JBrowse 1.13.1

Minor improvements

• Gene, ProcessedTranscript, and Segments glyphs can now render third-level subfeatures
  (such as stop_codon_read_through features) as simple boxes that draw on top of the
  main segment glyph. Thanks to @mpoelchau for pointing out the need for this!
  (issue #584, @rbuels)

• CanvasFeatures tracks, when guessing which glyph to show for a feature in a track
  that does not specify glyphs in its configuration, will now use a Segments glyph
  instead of a Box glyph if the feature in question has subfeatures, and is not
  otherwise recognized as a gene or processed transcript. @rbuels

• Added a check in the setup.sh script for NodeJS >= 6 and NPM >= 3.
  (issue #1026, @rbuels)

• Plugins that don't need CSS can now set jbrowsePlugin.css to false in their
  package.json files to prevent JBrowse trying to load their css/main.css file,
  if they don't use any CSS. (@rbuels)

• Add ability for the CanvasFeatures feature labels to stay visible on the screen.
  (issue #390, pull #971, @cmdcolin, @rbuels)

• Improve VCF tracks support for GVCF generated by GATK, and fix a number of related
  VCF details display bugs. (pull #991, @cmdcolin)

• generate-names.pl now supports indexing GFF3 files, enabling better use of
  GFF3Tabix tracks. Thanks to @billzt for the initial implementation!
  (issue #780, pull #900, @rbuels)

• CanvasFeatures ProcessedTranscript and Gene glyphs now support a "style→utrHeightPercent" configuration variable that sets the percentage of the overall feature's height that a UTR have. This was previously hardcoded to 65, now it is customizable, defaulting to its old value of 65. @rbuels

Bug fixes

• Updated NeatCanvasFeatures and NeatHTMLFeatures plugins to support a gradient
  configuration variable, fix rendering of outrons, restore their default
  gradient-drawing behavior, disable gradients by default on Alignments and
  Alignments2 track types, and clean up their documentation. (issue #931, issue #982,
  issue #985, issue #931, issue #992, pull #1011, @enuggetry)

• Fixed a bug with plugin loading that was preventing some plugins from working
  correctly. (issue #1025, @rbuels)

• flatfile-to-json.pl will now refuse to format a track if the trackLabel
  contains a '/' character. Thanks to @dytk2134 for pointing this out, and @cmdcolin
  for the fix! (issue #1023, @cmdcolin)

• Fixed a bug in which the viewing location would not be preserved across page reloads
  if generate-names.pl had not been run, or a names store had not otherwise
  been defined. Thanks to @cmdcolin for the bug report. (issue #1016, @rbuels)

JBrowse 1.13.0

Major improvements

• JBrowse now uses a Webpack-based build system, which greatly speeds up JBrowse's
  initial loading time. Going forward, this change will also enable us to make
  much more effective use of the huge node.js ecosystem that has grown up in
  recent years, as well as to use newer versions of JavaScript itself while
  still maintaining compatibility with older web browsers.

• Behind the scenes, the way JBrowse plugins are discovered and loaded has also
  changed significantly. The most visible consequence of this change is that
  installations that use plugins must now use the JBrowse-1.13.0-dev.zip release
  (or check out the master branch from GitHub), and must re-run the webpack build
  (most easily by running setup.sh) every time a plugin is added or removed from
  JBrowse. Although we think that most users of plugins will not experience any
  problems, we recommend that installations that make use of plugins other than the
  standard built-in plugins (Neat*Features, RegexSearch, etc) test the compatibility
  of their plugins thoroughly before deploying this release, and report any problems
  either to the JBrowse issue tracker on GitHub, or to the gmod-ajax mailing list.

• Again, concisely: if you use JBrowse plugins other than the "stock" ones that
  come with JBrowse, you must now use the dev release of JBrowse, and re-run either
  setup.sh or npm run build every time you add or remove a plugin.
  (issue #981, @rbuels)

• JBrowse plugins can now be published and installed with NPM. Simply publish your
  plugin using the standard npm publish machinery, and make sure its package name
  ends with "-jbrowse-plugin". For example, if you have a plugin named "foo", publish
  it to npm as "foo-jbrowse-plugin". However, if your plugin is named MyAwesomePlugin,
  which is not compatible with npmjs.org's naming conventions, you will want to publish
  it as something like "myawesome-jbrowse-plugin" and add a configuration stanza to its
  package.json file telling JBrowse its real plugin name. Example:

  {
      ...
      "jbrowse": {
          "pluginName": "MyAwesomePlugin"
      },
      ...
  }
  

Minor Improvements

• Added disableCollapsedClick and enableCollapsedMouseover track configuration options.
  The enableCollapsedMouseover option is useful when features do not overlap e.g.
  chromosome segmentation and disableCollapsedClick is useful when the collapsed features
  are very dense. Thanks to @rdhayes for tips (issue #544, pull #870, @cmdcolin)

• Removed JBrowse 1.2.1 compatibility. Please use JBrowse 1.12.5 or earlier
  if you still have old data formatted with JBrowse 1.2.1. (@rbuels)

• For npm installations of JBrowse, jb_run.js and jb_setup.js are now installed into
  the standard node_modules/.bin location. (issue #1021, @rbuels)

Bug fixes

• Fixed a bug in which adding setting tracklabels=0 in the URL failed to hide
  track labels when nav=0 was also set in the URL. Thanks to Vaneet Lotay for reporting
  the problem, and @cmdcolin for the fix. (issue #1017, pull #1018, @cmdcolin)

JBrowse 1.12.5

Minor improvements

• Safari versions 10 and 11 will now see buttons for downloading feature FASTA
  sequences, as well as other sequences. These were turned off for all Safari
  browsers back when no version of Safari could download a client-generated file,
  but Safari 10 and 11 support it now. Thanks to @kkara for noticing the button
  was missing and prodding us to look into it. (issue #714, @rbuels)

• Changed the default color for HTMLFeatures features to be a darker gray that
  is easier to see. Many thanks to @colindaven for the fix! (pull #980, @colindaven)

• Added the ability to manually specify a reference sequence ordering in the
  configuration. Users can now set refSeqOrder: "by_list" and then set
  refSeqOrderList: "ctgX,ctgY,ctgZ" to manually specify an ordering.
  Thanks to @dsenalik, @liub1993, @wkpalan, and @cmdcolin for valuable
  discussions about this, and @rdhayes for the prototype implementation.
  (issue #867, issue #919, pull #1007, @rdhayes)

• Added a --noSort option to prepare-refseqs.pl that preserves the reference
  sequence ordering in the input file, instead of sorting the reference sequences
  alphabetically in the JSON. Thanks to @dsenalik for the prototype implementation
  of this, and @cmdcolin and @rdhayes for valuable discussions.
  (issue #925, pull #924, pull #1007, @dsenalik)

• Feature tracks now support a showNoteInAttributes flag that force the feature's
  Notes attribute to be displayed as a regular attribute in the feature detail
  popup. This is to support the case in which users want the blue description text
  on a feature to be different from the feature's Notes attribute, but still display
  the Notes attribute in the detail dialog. Thanks to @loraine-gueguen and @cmdcolin
  for the idea and the implementation. (pull #885, @cmdcolin)

• When users click on an item in the dropdown autocompletion for the browser search
  box, the browser will go directly to that item immediately, eliminating the extra
  step of the user having to click "Go". Many thanks to @enuggetry for noticing the
  opportunity for this nice usability enhancement! (issue #616, pull #1001, @rbuels)

• The global highResolutionMode configuration is now set to auto, meaning that
  JBrowse by default will now auto-detect high-DPI displays (Apple Retina displays
  and similar) and draw canvas-based tracks more clearly on them. This capability
  has been present in the JBrowse code for a long time, but has been turned off
  by default. (@rbuels)

• Added support for two new configuration variables for SNPCoverage tracks:
  indicatorProp and indicatorDepth, which set the minimum proportion (indicatorProp)
  and minimum depth (indicatorDepth) of alternative alleles required to render the
  SNP indicator below a SNPCoverage track. Big thanks to Nathan Haigh for the idea
  and implementation! (pull #951, @nathanhaigh)

• Added a basic loading screen for when the page is initially loading (pull #1008,
  @cmdcolin)

• The subfeatureDetailLevel configuration variable for tracks now defaults to a value
  of 2, meaning that the builtin JBrowse default feature detail popup dialogs will only
  show one level of subfeatures by default. Most feature tracks have only one level of
  subfeatures anyway, but for very complex data (like gene models with many transcripts,
  each with many introns and exons), this new default will prevent a rather confusing
  problem some users were seeing in which JBrowse would seem to 'hang' when clicking a
  gene model to see its details. Thanks to @cmdcolin for the original implementation of the
  subfeatureDetailLevel configuration variable, @kshefchek for a good bug report that
  shows it, and @nathandunn and @selewis for valuable discussions.
  (issue #559, pull #1010, @rbuels)

Bug fixes

• Fixed a security issue with JBrowse error messages. Thanks to @GrainGenes for
  noticing and reporting it! (issue #602, @rbuels)

• Fixed an off-by-one error in the "Next segment position" field of BAM features.
  Thanks to @keiranmraine for reporting it, and @rdhayes for tracking down the fix!
  (issue #907, pull #986, @rdhayes)

• Fixed the broken demo track data source in the modENCODE sample data. Thanks
  to @cmdcolin for the fix! (pull #999, @cmdcolin)

• Fixed bug in which dragging an Alignments or Alignments2 track into a combination
  track caused the combination track to crash. (issue #771, @cmdcolin)

• Feature detail dialogs for variant tracks now correctly display "no-call" in
  the genotype details table for "./." alleles. Thanks to @carrere for reporting
  it, and @cmdcolin for the fix. (issue #980, pull #990, @cmdcolin)

• Fix parsing of the END field in VCF tracks, enabling things like CNV and deletion
  variants to be visualized from variant tracks. (pull #847, @cmdcolin)

• Fixed a long-standing bug in JBrowse configuration template parsing that
  prevented use of dot-notation nested variable names, e.g. {foo.bar}, in
  JBrowse configuration, as well as whitespace inside the braces. Big thanks to
  @wuroger for finding this bug. (issue #1012, @rbuels)

JBrowse 1.12.4

Minor improvements

• Fixed SEVERE performance regression that basically made flatfile-to-json.pl
  unusable on Perl 5.18 and higher. Huge thanks to Colin Diesh for tracking
  this down. (issue #470, pull #912, @cmdcolin)

• Added code to calculate feature density histograms for Tabix-indexed GFF3
  (GFF3Tabix) data sources. Thanks to @nathandunn for noticing and fixing
  this! (pull #956, @nathandunn)

• Added a new "Hide unspliced reads" menu item to Alignments and Alignments2
  tracks that filter out reads that have no Ns in their CIGAR strings.
  Thanks to Deepak Kunni and Nathan Dunn for their work on this.
  (pull #921, @deepakunni3)

• setup.sh now uses npm instead of Bower (which is deprecated) to install
  dependencies. @enuggetry

• Removed legacy wig-to-json.pl and bam-to-json.pl scripts. @rbuels

• Added a --trackConfig option to prepare-refseqs.pl to allow injecting
  refseq configuration variables at format time. (pull #884, @erasche)

• Added trackLabels: "no-block" config feature. Moves track labels/menus
  above the features so as not to obscure the features. (issue #901, #490)

• Added a --category option to add-bw-track.pl and add-bam-track.pl to
  set the new track's category. Thanks to @loraine-gueguen for the implementation!
  (pull #911, @loraine-gueguen)

• Made jbrowse installable using npm. @cmdcolin and @enuggetry.

• Implemented a built-in node.js Express server jb_run.js for quick JBrowse launching.
  @enuggetry

• Added an --unsorted option to prepare-refseqs.pl that formats reference sequences
  in the same order in which they appear in the input sequence file. Thanks to
  @dsenalik for the suggestion and implementation! (pull #924, @dsenalik)

• Allows for dot-notation instead of JSON (pull #952) for addTracks, addBookmarks,
  and addStores. #952. Address security concerns
  adding JSON to GET (https://nvd.nist.gov/vuln/detail/CVE-2016-6816) @nathandunn.

• If a track has no key set in its track configuration, JBrowse will now look for
  a key in its track metadata, and use that if it is present. Thanks to Loraine
  Guéguen for the idea (issue #957, pull #958). @rbuels

• Fixed bug in maker2jbrowse script that allows maker2jbrowse to be installed
  in system executable directories, and adds a --sortMem option.
  (pull #877, @cmdcolin)

• Fixed a cosmetic/styling bug with malformed DOM structure in feature detail popup
  dialogs. Thanks to Erik Rasche for noticing and fixing this! (pull #882, @erasche)

• Added a configuration option that can disable JBrowse's behavior of updating the
  browser's title text as the view changes. Thanks to Luka Jeran, Primož Hadalin,
  and Nathan Dunn for this! (pull #904, @lukaw3d)

• Suppress execution of biodb-to-json.pl on sample data while running setup.sh
  on MacOS High Sierra with stock Perl due to an issue with the stock Perl having
  broken BerkeleyDB integration, which is needed by Bio::DB::SeqFeature::Store,
  the main storage engine used by biodb-to-json.pl. Bug was manifesting as the script
  running indefinitely and taking all available disk space.
  (pull #945, issue #946, @deepakunni3 and @rbuels)

• Mitigate race condition that could sometimes cause duplicate tracks to be shown
  when the browser is started with the loc query parameeter set to the name of
  a feature. Thanks to Colin Diesh for the fix. (issue #567, @cmdcolin)

• Fixed issue in which JBrowse crashed when negative numbers were supplied for highlight
  coordinates in the URL. Thanks to @h2akim for reporting, and @cmdcolin for debugging help.
  (issue #769, @rbuels)

• Add --config command-line option to add-bw-track.pl and add-bam-track.pl
  scripts. Thanks to Chris Childers for suggesting this! (issue #620, @rbuels)

• Fixed a "cannot read property 'offsetLeft'" error when using touch screens without
  the old simple track selector active. (issue #893, @rbuels)

• Upgraded to use new Google Analytics API for usage reporting. (@rdhayes)

• Fixed bug in which start/stop codons were sometimes not displayed in the sequence
  track at certain zoom levels (issue #858, pull req #859, @cmdcolin)

• Fixed a regression in which the defaultTracks configuration variable was no longer
  respected when set to a comma-separated list. (issue #892, pull #896, @rdhayes)

• Made a cosmetic change to Alignments track detail popups, changing "Length on ref" to
  be displayed as "Seq length on ref", so that it is displayed more usefully next to
  "Seq length". Thanks to @colindaven for the suggestion and implementation!
  (pull #939, @colindaven)

• Improved the error messages displayed when a JBrowse glyph class fails to load. Thanks
  to @scottcain and @cmdcolin for tracking down the issue and improving the error
  handling! (issue #968, @cmdcolin)

• Added support for an addFeatures URL query parameter that can inject features from
  the URL query string. (issue #976, @nathandunn)

• Changed the project's git workflow to utilize a dev branch that is separate from
  master, with master only being updated when a new release of JBrowse is published.
  (issue #975, @enuggetry)

• Implemented automated deployment of JBrowse releases to GitHub releases and npm.
  Thanks to @abretaud, @nathandunn, @erasche, and @cmdcolin for valuable discussions.
  (issue #822, pull #979, pull #984, @rbuels)

• Added a --bigwigCoverage option to add-bam-track.pl to support configuring pregenerated
  coverage histograms from the command line. Thanks to @loraine-gueguen for the suggestion
  and implementation! (pull #972, @loraine-gueguen)

• Improved documentation of the CategoryURL plugin. (pull #985, @enuggetry)

JBrowse 1.12.3

Release 1.12.3 2017-05-02

Pre-Packaged downloads: http://jbrowse.org/jbrowse-1-12-3/

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).

1.12.2 (SPECIAL) release to correspond with Apollo 2.0.3 release

1.12.2 release to correspond with Apollo 2.0.3 release.

JBrowse 1.12.1

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