JBrowse 1.16.1

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)

JBrowse 1.16.0

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.
  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)

• Added support for indexing arbitrary fields from GFF3Tabix files by setting
  nameAttributes in the track config e.g. nameAttributes=name,id,customfield.
  (issue #1115, pull #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
  (pull #1228, pull #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, pull #1230, @cmdcolin)

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

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

• Added a config datasetLinkToParentIframe to make the dataset selector use
  window.parent for when jbrowse is in an iframe (pull #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 (pull #1235, @cmdcolin)

• Added useTS coloring option for RNA-seq strandedness, similar to the useXS
  that existed previously (pull #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, pull #1282, @cmdcolin).

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
  #1236, @cmdcolin)

• Fixed issue where instantiating JBrowse via standalone.js didn't work when
  in a production build with JBROWSE_PUBLIC_PATH overridden (issue #1239,
  @garrettjstevens)

• Small fix for issue where SNPCoverage would crash on some feature filters
  (issue #1241, @cmdcolin)

• Fixed issue where JBrowse Desktop was not able to access remote files (issue
  #1234, pull #1245, @cmdcolin)

• Fix issue where the Hierarchical track selector contained a bunch of blank
  whitespace. Thanks to @nathanhaigh for reporting! (issue #1240, pull #1253,
  @cmdcolin)

• Fixed issue where whitespace surrounding GFF3 attributes and attribute names
  was incorporated (issue #1221, pull #1254, @cmdcolin)

• Fixed issue with some GFF3Tabix tracks having some inconsistent layout of
  features (issue #1244, pull #1260, @cmdcolin)

• Fixed CRAM store not renaming reference sequences in the same way as other
  stores (pull #1277, @rbuels, @cmdcolin)

• Fixed bug where older browsers e.g. IE11 were not being properly supported via
  babel (issue #1259, pull #1267, @cmdcolin)

• Fixed bug where some files were not being fetched properly when changing
  refseqs. Thanks to @luke-c-sargent for the report (issue #1252)

• Fixed storeTimeout on CRAM files being unused which can result in excessive
  fetches (pull #1235, @cmdcolin)

• Fixed issue where JBrowse would load the wrong area of the refseq on startup
  resulting in bad layouts and excessive data fetches. Thanks to @hkmoon,
  @cmdcolin, and @garrettjstevens for debugging (issue #1190, pull #1235, pull
  #1187)

• Fixed issue where CRAM layout and mouseover would be glitchy due to ID
  collisions on features (issue #1271, @cmdcolin)

• Fixed parsing of certain bigBed files that were hanging on track startup
  (issue #1226, pull #1229, @cmdcolin)

• Fixed issue where some parts of a CRAM file would not be displayed in JBrowse
  due to a CRAM index parsing issue (@cmdcolin)

• Fixed an issue where BAM features were not lazily evaluating their tags
  (@cmdcolin)

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).

JBrowse 1.15.4

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)

• 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, pull #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, pull #1209, @rbuels)

• Added hideSequenceBox config to allow hiding the FASTA boxes in the View details
  popups. Thanks to @andreamini for reporting (issue #1211, pull #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, pull #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, pull #1209, @rbuels)

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

JBrowse 1.15.3

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)

JBrowse 1.15.2

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)

• 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, pull #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, pull #1173, @cmdcolin)

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)

JBrowse 1.15.1

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.
  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
  read versus the reference with the renderAlignment configuration. (issue #1126,
  pull #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! (pull #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, 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
  display but this generally seems to be due to limited use case such as secondary
  alignments in RNA-seq (issue #1108, pull #1145, @cmdcolin)

JBrowse 1.15.0

Major improvements

• Added support for displaying alignments from CRAM files, using the new npm module @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
  configuration with names.dialog entry, or disable search dialog with disableSearch.
  Thanks to the #GCCBOSC hackathon for the idea and feedback (pull #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, 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').
  Thanks to @nvteja for motivating this! (issue #1068, pull #1074, @cmdcolin)

• Added cache-busting for track config files which actively prevents stale configuration files
  from being loaded (pull #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.
  (pull #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, pull #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. (pull #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, pull #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 (pull #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, pull #1119, @nathanhaigh)

• Fixed setup.sh behavior when node is not installed, printing a decent error message. (issue #1082, pull #1083, @cmdcolin)

JBrowse 1.14.2

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, pull #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, 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
  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

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

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: html <div class="jbrowse" data-config='"baseUrl": "../jbrowse"' id="GenomeBrowser" style="height: 600px; width: 100%; padding: 0; border: 0;" > </div> would tell JBrowse to look for its configuration and assets at the relative base URL "../jbrowse". @rbuels

• JBrowse now has a favicon! (issue #973, @rbuels)

• Added additional caching code to SequenceChunks and NCList stores, reducing duplicate network requests and increasing performance in some circumstances (issue #855, @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