014-03-07 13:05:57 EST5EDT
## Minor improvements
* Added a "Zoom to this" item in the default right-click menus for
canvas-based feature tracks. Thanks to Paul Hale for the initial
implementation of this.
* Allow the user to set the document.domain property via jbrowse.conf
which can be helpful especially if jbrowse is embedded in a iframe.
Thanks to Kieran Raine for the idea and Colin Diesh for the bugfix
(issue #440)
* Improved the graphic design of the "Add sequence search" dialog box
to make it clearer how to switch between providing an amino acid
and a nucleotide sequence. Thanks to Kevin Mohamed for the initial
implementation of this (issue #436).
* Expanded the default color set of `Alignments2` tracks to show
different shades of color indications of reads with missing mate
pairs, improperly aligned reads, and reads with mate pairs on
different reference sequences. Thanks to Keiran Raine for
implementing this (issue #443).
* Added support to customize specific parts of the 'View details'
popups using callback functions. Thanks to Kieran Raine for the
idea and Colin Diesh for the implementation (issue #421).
* The File->Open tool will now can add files named `*.coverage.*` or
`*.density.*` as histograms to newly-opened tracks if the file
basenames match. For example, if both `mysample.bam` and
`mysample.coverage.bw` are present, `mysample.coverage.bw` will be
added as a histogram source for `mysample.bam`. Thanks to Keiran
Raine and Alexander Stoddard for suggesting this (issue #423).
## Bug fixes
* Fixed a problem where the feature arrowhead would get stuck in the
middle of the screen at high zoom levels. Thanks to Colin Diesh for
the fix (issue #449).
* Disabled the FASTA download button in the "View details" page on
Safari (issue #412). This feature can't be supported in Safari at
this time, but it is still supported in most other browsers. Rob
Buels and Colin Diesh contributed fixes to this issue.
* Fixed a bug in the client-side GFF3 parser pointed out by Andrew
Warren. Thanks Andrew! (issue #452).
* Fixed the problem of translation frames being switched around at
different zoom levels. Thanks to Kieron Taylor for the bug report
and Colin Diesh for the bugfix (issue #435)
* Fixed a bug where gene features in GFF tracks would not have
arrowhead markers. Thanks to Colin Diesh for finding and fixing
this issue (issue #454)
# Release 1.11.2 2014-02-10 19:11:33 EST5EDT
## Minor improvements
* Added some user interface elements to set the height in pixels of a
single quantitative track, or of all visible quantitative tracks.
Thanks to Evan Briones for implementing this!
* Added a `JBrowse/View/FeatureGlyph/Diamond` glyph that draws
diamond-shaped features instead of boxes. Thanks to OICR Co-op
student Kevin Mohamed for implementing this!
* Reference sequence tracks now display a "no sequence" message
instead of a bunch of blank blocks when the reference sequence
basepairs aren't available. Thanks to Kevin Mohamed for
implementing this (issue #422).
* Persistent session state is now stored on a per-dataset basis,
which improves user experience when switching between multiple
datasets in JBrowse. Thanks to Richard Hayes for pointing this
issue out, and Kevin Mohamed for the fix (issue #410).
* "Hide sites not passing ..." settings in VCF track menus now show
the filter's long description when hovered over. Thanks to Keiran
Raine for suggesting this (issue #420).
* Tweaked display of track labels and added a slight border at the
top edge of each track to make it more clear which track data
belongs to. Thanks to Keiran Raine for suggesting this, and Kevin
Mohamed for the initial implementation (issue #432).
* Added a `--config` option to `flatfile-to-json.pl` that accepts
additional configuration variables that will be merged into the top
level of the track configuration. Thanks to Mikael Brandström
Durling for the initial implementation of this.
## Bug fixes
* `generate-names.pl` now indexes VCF files from track definitions in
`tracks.conf` files. Thanks to Paul Halle for pointing this out
(issue #434).
* Added a missing dependency for the server side formatting tools on
List::MoreUtil 0.28 or higher. Thanks to Cris Lawrence and Keiran
Raine for troubleshooting this!
# Release 1.11.1 2014-01-07 15:48:39 EST5EDT
## 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).
# Release 1.11.0 2013-12-19 15:51:37 EST5EDT
## Major improvements
* Introduced density/coverage histogram support for CanvasFeatures,
CanvasVariants, and Alignments2 tracks. These track types now
support an optional `histograms` configuration subsection that can
contain a definition for a second datastore that holds quantitative
data (usually either coverage depth or feature density) to be
displayed when zoomed further out than `featureScale` (or if
`featureScale` is not set, the scale determined by the store's
feature density divided by `maxFeatureScreenDensity`). Thanks to
Richard Hayes for pushing hard for this feature.
* Added a new "Hierarchical" track selector that shows tracks in a
hierarchy of collapsible categories, which is now the default track
selector. To assign categories and subcategories to your tracks,
set `category` or `metadata.category` attributes on each configured
tracks in your `trackList.json`. Thanks to the many users who have
requested this at one time or another.
* JBrowse now supports a new plaintext configuration format that
users of GBrowse will find very familiar, since it is designed to
be very similar to it. This syntax is also much easier to
hand-write than JSON. The JSON configuration syntax is not going
away, and will continue to be supported.
Thanks to Erik Derohanian for the original implementation of this
configuration adaptor, and Richard Hayes and Keiran Raine for
motivating the work to polish and more fully integrate it.
* Variables in configuration files can now be based on the contents
of other variables. For example, setting
"myCustomVariable": "/some/custom/path",
"include": "{myCustomVariable}/conf.json"
will try to include a configuration file located at
"/some/custom/path/conf.json". Interpolation is done as the final
step in configuration loading, so variables can come from anywhere
in the configuration.
* When JBrowse is started, if there are no reference sequences found
in the default `dataRoot`, but the dataset selector is configured,
JBrowse shows a simple list of links to available datasets instead
of the "Congratulations, JBrowse is on the web" page. Thanks to
Saulo Aflitos for the idea and its initial implementation.
* For users wishing to convert existing JSON configuration files to
the new format, there is a new script, `bin/json2conf.pl`, that
does a fair job. Run `bin/json2conf.pl -?` for details on how to
use it.
* Added a new REST backend for name lookup and autocompletion. See
http://gmod.org/wiki/JBrowse_Configuration_Guide#JBrowse_REST_Names_API
for details. Thanks to Erik Derohanian for implementing this, and
Ben Booth for suggesting an API design (issue #267).
* Major performance and scalability improvements for
`generate-names.pl`. Now uses a different algorithm that is faster
and more scalable than before, and no longer relies on BerkeleyDB
for temporary storage. This should also alleviate the need to run
generate-names.pl with `--safeMode` in Perl 5.10 and earlier. In
fact, the `--safeMode argument` to generate-names.pl no longer has
any effect. Thanks to Cris Lawrence for pointing out the
continuing need for more scalability.
## Minor improvements
* Detail popups for CanvasVariants and HTMLVariants tracks now
display the reference sequence itself instead of just "ref" in
genotype displays. Thanks to Cris Lawrence for requesting this.
* Added a "save as FASTA" button to default feature detail popups
that downloads a FASTA file with the displayed piece of reference
sequence (issue #299).
* `chunkSizeLimit` for VCF files now defaults to 1 MiB. It used to
be 15 MiB, which was really far too big for browsers to handle.
* Added support for a `--nameAttributes` argument to
`flatfile-to-json.pl` that takes a comma-separated list of feature
attributes to index for name searching and completions, or 'none'
to not make names searchable.
* Added support for a `nameAttributes` variable in `biodb-to-json.pl`
track configurations that can be set to an array of feature
attribute names to to index for name searching and completions, or
'none' to not make names searchable.
* Add a `--category` argument to bin/wig-to-json.pl that can be used
to set the `metadata.category` of a track.
## Bug fixes
* Fixed a bug in NCList data backed in which feature histograms were
often calculated very incorrectly.
* Fixed a bug in the VCF data backend that caused not all VCF
features to be shown in some files at some zoom levels.
# Release 1.10.12 2013-12-10 16:09:42 EST5EDT
## Minor improvements
* `bam-to-json.pl` and `flatfile-to-json.pl` now support a
`--metadata` argument that can add a `metadata` stanza to track
configurations they generate.
* Multi-valued attributes in feature detail popups are displayed as a
string of boxes, each containing a value, to avoid
misinterpretation. Before, each value was just separated from the
previous one by whitespace. Thanks to Cris Lawrence for pointing
out the need for this.
## Bug fixes
* Re-enabled usage analytics reporting, which had been disabled by a
stray piece of debugging code since the 1.10.7 release.
* Fixed a bug in which the tooltip in canvas-based feature tracks
would sometimes display incorrect label or description text.
# 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
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).
# Release 1.10.10 2013-11-21 09:31:53 EST5EDT
## Minor improvements
* Spacing between tracks is now configurable by setting
`view.trackPadding` in the configuration. Thanks to Chenchen Zhu
for suggesting this (issue #377).
* If reference sequences are defined, but no tracks are yet added,
JBrowse will start normally instead of going to the
"Congratulations, JBrowse is on the web" page.
* `generate-names.pl` now supports a `--compress` option that
compresses the name index files to save server disk space. Thanks
to Richard Hayes for pointing out the need for this (issue #378).
## Bug fixes
* `generate-names.pl` now uses IO::Uncompress::Gunzip instead of
PerlIO::gzip to read compressed VCF files. This fixes a bug in
which only the first few hundred names in a VCF were indexed.
Thanks to Cris Lawrence for pointing this out (issue #380).
* Fixed a bug in which `generate-names.pl` would crash if run with
`--incremental` and no existing names index. Thanks to Richard
Hayes for pointing this out (issue #379).
* Fixed a bug in which `generate-names.pl` would sometimes choose the
wrong number of hash bits when performing incremental updates,
leading to the old data being lost. Thanks to Richard Hayes for
lots of help troubleshooting this.
* Fixed bug where other tracks are visible underneath pinned tracks
when the display is scrolled down. Thanks to Ed Lee for pointing
this out.
* Fixed a bug in which tooltip does not hide after the mouse leaves a
Wiggle track in Safari 5 and 6. Thanks to Charles Girardot for
pointing this out.
* Fixed a bug in which the `main.css` file for plugins was not being
correctly loaded in some installations. Thanks to Matt Bomhoff for
pointing this out.
# Release 1.10.9 2013-11-08 15:22:50 EST5EDT
## Minor improvements
* `generate-names.pl` now supports a `--incremental` or `-i` option
that adds names to an existing index. Thanks to Richard Hayes for
reminding me that this wasn't done yet (issue #373).
* Added a lower-performance, but more backward-compatible indexing
backend to generate-names.pl that can be activated by passing the
`--safeMode` command-line argument. The recent performance
improvements to generate-names.pl have apparently tickled some bugs
that are present in some installations. Thanks to Josie Reinhardt
and GitHub user raj76 for their continued help troubleshooting
this. If you find that name indexing is not working correctly, try
running it again with `--safeMode`, and report to the mailing list
if it helps.
* Added support for using the JBrowse in-memory GFF3 adaptor to
display web-accessible GFF3 files directly. See
docs/tutorial/data_files/volvox.gff3.conf for an example
configuration. Thanks to David Goodstein and Richard Hayes for
motivating this.
## Bug fixes
* `flatfile-to-json.pl` now depends on the latest
Bio::GFF3::LowLevel::Parser 1.8, which fixes a bug in which
features with no ID, Parent, or Derives_from attributes were not
being included in parsed data. Thanks to Gwendoline Andres for
pointing this out.
* Tweak BioPerl-handling code in biodb-to-json.pl to hopefully work
better with BioSQL backends. Thanks to Brian Osborne for pointing
this out.
# Release 1.10.8 2013-10-25 11:13:30 EST5EDT
## Minor improvements
* Added a new `navigateTo` action usable for customizing feature
left-clicks and right-click menus. Thanks to Scott Cain for
requesting this.
* Added a new `feature_range_cache` option for the REST data backend.
If set to true, the REST backend will more aggressively cache
ranges of feature data. Thanks to Daniel Troesser for pointing out
the need for this (issue #369).
* `maker2jbrowse` now, by default, runs `generate-names.pl` to
generate names indexes. Also added a `--no_names_index` option to
turn this off. Thanks to Josie Reinhardt for making me notice this
was missing.
* Tweaked `generate-names.pl` default indexing parameters to
emphasize indexing speed more. Now defaults to a smaller average
file size for the on-disk JSON files it produces, which is much
faster to generate and write (up to 8 or 10x faster). However, the
on-disk index is about 2-2.5x larger overall.
* Removed support for the `--refids` command-line argument to
`prepare-refseqs.pl`, which has probably never really worked.
* Improved `prepare-refseqs.pl` support for Bio::DB::Das::Chado
database backends. Thanks to Gwendoline Andres for helping
troubleshoot this.
## Bug fixes
* Fixed generate-names.pl making incorrect name indexes when using 16
or more bits of hashing (when the number of index entries exceeds
about 4 million). Thanks to Josie Reinhardt for helping
troubleshoot this (issue #370).
* The faceted track selector no longer refuses to display track
unique labels even if they are explicitly included in the
`displayColumns` setting.
# Release 1.10.7 2013-10-15 16:50:00 EST5EDT
## Minor improvements
* Added an optional `stats/regionFeatureDensities` endpoint to the
REST API that makes it possible to provide binned feature counts
that HTMLFeatures tracks can use to display feature histograms.
Thanks to Stuart Watt and Daniel Troesser for pointing out the need
for this (issue #365).
## Bug fixes
* Fixed a bad bug introduced in 1.10.6 in which FASTA files with line
lengths longer than the configured chunk size were not correctly
formatted. Thanks to Jean-Jack Riethoven for pointing this out
(issue #363).
* Fixed a bug introduced in 1.10.6 in which prepare-refseqs.pl would
not respect the --noseq command-line option when using --fasta.
* Fixed bug in which `name` or `seq_id` attributes are required for
reference sequence features. Thanks to Daniel Troesser for
pointing this out.
* Fixed a bug that may have prevented some types of VCF files from
being displayed (error message referring to `inheritedFilters`).
* Fixed a bug in which "Zoom in to see feature" in Sequence tracks
would wrap downwards below track at some zoom levels and window
widths.
* Fixed an off-by-one error in UTR attributes manufactured by the
`impliedUTRs` mechanism of the ProcessedTranscript glyph. Thanks
to Ben Booth for pointing this out (issue #362).
* Fixed a bug in which `score` attributes of features were not being
recorded by `biodb-to-json.pl`. Thanks to HongKee Moon for
pointing this out (issue #364).
* Removed a stray use of Carp::Always in GFF3-processing Perl code
that may have caused problems in some installations.
# Release 1.10.6 2013-10-07 21:06:51 EST5EDT
## Minor improvements
* Made the `impliedUTRs` option for ProcessedTranscript and Gene
glyph still attempt to create UTRs if only '''one''' of the UTRs is
missing from a transcript. Thanks to Ben Booth for pointing out