JBrowse 1

JBrowse 1.16.1 maintenance release

December 27, 2018

I'm pleased to announce the release of JBrowse 1.16.1! This release offers a variety of small bugfixes for cross-origin resource fetching, BAM files, and JBrowse desktop.

It also contains a fix that helps very large track lists to have a faster initial load for the Hierarchical track selector specifically.

Enjoy browsing!

Minor improvements

  • Made a change to make Hierarchical track selector much faster on intial browser load for very large tracklists (@cmdcolin)

  • Updated to webpack 4 for some faster build times (issue #1270, @cmdcolin)

  • Updated to use dojo/dijit/dojox 1.14 (@cmdcolin)

  • Updated NeatCanvasFeatures to allow non-coding transcripts to be colored differently with style->unprocessedTranscriptColor. Thanks to @billzt for the bug report (issue #1298, @cmdcolin)

Bug fixes

  • Fixed issue where data directories with spaces in them were giving errors due to CORS on JBrowse Desktop (issue #1285, @cmdcolin)

  • Fixed issue where the name store could be queried before being initialized (issue #1286, @cmdcolin)

  • Fixed an issue for large BAM headers failing to load post-@gmod/bam integration (@cmdcolin)

  • Fixed access to some cross-origin resources (issue #1289, issue #1292, @cmdcolin)

JBrowse 1.16.0 maintenance release

December 13, 2018

I am very pleased to announce the release of JBrowse version 1.16.0!

A major new feature of this release is the introduction of paired read visualization options!

And rather than delivering just one type of paired read visualization, there are many options for this including:

  • Pileup - standard alignments view but with connections between pairs
  • Read cloud - plotting by insert size
  • Arc view - plotting paired reads as connected arcs

There are also multiple coloring options for each type of view, including coloring by insert size (so abnormally large inserts are colored red for example) or pair orientation. Here are some example screenshots to help demonstrate

Figure 1.standard pileup view with paired and unpaired modes on the same data.

Figure 2. arc view which shows many long-range connections from a mate pair dataset.

Figure 3. The read cloud view showing color by orientation and size (red being abnormally large insert size, and turquoise and blue being incorrect pair orientations)

JBrowse version 1.16.0 also contains many other features and bug fixes, so please review the changelog below! Also make sure to view the paired read documentation for more information on the paired read options.

Major improvements

  • Added ability to view paired read data as connected entities for BAM and CRAM store classes. There are multiple different viewing options for this including plotting by insert size, plotting as connected arcs, or pileup views for the paired reads. Additonally multiple color schemes are available for coloring by insert size, pair orientation, mapping quality, and more. Thanks to @garrettjstevens, @rbuels, @AndyMenzies, and @keiranmraine for testing. Also a big thanks to @jrobinso from @igvteam for contributions to CRAM code related to paired reads (issue #1235, @cmdcolin)

Minor improvements

  • For users with the "dev" or compiling JBrowse from source code, the ./setup.sh now performs a full webpack production build (issue #1223, @cmdcolin)

  • Created new BAM parsing mechanism using the npm module @gmod/bam. Users might see some modest performance improvements due to enhanced tooling. Thanks to @rbuels and others for testing and feedback (issue #1215, issue #1178, @cmdcolin)

  • setup.sh now supports setting a JBROWSE_PUBLIC_PATH environment variable for more flexibility in iframeless embedding scenarios (issue #1213, @rbuels)

  • Added support for indexing arbitrary fields from GFF3Tabix files by setting nameAttributes in the track config e.g. nameAttributes=name,id,customfield. (issue #1115, issue #1222, @cmdcolin)

  • Add support for generate-names to index VCF features that have multiple IDs in the ID column (@cmdcolin)

  • Added documentation on embedding JBrowse in an iframe and in a div, including how to embed JBrowse using a custom JavaScript object as a configuration (issue #1228, issue #1243, @rbuels and @garrettjstevens)

  • Added ability to render non-coding transcript types to the default Gene glyph which helps when a gene feature has a mix of coding and non-coding subfeatures (issue #1106, issue #1230, @cmdcolin)

  • Created new VCF parsing mechanism using the NPM module @gmod/vcf. Thanks to @cmdcolin and others for testing and feedback (issue #1227, issue #1199, @garrettjstevens)

  • Added ability to open "chrom.sizes" files from the Open sequence dialog (issue #1250, issue #1257, @cmdcolin)

  • Added a config datasetLinkToParentIframe to make the dataset selector use window.parent for when jbrowse is in an iframe (issue #1248, @enuggetry)

  • Improved error message that is displayed when a data file cannot be fetched via CORS (@rbuels)

  • Added some word wrapping for long unbroken fields in the View details popups. Thanks to @luke-c-sargent for the idea (issue #1246).

  • Added hideImproperPairs filter for Alignments2/SNPCoverage tracks which disambiguates from missing mate pairs (issue #1235, @cmdcolin)

  • Added useTS coloring option for RNA-seq strandedness, similar to the useXS that existed previously (issue #1235, @cmdcolin)

  • Added a --bgzip_fasta option for prepare-refseqs.pl and also the ability to index reference sequence names if they are manually specified as a fasta index e.g. refSeqs=genome.fai. Thanks to @FredericBGA for the report! (issue #1281, issue #1282, @cmdcolin).

Bug fixes

Notable changes

  • Rendering of features in popups, mouseover tooltips, and feature labels were made to escape HTML. If you are using literal HTML labels in these places then set the attribute unsafePopup, unsafeMouseover, or unsafeHTMLFeatures on your tracks. Thanks to @garrettjstevens (issue #1263, @cmdcolin).

JBrowse 1.15.4 maintenance release

October 5, 2018

JBrowse 1.15.4 has been released! This release allows you to use bgzip indexed FASTA, adds a new categoryOrder config for sorting the Hierarchical track selector, and more! Thanks to everyone for their feature requests and bug reports, and enjoy!

Minor improvements

  • Added support for bgzipped indexed FASTA. To use, bgzip your FASTA with bgzip -i file.fa, which generates file.fa.gz and file.fa.gzi and then use samtools faidx file.fa.gz. If you specify the .fa.gz in the track config e.g. "urlTemplate": "file.fa.gz" and have all three files in your data directory, then they will automatically be detected (issue #1152, issue #1200, @cmdcolin)

  • Allow fna and mfa file extensions for FASTA to be recognized by default in the Open sequence dialog (issue #1205, @cmdcolin)

  • Improve the layout slightly for dense features (issue #1210, @cmdcolin)

  • Added a topLevelFeaturesPercent configuration variable that can be used to correct feature statistics estimates when topLevelFeatures is being used for a track, or when it contains deeply-nested features. This configuration variable is currently only used by BAM, BEDTabix, GFF3Tabix, and VCFTabix stores. (issue #1147, issue #1209, @rbuels)

  • Tabix-based data stores use a new storage backend based on the @gmod/tabix npm module. Users should see some modest performance improvements for Tabix-based tracks. (issue #1195, issue #1209, @rbuels)

  • Added hideSequenceBox config to allow hiding the FASTA boxes in the View details popups. Thanks to @andreamini for reporting (issue #1211, issue #1219, @cmdcolin)

  • Added categoryOrder config to allow sorting the categories in the Hierarchical track selector. For example, categoryOrder=VCF,Quantitative/Density,BAM. Note that we specify a lowest level subcategory e.g. Quantitative/Density to sort the parent category Quantitative to a position (issue #1203, issue #1208, @cmdcolin)

Bug fixes

  • Fixed a bug in which feature labels would sometimes be repeated across the view, in the wrong locations. (@rbuels)

  • Fixed error where a chunk size limit error during histogram display would not be displayed (@cmdcolin)

  • Fixed issue where Open sequence dialog will open up the default "data" directory instead of a blank instance (issue #1207, @cmdcolin)

  • Added check for PCR duplicates for CRAM features (@cmdcolin)

  • Fixed issue where editing the track names and types in the "Open track" dialog box was not working when editing multiple tracks (issue #1217, @cmdcolin)

  • Fixed issue in which large VCF headers were not always correctly parsed by JBrowse (issue #1139, issue #1209, @rbuels)

  • Fixed issue where the histogram Y-scale bar would appear over features (issue #1214, issue #1218, @cmdcolin)

JBrowse 1.15.3 maintenance release

August 29, 2018

JBrowse 1.15.3 has been released! This contains an bugfix introduced in 1.15.0 where typing a reference sequence name in the search bar did not navigate to it properly. It also contains a cool feature where "ultra minimal configs" can be specified by simply specifying a track label and urlTemplate

For example, a directory containing indexed files like VCF, BAM, GFF3 tabix, and indexed FASTA can have a config simply like this in tracks.conf

[GENERAL]
refSeqs=volvox.fa.fai
[tracks.refseq]
urlTemplate=volvox.fa
[tracks.bam]
urlTemplate=volvox-sorted.bam
[tracks.cram]
urlTemplate=volvox-sorted.cram
[tracks.vcf]
urlTemplate=volvox.filtered.vcf.gz
[tracks.gff]
urlTemplate=volvox.sort.gff3.gz
[tracks.bed]
urlTemplate=volvox.sort.bed.gz

Enjoy browsing!

Minor improvements

  • Add ability to automatically deduce the storeClass and trackType of files based on the file extension of urlTemplate. This allows very minimal configs where only track label and urlTemplate can be specified. (issue #1189, @cmdcolin)

Bug fixes

  • Fixed an issue with servers that use HTTP Basic Authentication on certain browsers, notably some Chromium, Firefox 60 and earlier, and Safari. Thanks to Keiran Raine for reporting and @cmdcolin for debugging. (issue #1186, @rbuels)

  • Fix issue where searching for reference sequence names would not be navigate to the typed in reference sequence (issue #1193, @cmdcolin)

JBrowse 1.15.2 maintenance release

August 16, 2018

JBrowse 1.15.2 has been released! This contains a couple nice features including estimating feature density directly from the index file of BAM, VCF, and other tabix formats. We also updated the website with a new blogging and documentation platform! Please try it out and give us feedback.

Enjoy browsing!

Minor improvements

  • Created "index stats estimation" which overrides the older "global stats estimation" that randomly samples genomic regions of BAM, VCF, etc to find feature density. This allows initial track load to be faster automatically. (issue #1092, issue #1167, @cmdcolin)

  • Removed the "full" or "dev" releases from the build. If you need a "dev" release, you can simply download the JBrowse "source code" link from the GitHub releases page, or use a git clone of the JBrowse repository. This will behave the same as the "dev" release. (issue #1160, issue #1170, @cmdcolin)

  • JBrowse now uses a new binary-file caching and fetching backend based on the http-range-fetcher and tenacious-fetch npm modules. Users may see slightly higher performance when viewing indexed binary formats such as BAM, CRAM, 2bit, etc. (issue #1155, issue #1175, issue #1165, @rbuels)

  • Updated the main jbrowse.org website to use the docusaurus platform. The main docs for the website are now moved from the GMOD.org server to jbrowse.org. You can find the latest documentation in the header bar. We hope you will enjoy this upgrade! There is also a new quick start guide based on setting up JBrowse with indexed file formats. (issue #1153, issue #1137, issue #1173, @cmdcolin)

Bug fixes

JBrowse 1.15.1 maintenance release

August 1, 2018

JBrowse 1.15.1 has been released!

Files for download

Minor Improvements

  • Add a internal code attribute for XHR requests that use byte-range headers so that if a server does not support it, an error is returned immediately. Thanks to @theChinster for the motivating example (issue #1131, issue #1132, issue #1134, @cmdcolin).

  • Speed up TwoBit file processing with a robust implementation of the file spec. The improvements are contained in a new npm module @gmod/twobit. Thanks to @cmdcolin for some testing and motivating examples. (issue #1116, issue #1146, @rbuels)

  • Added feature.get('seq') to CRAM features which enables detailed comparison of the read versus the reference with the renderAlignment configuration. (issue #1126, issue #1149, @rbuels)

  • Added support for 1000genomes CRAM 2.0 codecs via updates to the @gmod/cram npm module. (@rbuels)

  • Add some better formatting for rich metadata in the "About this track" dialog boxes for tracks. Thanks to Wojtek Bażant for the idea and implementation! (issue #1148, @wbazant)

Bug fixes

  • Fix bug where prepare-refseqs with indexed FASTA would allows scrolling past the end of the chromosome (@cmdcolin).

  • Fix long standing bug related to not being able to configure dataRoot in the config file. Now you can set dataRoot=mydirectory to make JBrowse load mydirectory instead of the default data by default (issue #627, issue #1144, @cmdcolin).

  • Added hashing of the BAM feature data to generate unique IDs in order to distinguish reads that have nearly identical information (same read name, start, end, seq, etc). If the reads literally have identical information in them JBrowse is still unable to display but this generally seems to be due to limited use case such as secondary alignments in RNA-seq (issue #1108, issue #1145, @cmdcolin)

JBrowse 1.15.0 release - CRAM support, CSI indexes, and on the desktop!

July 19, 2018

JBrowse 1.15.0 has been released! This is a really big one.

At long last, JBrowse can open and view CRAM v2 and v3 files just like BAM. In fact, viewing CRAM files can sometimes be even faster than viewing BAM files, because there is less data to move around! Enjoy CRAM support, we all worked really hard to bring it to you! Getting started with CRAM is easy, just use the JBrowse/Store/SeqFeature/CRAM store and the Alignments2 track type, just as you probably are already with BAM files. It works with local files too, of course!

Another big development, JBrowse Desktop has matured to the point where we can recommend it without reservation to those looking for a fast, easy to use desktop genome browser for local and remote files. From now on, we'll be publishing builds of JBrowse Desktop for Windows, Mac OS, and Linux alongside the regular JBrowse releases. Download it and give it a try, let us know what you think! Huge congratulations to Colin Diesh (who is now a full-time JBrowse developer!) for thinking of this, and seeing this amazing development through. I think you will be quite pleased with how well JBrowse runs on the desktop!

Also, JBrowse now supports CSI format indexes for BAM fiels and Tabix-indexed (VCF, GFF3, etc) files. Now your BAM files can be even bigger. As if they weren't huge enough already. This continues our very serious commitment to make JBrowse effortlessly usable on even the biggest datasets.

Lastly, JBrowse now sports a nice new text-searching interface accessible from the View → Search menu item in the top bar. This was a cool idea that came out of discussions last month at the GCCBOSC 2018 CollaborationFest, and was executed with alacrity by Colin!

As always, read on below the fold for the full release notes, including minor improvements and bugfixes. And thanks for using JBrowse. 😁

Files for download

Major improvements

  • Added support for displaying alignments from CRAM files, using the new npm module [@gmod](https://www.npmjs.com/package/<a href=)/cram">@gmod/cram. Thanks to @keiranmraine, @cmdcolin, @nathanhaigh, and the authors of htslib and htsjdk for invaluable test data and suggestions during this major effort. (issue #546, issue #1120, @rbuels)
  • Added support for the CSI index format for tabix VCF/BED/GFF and BAM files! This allows individual chromosomes longer than ~537MB (229 bases) to be used in JBrowse. To enable, use the csiUrlTemplate config to point to the file. The "Open track" dialog also allows CSI to be used. Thanks to Keiran Raine for initial report and Nathan S Watson-Haigh for catching a bug in the initial implementation! (issue #926, issue #1086, @cmdcolin)
  • Added a new search dialog box via the View->Search features menubar. It will search the currently configured store for features. You can also configure the dialog class in the configuration with names.dialog entry, or disable search dialog with disableSearch. Thanks to the #GCCBOSC hackathon for the idea and feedback (issue #1101, @cmdcolin).

Minor improvements

  • Re-enabled JBrowse Desktop builds for releases! The Windows, Mac, and Linux binaries for JBrowse Desktop are uploaded automatically to GitHub releases page. JBrowse Desktop is a standalone app that can be used without a web server, similar to IGV or IGB (@cmdcolin)
  • Added a dontRedispatch option for GFF3Tabix stores. Example: set dontRedispatch=region if there are very large region biotype features in the GFF that do not have subfeatures which will speed up loading times significantly (issue #1076, issue #1084, @cmdcolin)
  • Add auto-lower-casing to the feature.get('...') function, commonly used for callback customizations. Now, for example, feature.get('ID') works as well as feature.get('id'). Thanks to @nvteja for motivating this! (issue #1068, issue #1074, @cmdcolin)
  • Added cache-busting for track config files which actively prevents stale configuration files from being loaded (issue #1080, @cmdcolin)
  • Added indexing of both Name and ID from GFF3Tabix files from generate-names.pl. Thanks to @billzt for the implementation! (issue #1069)
  • Made the color of the guanine (G) residue more orangey than yellow to help visibility. Thanks to Keiran Raine for the implementation! (issue #1079)
  • Refactored NeatCanvasFeatures and NeatHTMLFeatures as track types. You can enable the track style on specific tracks instead of globally this way by modifying the track type to be NeatCanvasFeatures/View/Track/NeatFeatures or NeatHTMLFeatures/View/Track/NeatFeatures. (issue #889, @cmdcolin).
  • In the location box, allow strings with format ctgA:1-100 e.g. with a hyphen instead of ... Big thanks to Nathan S Watson-Haigh for the idea and implementation! The default display remains .. but - is allowed. (issue #1100, issue #1102, @nathanhaigh)
  • Allow sequences with a colon in their name to be used in the location box. This includes the HLA reference sequences in hg38. Thanks again to Nathan S Watson-Haigh for the implementation of this feature. (issue #1119, @nathanhaigh)
  • Fix sensitivity to .gff.gz vs .gff3.gz in GFF3Tabix tracks opened via the "Open track" dialog for GFF3Tabix. (issue #1125, @cmdcolin)
  • Feature detail dialog boxes now display subfeatures of features on the reverse strand in upstream-to-downstream order, instead of in genomic coordinate order. Thanks to @nathanhaigh for suggesting this and contributing the fix! (issue #1071, issue #1114, @nathanhaigh)

Bug fixes

  • Fixed a potential cross-site-scripting (XSS) vulnerability by disallowing dataRoot config values or ?data= URL parameters that point to a different server from the one serving JBrowse. Users can disable this security check by setting allowCrossOriginDataRoot = true in their configuration. (@cmdcolin, @rbuels)
  • Fixed a memory leak that was introduced in JBrowse 1.13.1 in generate-names.pl. Thanks to @scottcain for reporting (issue #1058, @cmdcolin)
  • Fix the error checking in setup.sh if no node is installed at all (issue #1083, @cmdcolin)
  • Fix calculation of histograms on GFF3 and GFF3Tabix stores. Thanks to @thomasvangurp for the bug report and sample data! (issue #1103, @cmdcolin)
  • Fix the representation of array-valued attributes in column 9 for GFF3Tabix. Thanks to @loraine-gueguen for the bug report! (issue #1122, @cmdcolin)
  • Fixed a bug in which visibleRegion() in GenomeView.js sometimes returned a non-integer value for end, which interfered with some scripts and plugins. Thanks to @rdhayes for noticing and contributing the fix! (issue #491, @rdhayes)
  • Fixed bug where reference sequences with names containing the : character could not be switched to by typing their name in the search box. (issue #1118, issue #1119, @nathanhaigh)
  • Fixed setup.sh behavior when node is not installed, printing a decent error message. (issue #1082, issue #1083, @cmdcolin)

JBrowse 1.14.2 maintenance release

June 4, 2018

JBrowse 1.14.2 has been released!

Files for download

Minor improvements

  • Added a datasetSelectorWidth configuration key that sets the width of the dataset selector. The width defaults to 15em. Example setting in tracks.conf: [GENERAL] classicMenu = true datasetSelectorWidth = 20em Thanks to @srobb1 for pointing out the need for this. (issue #1059, @rbuels)

  • When exporting GFF3 from the 'Save track data' menu, the ##sequence-region pragma now specifies the exact sequence region that was exported from the UI. Thanks to @mwdavis2 for pointing this out! (issue #905, @rbuels)

  • Improved the welcome screen for the desktop version of JBrowse (issue #1045, issue #1050, @cmdcolin)

Bug fixes

  • Fixed the --config option for add-bw-track.pl. Although documented in the script's POD, it was not actually being processed. Thanks to @loraine-gueguen for noticing it, and for contributing the fix! (issue #1063, issue #1064, @loraine-gueguen)

  • Fixed a bug in which setup.sh failed if run twice in a row under some circumstances. (issue #1053, @cmdcolin)

  • Fixed a bug in which setup.sh did not accept nodejs version 10 as sufficiently recent. (issue #1048, @cmdcolin)

  • Fixed a bug in which the "Loading..." message erroneously appeared at the top of the dataset-selection page. Many thanks to @srobb1 for noticing this and reporting it! (issue #1057, @rbuels)

  • JSON syntax errors in the new configuration loading code now have better error messages. Thanks to @billzt for pointing out the need for this! (issue #1061, @rbuels)

JBrowse 1.14.1 maintenance release

May 2, 2018

JBrowse 1.14.1 has been released!

Files for download

Minor improvements

  • JBrowse now supports .idx indexes for VCFs that are generated by igvtools or GATK. Currently only VCF files can be used with this index type, but this could be expanded to other file types if users are interested. Thanks to @thon-deboer for suggesting this! (issue #1019, @rbuels)

  • The dropdown dataset selector in "classic menu" mode is now a type-ahead combo box, enabling fast searching through large numbers of datasets. Thanks to @keiranmraine for the suggestion! (issue #752, @rbuels)

  • There is now a new event named /jbrowse/v1/n/tracks/redrawFinished that fires after the view is refreshed, when all of the visible tracks are finished drawing (or have errored). Thanks to @scottcain for suggesting this. (issue #1027, @rbuels)

  • Improve the calculation of feature density for GFF3Tabix and add new one for GFF3 in-memory. Thanks to @hkmoon for the suggestion! (issue #1039, issue #913, @cmdcolin)

  • Re-enabled JBrowse Desktop builds based on automatically building on Travis-CI (issue #1028, @cmdcolin)

Bug fixes

  • Fixed several bugs related to the file-opening dialog's handling of indexed file types (bam+bai, gz+tbi, etc). Thanks to @sletort for submitting the bug report! (issue #1033, @rbuels)

  • The Perl formatting tools now properly read include-ed configuration files. Thanks to @carrere for pointing out this bug. (issue #551, @rbuels)

  • Fixed a bug in which the faceted track selector was nonfunctional in Internet Explorer 11. (issue #1036, @rbuels)

JBrowse 1.14.0 release - iframe-less embedding, BigBed support

April 18, 2018

JBrowse 1.14.0 has been released!

This release includes two major improvements, the first being that it's no longer strictly necessary to run JBrowse inside an <iframe> when embedding it in another site or webpage. Big thanks to Lacey Sanderson for championing this feature, and we look forward to working with the Tripal team toward a better JBrowse integration!

The second major improvement is in displaying data from BigBed files. Not only can JBrowse can now open BigBed files both locally, and over the web, but it now natively displays BED-type thick/thin features and feature blocks rather than converting them to GFF3-style feature hierarchies. This makes both BigBed and BED fast and responsive. The new BED glyph will also use each feature's RGB color if it has one.

There are many more features coming that enhance JBrowse's compatibility with UCSC-format data, stay tuned for future JBrowse releases!

As always, read on below the fold for the full release notes, including minor improvements and bugfixes.

Files for download

Major improvements

  • JBrowse now behaves much better when embedded in a webpage without using an iframe. See tests/drupal.htm in the JBrowse code for an example of this usage. Thanks to @laceysanderson for her patiently championing this feature all the way through the long road to completion! (issue #777, issue #844, @cmdcolin)
  • There is a new BigBed store type, for opening BigBed files. An example BigBed track configuration:
    [tracks.GENCODE]
    storeClass = JBrowse/Store/SeqFeature/BigBed
    type = CanvasFeatures
    urlTemplate = gencode.bb
    style.label = gene_name,name,id
    style.description = gene_bio_type
  • JBrowse now has much better support for UCSC-style BED and BigBed features, via the new BED glyph type for CanvasFeatures. Rather than rendering a complex feature hierarchy like many of the other CanvasFeatures glyphs, the BED glyph draws sub-blocks with thick and thin regions, for compatibility with the UCSC browser. CanvasFeatures will automatically use the JBrowse/View/FeatureGlyph/UCSC/BED glyph type if a feature has no subfeatures, but has blockCount or thickStart attributes. This means that, in practice, a BigBed file will display very well with just the default configuration. Also for compatibility with the UCSC browser, JBrowse will set a BED feature's background color if one is included in the feature data (turn this off by setting itemRgb = false).

Minor improvements

  • The current dataset name is now displayed in the top right portion of the menu bar. (issue #767, @rbuels)
  • prepare-refseqs.pl now accepts a --gff-sizes option to allow defining reference sequence sizes from the ##sequence-region directives in a GFF3 file. @rbuels
  • Some store types now support a topLevelFeatures configuration variable, which allows tracks to treat certain types of features as 'top-level', even the actual track data has them as children of other features. One common use case for this would be if you have gene models in a GFF3 structured as gene→mRNA→exon/CDS/UTR, but you want to display the "mRNA" features as top-level, i.e. ignore the gene container that they are in. Now you can set topLevelFeatures = mRNA in the track configuration, and the track will display only "mRNA" features on the top level, ignoring any other existing top-level features, and ignoring the containing "gene" features. This helps address what seems to be a common pain point of having to "filter" tabix-formatted GFF3 before using it with Apollo. One important caveat is that users that configure tracks to use an "out of band" source of feature density or coverage data, like a separate wiggle file that shows feature density, will have to make sure that the density data is correct for this filter setting if they use it. Thanks to @Yating-L, @nathandunn, and @cmdcolin for valuable discussions. Stores that support topLevelFeatures currently are: GFF3Tabix, GFF3, BED, BEDTabix, GTF, and REST (issue #974, issue #969, @rbuels)
  • JBrowse can now accept additional configuration from a data-config attribute on its container element. This is useful for embedding JBrowse in other sites, particularly in cases where the JBrowse assets and configuration are stored or referenced from a different location from the page displaying the embedded JBrowse. For example:
would tell JBrowse to look for its configuration and assets at the relative base URL "../jbrowse". [@rbuels](https://github.com/rbuels) * JBrowse now has a favicon! ([issue #973](https://github.com/gmod/jbrowse/issues/973), [@rbuels](https://github.com/rbuels)) * Added additional caching code to SequenceChunks and NCList stores, reducing duplicate network requests and increasing performance in some circumstances ([issue #855](https://github.com/gmod/jbrowse/pull/855), [@cmdcolin](https://github.com/cmdcolin))

Bug fixes

  • Fix a bug in which saving exported data to a file was nonfunctional for some export data types. @rbuels
  • Fix a bug in which subfeatures were not always fetched correctly when using the GFF3Tabix store (issue #780, @rbuels)
  • Fixed several bugs with specific cases of relative URLs used in configuration. @rbuels
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