GMOD/jbrowse

🐛 Bug fixes

• Fix URL accessible reflected XSS in ?loc= parameter (pull #1657)

📦 Minor improvements

• Add optional track label field for RegexSequenceSearch (issue #1553,
• @cmdcolin, @Rhinogradentia)
• Bump @gmod/tabix for textdecoder speedup for very large tabix files
• (@arpanda, @cmdcolin, pull #1569)
• Increase GFF3Tabix chunkSizeLimit to avoid it being hit on relatively small
• files

🐛 Bug fixes

• Bump @gmod/cram for fix for ultra long reads (https://github.com/GMOD/cram-js/pull/84)
• Fix issue that some users were seeing with "Commit hash required" when
• running setup.sh. Thanks to @GFJHogue and @hans-vg for reporting (issue #1555)
• Bump @gmod/bam which fixes some unsigned BAM tags being reported with a
• negative number
• Bump @gmod/bam and @gmod/tabix for some fixes with reg2bins and chunk
• merging for large chromosomes e.g. wheat. Thanks to @jrobinso for reporting
• (https://github.com/GMOD/tabix-js/issues/118)

📦 Minor improvements

• Added an optimization for BAM that helps for long reads especially
• (@cmdcolin)
• Added generation of the MD tag if none is specified in BAM (issue
• Added `customRefRename` and `replaceRefRename` global configs for
• extending and replacing ref renaming functionality respectively.
• Ref renaming helps things like chrM and chrMT to be loaded onto the
• same chromosome in jbrowse (@cmdcolin, pull #1506)
• Added support for a -f option for setup.sh. This option causes
• + 3 more

🐛 Bug fixes

• Fix the display of mismatches from hard clipped BAM sequences (pull #1513)
• Fix ability to use tracks from Open track dialog in combination tracks.
• Thanks to Sonny Arora for the repo (pull #1536)
• Fix mismatch/SNP calculation for reads with multiple skips, e.g. Iso-Seq
• (@cmdcolin)

📦 Minor improvements

• Added a 'Reset to defaults' menu item, which addresses a long standing
• issue. Thanks to a user with a very long github name for their
• contribution (pull #1496, issue #764).
• Disable coordinate indicator on tab switch, thanks @lukaw3d (pull #1497)
• Small optimization bumping @gmod/bam from version 1.0.35->1.0.36 (@cmdcolin)
• Add ability to include/hide variant filters instead of just hide
• (@cmdcolin, issue #1478)
• Add ability to color by TS tag. The useXS config now applies to `XS` and
• + 2 more

🐛 Bug fixes

• Fixed a race condition in the http-range-fetcher module that caused
• "Error: "failed to retrieve file size"" messages when many tracks
• were opened at once. Thanks to @russellmyers for the bug report!
• (issue #1473)
• Fixed error with exporting highlighted regions with Save track data,
• thanks to @lipan6461188 for reporting (issue #1488)
• Fixed ability to have custom mouseovers on features that have no
• default mouseover e.g. features with no name or ID. Thanks to
• + 12 more

🐛 Bug fixes

• Fixed an regression that made corrupted features around bgzip block
• boundaries. Related to @gmod/tabix 1.2.0->1.3.2 fileOffset based feature ID.
• Bug affected JBrowse 1.16.7 (issue #1464)

📦 Minor improvements

• Add name regularization for refseqs named MtDNA (pull #1408,
• @scottcain, @cmdcolin)
• Improved performance of startup time with large tracklists (pull #1412,
• @cmdcolin)
• Improve consistency of scrolling behavior across browsers using
• normalize-wheel npm package (@cmdcolin, @scottcain, pull #1429)
• Add trackMetadata->sortFacets boolean flag which can be set to false
• to disable sorting the facet categories in the left hand column of the
• + 6 more

🐛 Bug fixes

• Fix bug that has existed since 1.16.0 (since the introduction of @gmod/bam)
• that caused some BAM tags to be missed.
• Added a fix for a performance regularization for large tracklists that
• contain a lot of data. Thanks to @scottcain for reporting (#pull #1412,
• @cmdcolin)
• Fixed ability to access remote data directories in desktop app
• (issue #1413)
• Fixed ability to open FASTA files with the .fasta extension in the
• + 16 more

📦 Minor improvements

• Add name regularization for drosophila style chromsome naming so that
• 2L maps to chr2L and vice versa (@scottcain)
• Add ability to index names in a BEDTabix file, enabled by default.
• Thanks to @billzt for the idea and implementation (pull #1393)

🐛 Bug fixes

• Fix the side scrolling on Mac misbehaving and triggering the browser's
• back action (a bug that existed only in 1.16.5). Thanks to @nathandunn
• for debugging (issue #1397)

📦 Minor improvements

• Added better error reporting if there is a BAI file for a genome that
• is longer than 2^29 and requires a CSI index
• Added default dontRedispatch=chromosome,region which avoids long
• GFF3Tabix redispatching for common gff3 types that don't need it.
• Added a `hideIframeDialogUrl` option to hide the iframe url in a
• `iframeDialog` popup. Thanks to @mictadlo for the suggestion (issue
• Updated @gmod/tabix and @gmod/bam to unzip bgzf chunks as they are
• received instead of performing chunk merges. This also allows
• + 10 more

🐛 Bug fixes

• Fixed a long standing issue with BigWig files not accessing the
• lowest summary zoom level (e.g. the first one after unzoomed).
• (@cmdcolin, issue #1359)
• Fixed a bug with using the scoreType: maxScore configuration on
• Wiggle tracks failing at non-summary zoom levels. Thanks to
• @patrickcng90 for reporting
• Fixed a bug with name regularizing that particularly affected CRAM
• on mitochondrial chromosomes. Thanks to @sachalau for patience and
• + 12 more

📦 Minor improvements

• Added `indexedFeatures` tracklist attribute for GFF3Tabix track types
• which controls the feature types from a GFF3Tabix file that are
• indexed. Thanks to @loraine-gueguen for the idea and implementation!
• (pull #1337, @loraine-guegen)
• Added `inferHTMLSubfeatures` which automatically creates multiple
• mRNA transcripts from a single gene parent feature. Thanks to
• @abretaud for the idea and implementation! Note that this is enabled
• by default now (pull #1343, pull #1340)
• + 2 more

🐛 Bug fixes

• Added better error reporting to GFF3Tabix tracks for if a parsing
• error occured. Thanks to @nathanhaigh for reporting (@cmdcolin)
• Added fix for VCF that don't contain alternative alleles (@cmdcolin)
• Added better error handling if there is a case where a tabix file is
• loaded that is on a genome longer than 2^29. CSI indexes are needed for
• this. Old versions of tabix which hadn't invented CSI would generate
• invalid tabix indexes in this case. Thanks to Hans Vasquez-Gross for
• reporting (@cmdcolin)
• + 3 more

🐛 Bug fixes

• Fix BioPerl setup after changes to the BioPerl distribution caused
• setup.sh to fail in all past JBrowse versions (issue #1310, @cmdcolin)
• Fix issue with NeatCanvasFeatures not drawing gradients on some
• features. Thanks to @mara-sangiovanni for reporting (issue #1311,
• @cmdcolin)
• Fix issue for exporting GFF3 for some nested attributes by dumping
• JSON into the value field. Thanks to @dionnezaal for reporting
• (issue #1309, @cmdcolin)

📦 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 (pull #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, pull #1292,
• @cmdcolin)

📦 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 (pull #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 (pull #1223, @cmdcolin)
• Created new BAM parsing mechanism using the npm module [@gmod/bam](https://www.npmjs.com/package/@gmod/bam).
• Users might see some modest performance improvements due to enhanced tooling.
• Thanks to @rbuels and others for testing and feedback (pull #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)
• + 30 more

🐛 Bug fixes

• Fixed issue where some generate-names setups would fail to index features.
• Thanks to @BioInfoSuite for reporting (issue #1275, pull #1283, @cmdcolin)
• Fixed issue with getting feature density from BAM files via the index stats
• estimation (issue #1233, @cmdcolin)
• Fixed issue where some feature mouseovers where not working properly (issue
• Fixed issue where instantiating JBrowse via `standalone.js` didn't work when
• in a production build with JBROWSE_PUBLIC_PATH overridden (issue #1239,
• @garrettjstevens)
• + 29 more

📋 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 (pull #1263, @cmdcolin).

📦 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, pull #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)
• + 14 more

🐛 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
• + 4 more

📦 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. (pull #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)

📦 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, pull #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, pull #1170, @cmdcolin)
• + 10 more

🐛 Bug fixes

• Added a more robust HTML processing in Util.js. Thanks to @hkmoon for the idea and
• implementation. (pull #1169, @hkmoon)
• Remove utils/jb_run.js from the minified release (issue #1161, issue #1160, @cmdcolin)
• Fixes issue where navigating away from genome browser and returning would not remember
• the location. Thanks to Vaneet Lotay for reporting. (issue #1168, @cmdcolin)
• Fixes off-by-one in the display of the size of the genomic region being viewed. Thanks
• to @sammyjava for the bug report! (issue #1176, @cmdcolin)

📦 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, pull #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](https://www.npmjs.com/package/@gmod/twobit).
• Thanks to @cmdcolin for some testing and motivating examples. (issue #1116, pull #1146,
• @rbuels)
• Added feature.get('seq') to CRAM features which enables detailed comparison of the
• + 6 more

🐛 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, pull #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
• + 2 more

📦 Major improvements

• Added support for displaying alignments from CRAM files, using the new npm module [@gmod/cram](https://www.npmjs.com/package/@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, pull #1120, @rbuels)
• Added support for the CSI index format for tabix VCF/BED/GFF and BAM files! This allows
• individual chromosomes longer than ~537MB (2^29 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, pull #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
• + 2 more

📦 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, pull #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').
• + 22 more

🐛 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 (pull #1083, @cmdcolin)
• Fix calculation of histograms on GFF3 and GFF3Tabix stores. Thanks to @thomasvangurp for
• + 6 more

📦 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)
• + 5 more

🐛 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, pull #1064, @loraine-gueguen)
• Fixed a bug in which setup.sh failed if run twice in a row under some circumstances.
• (pull #1053, @cmdcolin)
• Fixed a bug in which setup.sh did not accept nodejs version 10 as sufficiently recent.
• (pull #1048, @cmdcolin)
• Fixed a bug in which the "Loading..." message erroneously appeared at the top of the
• + 4 more

📦 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).
• + 5 more

🐛 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)

📦 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
• + 13 more

🐛 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
• + 5 more

📦 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
• + 27 more

📦 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)

📦 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
• + 42 more

🐛 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
• + 10 more

📦 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 `N`s in their CIGAR strings.
• + 72 more

📦 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
• + 38 more

🐛 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
• + 28 more

📦 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