Release 1.16.3 2019-02-21 00:48:52 UTC

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)

Release 1.16.2 2019-02-01 03:31:36 UTC

Minor improvements

Allow configuring the cache busting behavior for adding random ?v= value to config file requests. This can be configured in index.html. Thanks to user @sandilyaamit for reporting, this is actually important to disable when using Amazon presigned URLs (@cmdcolin)
Adds fixBounds config for XYPlot tracks which can be set to false to disable the behavior of rounding up or down on the min_score/max_score variables for the ruler. Thanks to @scottcain for the suggestion (pull #1306, @cmdcolin)

Bug fixes

Fix ability to use CSI indexes with BAM files since 1.16.0 (@cmdcolin)
Fix ability to read some CRAM files with unmapped mates (@cmdcolin)
Fix issue with the browser loading NaN locations on startup (@cmdcolin)
Add fix for exporting GFF3 for newer browsers that have Array.values() enabled. Thanks to Scott Cain for reporting (@cmdcolin)
Improve error message when refSeqs=file.fai config fails to load (@cmdcolin)

Release 1.16.1 2018-12-28 02:24:11 UTC

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)

Release 1.16.0 2018-12-13 17:24:29 UTC

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).

Release 1.15.4 2018-10-05 13:02:55 UTC

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)

Release 1.15.3 2018-08-29 22:34:53 UTC

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)

Release 1.15.2 2018-08-16 21:02:27 UTC

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)

Release 1.15.1 2018-08-01 23:59:52 UTC

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)

Release 1.15.0 2018-07-20 00:24:49 UTC

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)

Release 1.14.2 2018-06-04 23:41:52 UTC

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)

Release 1.14.1 2018-05-02 22:04:33 UTC

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)

Release 1.14.0 2018-04-18 15:14:58 UTC

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, pull #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 (pull #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

Release 1.13.1 2018-03-28 23:49:27 UTC

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)

Release 1.13.0 2018-03-15 01:32:20 UTC

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)

Release 1.12.5 2018-02-28 20:08:35 UTC

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)

Release 1.12.4 2018-02-14 22:29:20 UTC

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. GMOD#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)

Release 1.12.3 2017-05-02 19:20:01 America/Los_Angeles

Minor improvements

Upgraded build system to install dependencies with bower and updated to dojo 1.9.8 (issue #718).
Added the ability to load tabix indexed GFF and BED files. Thanks to Colin Diesh and @zhjilin for contributing (issue #670).
Added ability to open BED files in the "Open track" user interface (issue #729).
Added ability to access SPARQL and other jbrowse data stores via CORS. Thanks to the WebApollo hackathon and Eric Rasche for contributing (issue #679).
Added extra coloring schemes for the Sequence track when using protein residues. Thanks to Eric Rasche for the idea and implementation (issue #673).
Added ability to specify custom exporter classes for the "Save track data" option, for example, adding exporter code in plugins (issue #682).
Added ability to specify custom name store classes via plugins, which allows plugins to implement their own search functionality (issue #732).
Added a timeout for the track feature density calculations which can aid problems like consistent chunkSizeLimit issues (issue #540, issue #730).
Added an option to specify multiple highlights, or bookmarks, using the config file, a remote service, or the URL bar (issue #668).
Added support for parsing BAM files from IonTorrent (issue #782, issue #568).
Added support for native file access to .2bit files (issue #759).
Added list of plugins in about box (issue #848).
Added cacheMismatches option to improve performance when viewing long-read alignments (issue #860).
Added subfeatureDetailLevel config item to make View details box only load subfeatures on demand (issue #861).
Added ability to draw scatter plot from BigWig tracks. Thanks to Keiran Raine for the contribution (issue #741).
Added a fullviewlink option for the URL bar to disable "View full link" attribute in embedded JBrowse. Thanks to Vivek Krishnakumar for contributing (issue #813).
Added URL parameter &tracklabels=0 and config parameter to hide track labels (issue #869).
Added renderAlignment option which creates a per-base alignment view of the read versus the reference (issue #795).
Added inferCdsParts option which creates CDS subfeatures from a continuous CDS region for CanvasFeatures glyphs. Thanks to Vivek Krishnakumar for the contribution (issue #872).
Added events tracks/focus, tracks/unfocus, allowing for context switching based on selected track.

Bug fixes

Made the menu bar widgets centered again (issue #680).
Fixed error where the sequence track would not load after "Open sequence file" (issue #831).
Fixed problem with persistant "Error reading from name store" message. Thanks to Anthony Bretaudeau for contributing the fix! (issue #820).
Reverted to standard eukaryotic codon set.
Fixed issue where saving session in JBrowse Desktop where plugins were not saved with session.
Fixed an error if there were numerical values being used as label or description for the CanvasFeatures type tracks. Thanks to Eric Rasche for reporting (issue #673).
Fixed some issues where the Gene glyph would not layout some features correctly. Thanks to Eric Rasche for reporting (issue #686).
Fixed an issue with JBrowse Desktop where saving session would not save the tracks that were not visible.
Added fix when using indexed fasta from prepare-refseqs.pl. Thanks to @billzt for the report (issue #719).
Added a fix for an issue where editing the configuration of files that were opened by a user didn't work. Thanks to @lpryszcz for the report (issue #569).
Fixed some inconsistencies where "Open sequence" on file with a .fasta file extension failed (issue #696).
Fixed issue where track labels would re-appear during scroll (issue #793).
Added handler for click scrolling in genome view. Thanks to @exogenesys for fixing (issue #709).
Fixed a rare error that only affected some versions of Chrome (issue #758).
Removed linear gradients from some NeatFeatures tracks (issue #721).
Fixed issue where saving GFF3 would fail if the source data was in VCF format (issue #800).
Fixed issue where there was a mix of plugin declarations (issue #866).

Release 1.12.2 2016-05-31 America/Los_Angeles

Special Release for Apollo

Release 1.12.1 2016-03-01 03:47:38 America/Los_Angeles

Minor improvements

Update Dojo to 1.8.10

Bug fixes

Fix RegexSearch plugin and NeatCanvasFeatures plugin - search track loading failure (issue #676)
Fix compat_121.html to access /css directory

Release 1.12.0 2015-12-18 17:40:39 America/Los_Angeles

New features

Added ability to open a new genome in FASTA format from the browser. Also supports indexed FASTA. Thanks to Bradford Powell for the original indexed FASTA contribution (issue #495, issue #647).
Support for inline reference sequence configurations.
Created stand-alone desktop version of JBrowse using the Electron platform for OSX, Windows, Linux (issue #647).

New plugins

NeatHTMLFeatures - Add the drawing of introns and gradient features to HTML tracks.
NeatCanvasFeatures - Add the drawing of introns and gradient features to Canvas tracks.
CategoryUrl - Implements a cat= URL option to display tracks for a given category (issue #618).
DebugEvents - a plugin to display global publish and milestone events on the debug console.
HideTrackLabels - Adds a toolbar button to toggle the display of track labels on and off (issue #614).

Minor improvements

Added new menu format to support loading your own genome. The open genome option can be hidden via hideGenomeOption in config, and the classic menu style can be restored via classicMenu in config.
Added ability to load custom histograms for tracks loaded from flatfile-to-json.pl (i.e. override a pre-existing histogram store). See (issue #612).
Added these options to add-bw-track.pl --clip_marker_color , --bg_color , --height (issue #510).
Added an option for Wiggle tracks, scoreType: 'avgValue', which helps preserve continuity when zooming in on certain tracks like GC-content. It complements the scoreType: 'maxValue' introduced in 1.11.6. Thanks to Han Lin for the pull request (issue #504).
Clarify track filter box description and feature search box "placeholder" text. (issue #611)
Implement option to have a separate location box from search box (issue #611, issue #652).
Move CSS files into css folder.
Added ability to specify the set of startCodons and stopCodons in the config files. Thanks to Eric Rasche for the contribution (issue #657)!

Bug fixes

Add Travis-CI and jshint linting to build (issue #628).
Fixed a bug where the BAM popup boxes would display some incorrect info due to byte packing. Thanks to Thomas Downs for contributing the fix.
Fixed a bug where grid lines wouldn't render at some particular zoom levels (issue #514).
Fixed a bug where the user's --workdir parameter would be deleted which could have unintended side effects if the --workdir was pointing to important data, but this is uncommon (issue #563).
Allow falsey values to be used in browser.cookie.
Fix minor issue where sometimes the length field of refSeqs.json was missing.
Fix some issues that occurred when a reference sequence was named '0' (issue #662, issue #610).

Release 1.11.6 2015-02-12 18:27:38 America/Chicago

Minor improvements

Added the ability to customize the contents of HTMLFeatures and CanvasFeatures mouseover tooltips more extensively. Thanks to David Muller for the original bug report and Colin Diesh for the fix (issue #480).
Added new options for BigWig files to use min/max summary values when zoomed out using scoreType. Thanks to Scott Cain for reporting the issue and to Colin Diesh for the fix (issue #518).
Added a checkbox for wiggle type tracks to have log scale. Thanks to Han Lin for the pull request (issue #502).
Added the ability to display paired-end reads in the same direction on Alignments2 tracks with the "Use reverse template" option. Thanks to Tomaz Berisa and Colin Diesh for their contributions (issue #485).
Added the ability to specify a codon table (or partial codon table) for the Sequence track.
Added the ability to show or hide the main menu bar using the configuration file.

Bug fixes

Fixed "boolean is not a function" error when using CanvasFeatures tracks with the Segments glyph in some situations.
Fixed a dialog box display issue for VCF variants with "no call" specified (issue #513).
Fixed loading files from certain filepaths with special characters. Thanks to Ben Bimber for reporting and helping diagnose the bug (issue #508).
Fixed popup-dialog callbacks not being called on BAM Alignments tracks in 1.11.5.
Fixed systemwide installations of JBrowse perl modules when using Module::Build.
Fixed a bug when displaying SNPs on hard clipped reads. Thanks to Thon de Boer for the bug report and to Colin Diesh for the fix (issue #516).
Fixed a bug when displaying SNPs on spliced alignments. Thanks to GitHub user 09140930 for the bug report and to Colin Diesh for the fix (issue #523).
Fixed a bug that affected some VCF and GFF popup dialogs in some browsers, particularly Chrome 38 (issue #522).
Fixed a bug with the incremental indexing with generate-names that associated the wrong track with the name store. Thanks to Richard Hayes for reporting this issue and to Colin Diesh for the fix (issue #526).
Fixed the --workdir parameter in generate-names.pl (issue #506).
Fixed the display of alternative alleles in the genotype for VCF pop-ups (issue #533).
Fixed an issue where some paired-end read data wouldn't display properly if they had the same start position (issue #521).
Output .htaccess file for generate-names.pl when using the compress option. Thanks to Sebastien Carrere for reporting the bug (issue #541).
Fixed a small bug with being able to scroll past end of chromosome when using the --sizes option to prepare-refseqs.pl (issue #535).
Fixed a small internal code inconsistency with the positioning of the vertical position line. Thanks to Anurag Priyam for the fix (issue #545).
Fixed a small bug with some stylesheets not being able to be used for the CanvasFeatures coloring, for example, LESS stylesheets. Thanks to Anurag Priyam for reporting the issue (issue #527).
Fixed a small bug with mouseovers on Wiggle type tracks. Thanks to Han Lin for finding and fixing this bug (issue #503).
Removed XS tag from the strand calculation for alignments and made it an optional rendering option for BAM files with the "Use XS" option. Thanks to Kieran Raine and the pull request (issue #473).
Added a bugfix that prevented viewing the details of haploid VCF files. Thanks to Colin Diesh for finding and fixing this bug (issue #536).
Added a bugfix for an issue that made browsing very buggy when using private browsing mode in Safari.
Fixed the shortDescription option for the mouseover description of tracks in the Hierarchical track list (issue #553).
Re-added filter options that were missing for SNPCoverage tracks.

Release 1.11.5 2014-09-04 16:03:22 America/Chicago

Minor improvements

Added the ability to disable sorting on the Hierarchical track selector using the sortHierarchical flag. Thanks to Chris Childers for the suggestion and Colin Diesh for the implementation (issue #477).
Added saving of the display mode setting on the CanvasFeature based tracks. Thanks to Jon Hinton for the idea and Colin Diesh for the fix (issue #469).
Added configurable click event handlers for Wiggle type tracks. Thanks to Richard Hayes for implementing this feature (issue #489).
Added more configuration options for 'View details' popups as well as the ability to customize the 'About track' popups. Thanks to Colin Diesh for the idea and implementation (issue #494).
Added the ability to load the category attribute from trackMetaData files to be used for the Hierarchical track selector.
Added the ability to specify initially collapsed categories in the Hierarchical track selector (issue #507).
Added beta touch-screen and tablet support by fixing a related bug. Thanks to Paul Hale and Kieran Raine for reporting bugs and to Emily Greenfest-Allen for the suggested fix (issue #505).

Bug fixes

Fixed a bug with VCF tabix file parsing that caused unnecessary chunkSizeLimit errors. Thanks to Richard Hayes for finding and debugging this issue (issue #486)!
Fixed a bug where the Variant popup boxes would not display complete genotype information in previous 1.11.* versions. Thanks to Nando for reporting the bug and Colin Diesh for the bugfix (issue #488).
Fixed a small error that occured when using variant type tracks with the REST API.
Added a bugfix that caused problems scrolling in dialog boxes for variant type tracks in 1.11.4 (issue #492).
Fixed the use of the --refs flag on prepare-refseqs.pl. Thanks to Audrey for finding & fixing this bug (issue #497).
Added missing template length flag to the Alignments popup dialogs. Thanks to Kieran Raine for the suggestion and Colin Diesh for the fix (issue #471).
Fixed the functionality of the --incremental flag in the generate-names.pl script. Thanks to Richard Hayes and Colin Diesh fixing the issue (issue #478).
Fixed legacy bam-to-json.pl support when running setup.sh due to samtools build modifications (issue #501).

Release 1.11.4 2014-05-14 12:04:54 America/Chicago

Minor improvements

Added high-resolution rendering for CanvasFeatures, SNPCoverage, BigWig tracks, and histograms. This allows rendering for canvas- based tracks to look much sharper on high-resolution displays and can even look sharper when zooming. The high-resolution rendering is disabled by default to avoid conflicts with existing instances, but feel free to test it out by setting "highResolutionMode" in jbrowse.conf. Thanks to Colin Diesh for the idea and implementation (issue #456)
Added the ability to run jbrowse scripts outside of the JBrowse root directory. Thanks to Chien-Chi Lo for the patch (issue #465).
Added basic GTF parser that can open files from the File->Open menu or by using the in-memory adaptor. Big thanks to Andrew Warren for the contribution (issue #453).
Added a change to the highlight button to allow the user to more easily clear highlights. Thanks to Paul Hale for the suggestion and Colin Diesh for the fix (issue #445).

Bug fixes

Fixed help page icons not loading since JBrowse 1.11.2. Thanks to Colin Diesh for catching the bug and fixing it (issue #460).
Fixed updating of the y-axis scale when using the resize quantitative tracks feature. Thanks again to Evan Briones for the original implementation and Colin Diesh for the fix (issue #461).
Changed the CanvasFeatures 'View details' pages to display the name and description of features in the dialog box. Thanks to Colin Diesh for the fix (issue #463).
Added a bugfix for non-compliant servers that add a trailing slash to the URL. Thanks to Colin Diesh for the fix (issue #462).
Fixed a broken link in the documentation for biodb-to-json.
Updated setup.sh to maintain compatibility with the latest BioPerl. Thanks to Thomas Sibley and Scott Cain for helping with this issue (issue #468).
Fixed a long standing bug with the coloring of nucleotides on the SNPCoverage/Alignments2 track. Thanks to Long Le for reporting this on the mailing list.
Fixed a long standing bug with the scrollbar in the dialog box on Chrome and Safari browsers. Thanks to the #dojo irc channel and and Colin Diesh for helping fix this problem (issue #386).
Fix a small rendering problem that causes one pixel gap to appear on Safari due to subpixel rendering issues. Thanks to Colin Diesh for the preliminary fix (issue #341).
Fix a bug with CanvasFeatures based tracks loading huge amounts of data to generate histograms instead of using pre-generated histograms. Also lowered the maxScreenFeatureDensity default on the CanvasFeatures tracks so that histograms can be displayed more readily. Thanks to Daniel Troesser for reporting this issue on the mailing list and Colin Diesh for the fix (issue #475).

Release 1.11.3 2014-03-07 13:05:57 EST5EDT

Minor improvements

Added a "Zoom to this" item in the default right-click menus for canvas-based feature tracks. Thanks to Paul Hale for the initial implementation of this.
Allow the user to set the document.domain property via jbrowse.conf which can be helpful especially if jbrowse is embedded in a iframe. Thanks to Kieran Raine for the idea and Colin Diesh for the bugfix (issue #440)
Improved the graphic design of the "Add sequence search" dialog box to make it clearer how to switch between providing an amino acid and a nucleotide sequence. Thanks to Kevin Mohamed for the initial implementation of this (issue #436).
Expanded the default color set of Alignments2 tracks to show different shades of color indications of reads with missing mate pairs, improperly aligned reads, and reads with mate pairs on different reference sequences. Thanks to Keiran Raine for implementing this (issue #443).
Added support to customize specific parts of the 'View details' popups using callback functions. Thanks to Kieran Raine for the idea and Colin Diesh for the implementation (issue #421).
The File->Open tool will now can add files named *.coverage.* or *.density.* as histograms to newly-opened tracks if the file basenames match. For example, if both mysample.bam and mysample.coverage.bw are present, mysample.coverage.bw will be added as a histogram source for mysample.bam. Thanks to Keiran Raine and Alexander Stoddard for suggesting this (issue #423).

Bug fixes

Fixed a problem where the feature arrowhead would get stuck in the middle of the screen at high zoom levels. Thanks to Colin Diesh for the fix (issue #449).
Disabled the FASTA download button in the "View details" page on Safari (issue #412). This feature can't be supported in Safari at this time, but it is still supported in most other browsers. Rob Buels and Colin Diesh contributed fixes to this issue.
Fixed a bug in the client-side GFF3 parser pointed out by Andrew Warren. Thanks Andrew! (issue #452).
Fixed the problem of translation frames being switched around at different zoom levels. Thanks to Kieron Taylor for the bug report and Colin Diesh for the bugfix (issue #435)
Fixed a bug where gene features in GFF tracks would not have arrowhead markers. Thanks to Colin Diesh for finding and fixing this issue (issue #454)

Release 1.11.2 2014-02-10 19:11:33 EST5EDT

Minor improvements

Added some user interface elements to set the height in pixels of a single quantitative track, or of all visible quantitative tracks. Thanks to Evan Briones for implementing this!
Added a JBrowse/View/FeatureGlyph/Diamond glyph that draws diamond-shaped features instead of boxes. Thanks to OICR Co-op student Kevin Mohamed for implementing this!
Reference sequence tracks now display a "no sequence" message instead of a bunch of blank blocks when the reference sequence basepairs aren't available. Thanks to Kevin Mohamed for implementing this (issue #422).
Persistent session state is now stored on a per-dataset basis, which improves user experience when switching between multiple datasets in JBrowse. Thanks to Richard Hayes for pointing this issue out, and Kevin Mohamed for the fix (issue #410).
"Hide sites not passing ..." settings in VCF track menus now show the filter's long description when hovered over. Thanks to Keiran Raine for suggesting this (issue #420).
Tweaked display of track labels and added a slight border at the top edge of each track to make it more clear which track data belongs to. Thanks to Keiran Raine for suggesting this, and Kevin Mohamed for the initial implementation (issue #432).
Added a --config option to flatfile-to-json.pl that accepts additional configuration variables that will be merged into the top level of the track configuration. Thanks to Mikael Brandström Durling for the initial implementation of this.

Bug fixes

generate-names.pl now indexes VCF files from track definitions in tracks.conf files. Thanks to Paul Halle for pointing this out (issue #434).
Added a missing dependency for the server side formatting tools on List::MoreUtil 0.28 or higher. Thanks to Cris Lawrence and Keiran Raine for troubleshooting this!

Release 1.11.1 2014-01-07 15:48:39 EST5EDT

Minor improvements

Alignments2 tracks now include right-click menu items to view the location of an alignment's mate pair or next segment in a popup or a new tab. Thanks to Keiran Raine for suggesting this (issue #406).
Alignments2 tracks now draw gaps and deletions in reads regardless of zoom level, as long as the alignment is at least 3 pixels wide in the display. Thanks to Keiran Raine for pointing out the need for this (issue #403).
Added support for a histograms.max variable for CanvasFeatures-based tracks that can be used to manually set the max value of a histogram display. Thanks to Keiran Raine for pointing out the need for this.
Added support for drawing clip markers (with their color set by histograms.clip_marker_color) in CanvasFeatures-based tracks. Thanks to Keiran Raine for pointing out the need for this (issue #402).
Canvas-based feature tracks now try to draw histograms, if available, when the data backend throws a data-overflow error (like when the BAM backend exceeds the chunkSizeLimit). Thanks to Keiran Raine for motivating this (issue #405).
Make it easier to set JS loading baseUrl by moving it into the initial dojo configuration. Thanks to Jillian Rowe for pointing out the need for this.
Enhanced new text-based config syntax to support arrays of values in a list like:
```
 [trackMetadata]
 sources =
   + data/mymeta.csv
   + data/more_meta.csv
```

Bug fixes

When a number is typed into the location box, JBrowse first checks if it is the name of a feature in the names index, and only interprets it as a coordinate if it is not found in the names index. Thanks to Richard Hayes for pointing this out (issue #407).
Fixed bug that caused client-side GFF3 tracks to appear as "Loading" forever if the GFF3 is malformed (like malformed GFF3 files that are opened with the File->Open tool).
Fixed bug in which no default value for maxFeatureSizeForUnderlyingRefSeq was being set, which made default feature detail popups try to fetch and display a feature's underlying reference sequence even if it is way too large, unless the variable was set explicitly in the configuration.
JBrowse now shows a more understandable error message when trying to open an uncompressed BAM file. Thanks to Keiran Raine for pointing this out (issue #404).
Fixed jbrowse.conf faceted track selector configuration examples not working as written. Thanks to Cris Lawrence for pointing this out.
Fixed a bug in which right-clicking on feature labels in an HTMLFeatures-based track did not bring up the right-click menu for a feature. Thanks to Cris Lawrence for pointing this out (issue #408).

Release 1.11.0 2013-12-19 15:51:37 EST5EDT

Major improvements

Introduced density/coverage histogram support for CanvasFeatures, CanvasVariants, and Alignments2 tracks. These track types now support an optional histograms configuration subsection that can contain a definition for a second datastore that holds quantitative data (usually either coverage depth or feature density) to be displayed when zoomed further out than featureScale (or if featureScale is not set, the scale determined by the store's feature density divided by maxFeatureScreenDensity). Thanks to Richard Hayes for pushing hard for this feature.
Added a new "Hierarchical" track selector that shows tracks in a hierarchy of collapsible categories, which is now the default track selector. To assign categories and subcategories to your tracks, set category or metadata.category attributes on each configured tracks in your trackList.json. Thanks to the many users who have requested this at one time or another.
JBrowse now supports a new plaintext configuration format that users of GBrowse will find very familiar, since it is designed to be very similar to it. This syntax is also much easier to hand-write than JSON. The JSON configuration syntax is not going away, and will continue to be supported.

Thanks to Erik Derohanian for the original implementation of this configuration adaptor, and Richard Hayes and Keiran Raine for motivating the work to polish and more fully integrate it.
Variables in configuration files can now be based on the contents of other variables. For example, setting
```
"myCustomVariable": "/some/custom/path",
"include": "{myCustomVariable}/conf.json"
```
will try to include a configuration file located at "/some/custom/path/conf.json". Interpolation is done as the final step in configuration loading, so variables can come from anywhere in the configuration.
When JBrowse is started, if there are no reference sequences found in the default dataRoot, but the dataset selector is configured, JBrowse shows a simple list of links to available datasets instead of the "Congratulations, JBrowse is on the web" page. Thanks to Saulo Aflitos for the idea and its initial implementation.
For users wishing to convert existing JSON configuration files to the new format, there is a new script, bin/json2conf.pl, that does a fair job. Run bin/json2conf.pl -? for details on how to use it.
Added a new REST backend for name lookup and autocompletion. See http://gmod.org/wiki/JBrowse_Configuration_Guide#JBrowse_REST_Names_API for details. Thanks to Erik Derohanian for implementing this, and Ben Booth for suggesting an API design (issue #267).
Major performance and scalability improvements for generate-names.pl. Now uses a different algorithm that is faster and more scalable than before, and no longer relies on BerkeleyDB for temporary storage. This should also alleviate the need to run generate-names.pl with --safeMode in Perl 5.10 and earlier. In fact, the --safeMode argument to generate-names.pl no longer has any effect. Thanks to Cris Lawrence for pointing out the continuing need for more scalability.

Minor improvements

Detail popups for CanvasVariants and HTMLVariants tracks now display the reference sequence itself instead of just "ref" in genotype displays. Thanks to Cris Lawrence for requesting this.
Added a "save as FASTA" button to default feature detail popups that downloads a FASTA file with the displayed piece of reference sequence (issue #299).
chunkSizeLimit for VCF files now defaults to 1 MiB. It used to be 15 MiB, which was really far too big for browsers to handle.
Added support for a --nameAttributes argument to flatfile-to-json.pl that takes a comma-separated list of feature attributes to index for name searching and completions, or 'none' to not make names searchable.
Added support for a nameAttributes variable in biodb-to-json.pl track configurations that can be set to an array of feature attribute names to to index for name searching and completions, or 'none' to not make names searchable.
Add a --category argument to bin/wig-to-json.pl that can be used to set the metadata.category of a track.

Bug fixes

Fixed a bug in NCList data backed in which feature histograms were often calculated very incorrectly.
Fixed a bug in the VCF data backend that caused not all VCF features to be shown in some files at some zoom levels.

Release 1.10.12 2013-12-10 16:09:42 EST5EDT

Minor improvements

bam-to-json.pl and flatfile-to-json.pl now support a --metadata argument that can add a metadata stanza to track configurations they generate.
Multi-valued attributes in feature detail popups are displayed as a string of boxes, each containing a value, to avoid misinterpretation. Before, each value was just separated from the previous one by whitespace. Thanks to Cris Lawrence for pointing out the need for this.

Bug fixes

Re-enabled usage analytics reporting, which had been disabled by a stray piece of debugging code since the 1.10.7 release.
Fixed a bug in which the tooltip in canvas-based feature tracks would sometimes display incorrect label or description text.

Release 1.10.11 2013-12-03 17:21:20 EST5EDT

Minor improvements

Made the sequence track's "zoom in to see sequence" placeholder take up less vertical space. Thanks to Scott Cain for pointing out that making it be the same height as it will eventually be when zoomed in to base level is silly.
By default highlighting features after searching for them by name is now turned off. Set the highlightSearchedRegions top-level conf variable to true to turn this back on. Turns out, most people seem not to like this behavior. Thanks to Gregg Helt and Cris Lawrence for pointing this out.
SNPCoverage tracks now correctly display "skipped" regions in alignments, such as those produced by TopHat. Thanks to Josh Orvis, Gustavo Cerquiera, and others for reminders that this was still an issue.
SNPCoverage tracks now provide per-strand counts of "reference" reads at each position, like they already were providing for reads with mismatches.
SNPCoverage tracks now accept a mismatchScale configuration variable that sets the viewing scale (i.e. zoom level, pixels per bp) above which base-level mismatches will be drawn. Defaults to 1/10. Making this value larger can speed up SNPCoverage tracks for high-coverage data at the cost of needing to zoom in further to see mismatches.
setup.sh now uses curl for downloading things instead of wget, since curl is more widely available. Thanks to Keiran Raine for suggesting and implementing this (issue #393).

Bug fixes

Fixed a bug in which generate-names.pl would sometimes report the incorrect number of hashing bits in verbose output, and would sometimes use the number of hashing bits for an existing index even if that index was being regenerated. Thanks to Richard Hayes for pointing out the incorrect log output.
Fix generate-names.pl crashing on some older versions of Perl with an error like Bareword "POSIX::O_RDONLY" not allowed while "strict subs" in use. Thanks to Chris Childers for pointing this out.
Fix setup.sh failing on some older versions of Perl. It now runs generate-names.pl with the --safeMode flag.
Fixed a bug where the value display in SNPCoverage tracks would sometimes report "NaN%" for the reference when no reads cover a region.
Fixed a bug in which activating rubberband zooming using the SHIFT key while in highlighting mode would cause all the tracks to be dragged when attempting to highlight a region afterward. Thanks to Erik Derohanian for pointing out and fixing this (issue #387).
Fixed the location of the dojo/nls directory in release zipfiles. Was erroneously in src/nls, supposed to be src/dojo/nls. Thanks to Matt Bomhoff for pointing this out.
The in-memory GFF3 parser now copes with a missing newline at the end of a GFF3 file. Previously, the last line was ignored if it did not end with a newline character. Thanks to Colin Davenport for pointing this out (issue #394).

Release 1.10.10 2013-11-21 09:31:53 EST5EDT

Minor improvements

Spacing between tracks is now configurable by setting view.trackPadding in the configuration. Thanks to Chenchen Zhu for suggesting this (issue #377).
If reference sequences are defined, but no tracks are yet added, JBrowse will start normally instead of going to the "Congratulations, JBrowse is on the web" page.
generate-names.pl now supports a --compress option that compresses the name index files to save server disk space. Thanks to Richard Hayes for pointing out the need for this (issue #378).

Bug fixes

generate-names.pl now uses IO::Uncompress::Gunzip instead of PerlIO::gzip to read compressed VCF files. This fixes a bug in which only the first few hundred names in a VCF were indexed. Thanks to Cris Lawrence for pointing this out (issue #380).
Fixed a bug in which generate-names.pl would crash if run with --incremental and no existing names index. Thanks to Richard Hayes for pointing this out (issue #379).
Fixed a bug in which generate-names.pl would sometimes choose the wrong number of hash bits when performing incremental updates, leading to the old data being lost. Thanks to Richard Hayes for lots of help troubleshooting this.
Fixed bug where other tracks are visible underneath pinned tracks when the display is scrolled down. Thanks to Ed Lee for pointing this out.
Fixed a bug in which tooltip does not hide after the mouse leaves a Wiggle track in Safari 5 and 6. Thanks to Charles Girardot for pointing this out.
Fixed a bug in which the main.css file for plugins was not being correctly loaded in some installations. Thanks to Matt Bomhoff for pointing this out.

Release 1.10.9 2013-11-08 15:22:50 EST5EDT

Minor improvements

generate-names.pl now supports a --incremental or -i option that adds names to an existing index. Thanks to Richard Hayes for reminding me that this wasn't done yet (issue #373).
Added a lower-performance, but more backward-compatible indexing backend to generate-names.pl that can be activated by passing the --safeMode command-line argument. The recent performance improvements to generate-names.pl have apparently tickled some bugs that are present in some installations. Thanks to Josie Reinhardt and GitHub user raj76 for their continued help troubleshooting this. If you find that name indexing is not working correctly, try running it again with --safeMode, and report to the mailing list if it helps.
Added support for using the JBrowse in-memory GFF3 adaptor to display web-accessible GFF3 files directly. See docs/tutorial/data_files/volvox.gff3.conf for an example configuration. Thanks to David Goodstein and Richard Hayes for motivating this.

Bug fixes

flatfile-to-json.pl now depends on the latest Bio::GFF3::LowLevel::Parser 1.8, which fixes a bug in which features with no ID, Parent, or Derives_from attributes were not being included in parsed data. Thanks to Gwendoline Andres for pointing this out.
Tweak BioPerl-handling code in biodb-to-json.pl to hopefully work better with BioSQL backends. Thanks to Brian Osborne for pointing this out.

Release 1.10.8 2013-10-25 11:13:30 EST5EDT

Minor improvements

Added a new navigateTo action usable for customizing feature left-clicks and right-click menus. Thanks to Scott Cain for requesting this.
Added a new feature_range_cache option for the REST data backend. If set to true, the REST backend will more aggressively cache ranges of feature data. Thanks to Daniel Troesser for pointing out the need for this (issue #369).
maker2jbrowse now, by default, runs generate-names.pl to generate names indexes. Also added a --no_names_index option to turn this off. Thanks to Josie Reinhardt for making me notice this was missing.
Tweaked generate-names.pl default indexing parameters to emphasize indexing speed more. Now defaults to a smaller average file size for the on-disk JSON files it produces, which is much faster to generate and write (up to 8 or 10x faster). However, the on-disk index is about 2-2.5x larger overall.
Removed support for the --refids command-line argument to prepare-refseqs.pl, which has probably never really worked.
Improved prepare-refseqs.pl support for Bio::DB::Das::Chado database backends. Thanks to Gwendoline Andres for helping troubleshoot this.

Bug fixes

Fixed generate-names.pl making incorrect name indexes when using 16 or more bits of hashing (when the number of index entries exceeds about 4 million). Thanks to Josie Reinhardt for helping troubleshoot this (issue #370).
The faceted track selector no longer refuses to display track unique labels even if they are explicitly included in the displayColumns setting.

Release 1.10.7 2013-10-15 16:50:00 EST5EDT

Minor improvements

Added an optional stats/regionFeatureDensities endpoint to the REST API that makes it possible to provide binned feature counts that HTMLFeatures tracks can use to display feature histograms. Thanks to Stuart Watt and Daniel Troesser for pointing out the need for this (issue #365).

Bug fixes

Fixed a bad bug introduced in 1.10.6 in which FASTA files with line lengths longer than the configured chunk size were not correctly formatted. Thanks to Jean-Jack Riethoven for pointing this out (issue #363).
Fixed a bug introduced in 1.10.6 in which prepare-refseqs.pl would not respect the --noseq command-line option when using --fasta.
Fixed bug in which name or seq_id attributes are required for reference sequence features. Thanks to Daniel Troesser for pointing this out.
Fixed a bug that may have prevented some types of VCF files from being displayed (error message referring to inheritedFilters).
Fixed a bug in which "Zoom in to see feature" in Sequence tracks would wrap downwards below track at some zoom levels and window widths.
Fixed an off-by-one error in UTR attributes manufactured by the impliedUTRs mechanism of the ProcessedTranscript glyph. Thanks to Ben Booth for pointing this out (issue #362).
Fixed a bug in which score attributes of features were not being recorded by biodb-to-json.pl. Thanks to HongKee Moon for pointing this out (issue #364).
Removed a stray use of Carp::Always in GFF3-processing Perl code that may have caused problems in some installations.

Release 1.10.6 2013-10-07 21:06:51 EST5EDT

Minor improvements

Made the impliedUTRs option for ProcessedTranscript and Gene glyph still attempt to create UTRs if only '''one''' of the UTRs is missing from a transcript. Thanks to Ben Booth for pointing out the need for this.

Bug fixes

Fixed bug in which the mouseover value displays for Wiggle and SNPCoverage tracks would not always be hidden when the mouse leaves the track.
Fixed a bad bug that prevented fixed-scale Wiggle and SNPCoverage tracks from displaying. Thanks to Jean-Jack Riethoven and Michael Axtell for pointing this out.

Release 1.10.5 2013-10-03 10:21:37 EST5EDT

Minor improvements

Greatly improved the speed and reduced the memory footprint when running prepare-refseqs.pl with the --fasta and --gff options.
Added an impliedUTRs option to the ProcessedTranscript and Gene glyphs for CanvasFeatures tracks. Thanks to Ben Booth for pointing out the need for this (issue #348).
Upgraded flatfile-to-json.pl to use a new version of Bio::GFF3::LowLevel::Parser for GFF3 parser, which has a lookback buffer limit that makes it easier to parse large GFF3 files that do not contain enough '###' directives.
Further improved the memory footprint and speed of generate-names.pl. Thanks to Richard Hayes for his continued help with testing improvements and reporting problems.
Removed explicit dependency on GD::Image, which is only used by the old tiled-image generation demo code. This will make dependency installation easier for many people, at a (very) small cost to backward compatibility.

Bug fixes

Fixed a bad bug that prevented combination tracks from working. Thanks to Harry Yoo for pointing this out (issue #351).
Fixed a bug in which one of the temporary files used by generate-names.pl was not being created in the correct location. Thanks to Richard Hayes for testing this.
Fixed a bug in which generate-names.pl could sometimes crash when run with the -v (verbose) switch, or in setup.sh.
Fixed odd behavior when entering coordinate ranges in the location box under Safari. Thanks to Keiran Raine for pointing this out (issue #341).

Release 1.10.4 2013-09-23 16:16:50 EST5EDT

Minor improvements

Rewrote many parts of generate-names.pl, making heavy use of temporary BerkeleyDB stores (using Perl's DB_File module). This improves generate-names.pl performance by more than 10x.
Added a File->Add sequence search track menu item that can make tracks that show which regions of the reference sequence contain a given (small) sequence, or match a given regular expression. Thanks to Daniel Kasenberg for the initial implementation of this (issue #315).
Added a CanvasVariants track type, similar to HTMLVariants, which utilizes the faster CanvasFeatures rendering backend for displaying variant data.
Added checkboxes to HTMLVariants and CanvasVariants track menus that allow filtering displayed features based on the FILTER attribute in a VCF file. In addition to filtering based on the presence or absence of PASS, users can filter based on the custom filters defined in the VCF header. Thanks to Keiran Raine and Andrew Uzilov for suggesting this (issue #344).
Added "Hide forward strand" and "Hide reverse strand" checkboxes to Alignments and Alignments2 track menus that allow alignments on the forward and/or reverse strands to be hidden.

Bug fixes

Fixed a bug that prevented indexing of feature aliases in the names index when running generate-names.pl.
Fixed a bug that prevented proper display of the "ibeam" feature class in HTMLFeatures tracks. Thanks to Ed Lee for pointing this out.

Release 1.10.3 2013-09-04 16:22:17 EST5EDT

Minor improvements

Added options to Alignments, Alignments2, and SNPCoverage tracks to allow hiding reads that are duplicates, fail vendor QC, have missing mate pairs, are secondary alignments, and/or are supplementary alignments. Thanks to Kieran Raine and Andrew Uzilov for pointing out the need for this, and for their input on its design (issue #332).
Added support for a variables configuration for SPARQL data stores that can be used to specify additional variables for interpolating into a SPARQL query. Thanks to Toshiaki Katayama for suggesting this.
Added the ability for Sequence tracks to display a 6- or 3-frame translation of the reference sequence. Thanks to Daniel Kasenberg for implementing this (issue #221).
Added checkboxes in the track menu of Sequence tracks that allow users to toggle the display of the forward strand, reverse strand, and 6-frame translation.
Added support for an addStores variable in the query string of the URL used to start JBrowse. This variable accepts store configurations (which are a way to specify data sources separately from track configurations, so multiple tracks can use the same data source) in JSON format. For example, to add a store called "urlbam" that points to a BAM file, you could use the JSON:
```
`{ "urlbam": { "type": "JBrowse/Store/SeqFeature/BAM", "urlTemplate": "/path/to/my/bamfile.bam" }}`
```
which, when URI-escaped and put in the query string, looks like:
```
`addStores=%7B%20%22urlbam%22%3A%20%7B%20%22type%22%3A%20%22JBrowse%2FStore%2FSeqFeature%2FBAM%22%2C%20%22urlTemplate%22%3A%20%22%2Fpath%2Fto%2Fmy%2Fbamfile.bam%22%20%7D%7D`
```
Slightly improved performance of generate-names.pl in cases where --completionLimit is zero. Also improved the POD documentation of the --completionLimit parameter for generate-names.pl. Thanks to Richard Hayes for his continued patience.

Bug fixes

Fixed some bugs that prevented proper display of BigWig files larger than 4GB. Thanks to Keiran Raine for pointing this out.
Fixed a major performance bug that unnecessarily slowed down display of large BigWig files with Wiggle tracks when autoscale is set to "local".
Fixed a bug that prevented display of BAM reads that had MD tags but no associated CIGAR string. Thanks to Keiran Raine for point this out (issue #330).
Fixed a bug in which FixedImage tracks (e.g. legacy image-based Wiggle tracks) never take down the "Loading" message when displaying on a reference sequence for which no image data has been provided.
Fixed a bug that prevented rendering of mismatches, insertions, and deletions in a BAM read that occurred after a skip. Thanks to Gregg Helt for noticing this and fixing it (issue #325).
Fixed a bug in which the SNP frequencies calculated by SNPCoverage tracks were sometimes incorrect. Thanks to Matthew Conte for pointing this out (issue #335).
Fixed a bug in which reference sequences with a start coordinate other than zero would cause the overview scale track to not be drawn correctly. Thanks to Gregg Helt for noticing this and working on an initial fix (issue #324).
Fixed a bug in which the most recent location visited on a given reference sequence was not properly being restored from the saved cookie. Thanks to Gregg Helt for the initial fix for this (issue #321).
Fixed a bug in which event handlers and blocks in CanvasFeatures tracks were not being properly cleaned up. The most prominent visible consequences of this were duplicate dialog boxes being opened when clicking on a canvas feature. Thanks to Keiran Raine for noticing this and making sure it was fixed (issue #329).
Fixed a bug with flatfile-to-json.pl parsing of GenBank locations. Thanks to Steve Marshall for pointing this out (issue #323).
Fixed a bug in which SNPCoverage tracks would not always properly display error messages when something goes wrong, particularly under IE 9.

Release 1.10.2 2013-08-15 13:57:16 EST5EDT

Added mouse-over 'tooltips' to to CanvasFeatures tracks that show the a feature's label and description when the mouse hovers over it. Thanks to Daniel Kasenberg for implementing this.
Strand arrowheads in CanvasFeatures tracks now attempt to stay visible on the screen, like they do in HTMLFeatures tracks. Thanks to Daniel Kasenberg for implementing this.
Fixed bugs and inefficiencies preventing JBrowse from handling very dense BigWig files. Thanks to Michael Axtell for pointing this out (issue #312).
Fixed a bug in which features were not always laid out correctly in CanvasFeature tracks when the display mode is set to "compact".
Fixed a bug causing the text labels of mismatching bases in Alignments2 tracks (i.e. Alignments canvas glyphs) to be slightly misaligned vertically when feature labels are turned on (they are off by default for Alignments glyphs).
Fixed a bug preventing the defaultTracks configuration variable from operating correctly.

Release 1.10.1 2013-08-06 15:32:21 EST5EDT

Added support in maker2jbrowse for user-defined source tags in GFF3 output from MAKER. Thanks to Carson Holt for contributing this fix.
NCList data stores (actually the array representation used therein) now store feature attribute names case-insensitively.
Fixed a bug in which features in canvas-based feature tracks could not be clicked in Firefox. Thanks to GitHub user mke21 for pointing this out, and to Daniel Kasenberg for fixing my fix to work with older versions of Chrome.
Fixed a bug with client-side GFF3 parsing in which the strand of features was not being correctly parsed.
Fixed bug preventing backward-compatibility with 1.2.1-formatted data. Thanks to Daniel Kasenberg for implementing this.
Fixed a bug in the Gene glyph that caused the browser to crash if a gene feature has no subfeatures.

Release 1.10.0 2013-07-30 14:25:06 EST5EDT

Major improvements

Added powerful combination tracks, which can combine data from multiple other tracks using range, arithmetic, or masking operations. For example, a BigWig track can be masked to highlight only regions that lie within features from a BAM track. Or the intersection of two or more feature tracks can be calculated. To create a combination track, select "File->Add combination track" from the menu bar, and then add tracks to the new combination track by dragging them into it. A huge thanks to OICR co-op students Julien Smith-Roberge and Daniel Kasenberg for implementing this powerful feature. It's a very significant accomplishment!
Added "normal", "compact", and "collapsed" feature layout options for canvas-based feature tracks (currently just Alignments2 tracks). Thanks to OICR co-op student Daniel Kasenberg for implementing this!
Greatly improved the JBrowse/View/Track/CanvasFeatures track type, to the point where it is probably ready for experienced JBrowse users to use in earnest. It renders features using a modular glyph system that GBrowse users will find very familiar. To give it a try, simply change the type key in an existing track configuration to "JBrowse/View/Track/CanvasFeatures" and add a glyph key to set which glyph to use. Glyphs that are currently implemented are:
- Box - draws a box, optionally with an arrow indicating strandedness.
- Segments - draws a series of boxes connected with a line, for features with subparts.
- ProcessedTranscript - draws CDS and UTR features, with UTRs a different color and thinner.
- Gene - draws a group of aligned ProcessedTranscript glyphs for mRNAs that are subfeatures of a top-level gene feature.
Each of these glyphs have been patterned as near-clones of the (very popular) analogous glyphs in GBrowse.
Added a SPARQL data backend to allow displaying features directly from a SPARQL endpoint. Many thanks to the NDBC/DBCLS BioHackathon 2012 and 2013 participants for suggesting this and helping with this work! See http://www.biohackathon.org for more on this fantastic (and I think very important) series of hackathons.
There is a new "Highlight" button next to the "Go" button that lets a user quickly and easily highlight a region with the mouse.
Added the ability to "pin" some tracks to the top of the display, so that they stay at the top of the pane while the rest of the tracks are scrolled vertically. Thanks to the WebApollo project for suggesting this.
Integrated a maker2jbrowse script into the core JBrowse distribution. You can now visualize your MAKER results in JBrowse with a single command: bin/maker2jbrowse -d /path/to/your/maker/master_datastore_index.log Thanks to the MAKER team and Yandell lab for providing the initial implementation of maker2jbrowse.

Minor improvements

Added support for an addFeatures variable in the query string of the URL used to start JBrowse. This variable accepts feature data in JSON format in the form:

[{ "seq_id":"ctgA", "start": 123, "end": 456, "name": "MyBLASTHit"},...}]

which, when URI-escaped and put in the query string, looks like:

addFeatures=%5B%7B%20%22seq_id%22%3A%22ctgA%22%2C%20%22start%22%3A%20123%2C%20%22end%22%3A%20456%2C%20%22name%22%3A%20%22MyBLASTHit%22%7D%5D

Developers integrating JBrowse into larger project may find this feature useful for displaying results from other non-JavaScript-based applications (such as legacy web BLAST tools) in JBrowse.

Features added to JBrowse in this way are available in a special data store named url, which can be specified in a track configuration by adding "store":"url".
Added support for an addTracks variable in the query string of the URL used to start JBrowse. This variable accepts track configurations in JSON format in the form:
```
`[{"label":"mytrack","store":"url","type":"JBrowse/View/Track/HTMLFeatures"},...]`
```
which, when URI-escaped and put in the query string, looks like:
```
`addTracks=%5B%7B%22label%22%3A%22mytrack%22%2C%22store%22%3A%22url%22%2C%22type%22%3A%22JBrowse%2FView%2FTrack%2FHTMLFeatures%22%7D%5D`
```
Added "Save track data" option to Alignments2 tracks. This option should have been there all along, but somehow slipped through the cracks. Thanks to Valerie Wong for pointing this out at the 2013 GMOD Summer School!
Statistics about a track's features are now shown in its "About this track" dialog, if available.
Added support for a --reftypes argument to prepare-refseqs.pl, allowing you to search a database for reference sequences based on the type of the reference sequences, e.g. 'chromosome'. Thanks to Gaelen Burke at the 2013 GMOD Summer School for pointing out the need for this, and for assistance in testing the new feature.
Added a --gbk option to flatfile-to-json.pl that accepts a GenBank-format text file as input for loading annotation data. Thanks to Justin Reese for the initial implementation of this.
When formatting features with flatfile-to-json.pl, multi-valued feature attributes are now only flattened (renamed foo, foo2, foo3, etc) for "name", "id", "start", "end", "score", "strand", "description", and "note" attributes. Formerly, all attributes were flattened. This improves the default display of features that have many values for some attributes, such as Dbxrefs or GO terms.
Further improved scrolling smoothness of HTML-based feature tracks.
Added a JBrowse/Store/SeqFeature/FromConfig feature store adapter that can display feature data that is specified directly in configuration. This is mostly used to implement the support for addFeatures in the JBrowse URL, but some administrators and developers may find it convenient as well to define feature data directly in the JBrowse configuration.
flatfile-to-json.pl now supports a --trackType option that can be used to set the JavaScript track class that will be used for the formatted data (e.g. "JBrowse/View/Track/CanvasFeatures" to use the new, improved HTML5 canvas-based feature tracks).
biodb-to-json.pl configuration files now support a trackType configuration key in each track configuration that can be used to set the JavaScript track class that will be used for the formatted data (e.g. "JBrowse/View/Track/CanvasFeatures" to use the new, improved HTML5 canvas-based feature tracks).
prepare-refseqs.pl can now format reference sequences from a common .sizes (aka .len) file that is just a two-column tab-separated list of reference sequence names and their lengths, run like: bin/prepare-refseqs.pl --sizes myrefs.sizes
prepare-refseqs.pl can now format reference sequences from a gzipped GFF3 if the file's name ends with the suffix ".gz".
Added a '--noSubfeatures' option for flatfile-to-json.pl to skip importing subfeatures (since --getSubfeatures is on by default for some time).
The style.label configuration variable in HTMLFeatures (and CanvasFeatures) tracks can now accept a comma-separated string of field names in addition to a function callback. Defaults to 'name,id';
The "Save track data" (data exporting) menu now has "Highlighted region" as one of the choices of which range to export, if there is a region currently highlighted.
The "JBrowse" link on the left side of the menu bar, and the browser title, now display the "About this browser" title instead of JBrowse, if aboutThisBrowser is set in the configuration. Thanks to Joanna Kelley at the 2013 GMOD Summer School for suggesting this.
Tweaked styling of inactive track handles in the default Simple track selector to make them look less like pressable buttons. Thanks to Pedro Pagan at the 2013 GMOD Summer School for pointing out the need for this, and helping to brainstorm how the new styles should look.
Horizontal mouse-wheel (or trackpad) events can now scroll the genome view horizontally. Thanks to Mara Kim for help testing this at the 2013 GMOD Summer School.
The "content" of configurable information popups (such as can be shown when clicking on features) can now accept a dojo/Deferred or other promise object that will provide the content to be shown asynchronously.
Added a track.maxFeatureSizeForUnderlyingRefSeq configuration variable, defaulting to 250 Kbp, that sets the maximum length of a feature for which the default feature detail popup will attempt to display the underlying reference sequence. Thanks to Colin Davenport for pointing out the need for this (issue #291).
Added the ability to specify the file name when exporting track data to a file. Thanks to Daniel Kasenberg for implementing this.
Added a track.noExportFiles configuration variable that, if set to true, disables exporting files from the "Save" menu of tracks.

Bug fixes

Fixed a bug that prevented clicking on features in Alignments2 (and other canvas feature tracks) in Internet Explorer.
Fixed a bad design decision with respect to track metadata stores. Before, a given metadata key ("Category", "Conditions", etc) was allowed to only be present in one source of track metadata (CSV file, configuration file, etc). The original thinking behind this was that it would be better for people to be forced to keep each kind of metadata in only one place. This was silly thinking. Thanks to the 2013 GMOD Summer School participants for helping me to see the error of my ways.
Fixed a bug in which turning off the HTMLFeatures track's "Show Labels" did not remove labels for features with descriptions.
Fixed a bug with prepare-refseqs.pl in which, when multiple definitions of a reference sequence are found (as in a GFF3 file with both ##sequence-region directives and a FASTA section), the seqChunkSize value is not recorded in refSeqs.json and the sequence bases cannot be displayed in the "Reference sequence" track.
Fixed a synchronization bug in NCList-based feature data stores that causes some features to be missing when displaying with a CanvasFeatures track. This bug may also have affected 'Save track data' (data export) in some situations.
Fixed a bug with GFF3 export in which the phase(!) column was missing. Thanks to Michael Campbell at the 2013 GMOD Summer School for helping track this down!
Fixed another bug with GFF3 export in which an extra comma would sometimes be added at the beginning of GFF3 lines for some child features.
Fixed a bug in which the global highlighted region was not correctly drawn when switching reference sequences.
Fixed a minor bug in which the REST store backend did not coerce start, end, strand, and score to be numeric if the input JSON had them as strings.

Release 1.9.8 2013-07-05 09:22:36 EST5EDT

Removed "XX has no data for this chromosome" popup warning message. It was just annoying and not very useful.
Added an optional "yScalePosition" element to track configs that allows configs with Y axes to have those axes positioned on the left or right side of the view, as well as in the center. Thanks to Alexis Grimaldi for making this change.
Fixed a bug in which NCList-based tracks display with an error for reference sequences on which they have no data. Thanks to Michael Axtell for pointing this out.
Improved GFF3 handling in the File->Open tool, fixed a bug in the GFF3 parser in which an empty (.) source column caused the GFF3 parser to crash.
Improved scrolling speed when many HTML feature tracks are active.
Fixed a bug in which the browser can fail to start for a reference sequence that has never been seen before.
Fixed a confusing behavior in JBrowse/Store/SeqFeature/REST in which the URLs it constructs to fetch from did not always have a '/' where one would expect. Thanks to Alex Kalderimis for pointing this out.

Release 1.9.7 2013-06-25 15:41:22 Asia/Tokyo

Fixed a bug in which the initial viewing location (passed from a URL parameter or similar) is not always set correctly in all parts of the browser. Thanks to Steffi Geisen for pointing this out.
Fixed a bug in which JavaScript paths for plugins were incorrectly calculated when a baseUrl global configuration variable was set. Thanks to Matt Bomhoff for pointing this out.
Fixed a bug in which XYPlot tracks sometimes failed to draw bars for data that was both below the graph origin and below the track's configured minimum value. Thanks to GitHub user drusch for pointing this out.

Release 1.9.6 2013-06-18 14:57:26 EST5EDT

Fixed a bug in which the reference sequence selection dropdown menu did not work for purely numeric reference sequence names. Thanks to Matt Bomhoff for pointing this out.
Fixed a bug with some types of BAM files in which not all BAM features would be displayed. Thanks to Ignazio Carbone for pointing this out. (issue #276).
Fixed bug in which File->Open failed to open GFF3 files with embedded sequences in a FASTA section.
Added a --workdir option to generate-names.pl to allow name index building on a faster filesystem than the one that will ultimately store the name index. Thanks to Alexie Papanicolaou for suggesting this. (issue #273).

Release 1.9.5 2013-06-12 12:35:53 EST5EDT

Added an trackSelector.initialSortColumn configuration variable to the faceted track selector that can be used to set the initial sort order for the grid in the faceted track selector. Thanks to Alexie Papanicolaou for suggesting this.
Made Wiggle density tracks indicate out-of-range values using separate clip markers at the top and bottom of the color field, rather than showing the out-of-range region as a third color (or black or white). Thanks to Gregg Helt for suggesting this.
Added support for a quickHelp configuration variable that lets administrators customize the contents of the Help->General dialog. Thanks to Gregg Helt for suggesting this.
Rewrote GFF3 direct-access backend to make it more standards-compliant and capable of parsing all attributes of a feature. Thanks to Jillian Rowe and Colin Davenport for pointing out the need for this.
Fixed arrowheads on HTMLFeatures not always being visible when the viewing region is being panned back and forth. Thanks to Gregg Helt for pointing this out.
Fixed a bug in which editing a track's configuration JSON through the track menu when the faceted track selector was enabled sometimes caused another track to be deactivated. Thanks to Steffi Geisen for pointing this out.
Fixed a subtle bug in which not completing a track-dragging gesture from the Simple track selector into the genome view caused the track handle to not disappear from the track selector when the track is turned on later. Thanks to Gregg Helt for pointing this out.
Fixed a bug in which prepare-refseqs.pl can crash when used with Bio::DB::Das::BioSQL. Thanks to Brian Osborne for contributing the fix.
Fixed failures of setup.sh legacy BAM support installation caused by samtools taking down their old SourceForge subversion repository.
Fixed a bug in which highlighted regions were not always drawn correctly at initial load time. Thanks to Steffi Geisen for pointing this out.
Added support for a plugins->[]->location configuration attribute, making it possible for plugins to be loaded from outside the JBrowse plugins directory.
Fixed a bug in which Wiggle track value displays behaved a bit oddly with some kinds of mouse movements. Thanks to Gwendoline Andres for pointing this out.
Added a logMessages global configuration variable that, if set to true, records messages on the JBrowse message bus in the browser log.
Added a workaround for problems with some types of nonstandard Perl installations. Thanks to Rebecca Boes for pointing this out.

Release 1.9.4 2013-05-22 14:03:32 EST5EDT

Fixed a bug with configuration handling that preventing disabling right-click feature menus, and probably had other undesirable effects. Thanks to Daniel Troesser for pointing this out (issue #260).
Fixed a bug in which facet renaming specified in the trackSelector.renameFacets configuration variable was not properly applied to facet titles in the accordion widget on the left side of the faceted track selector (issue #251). Thanks to Jason Gao for pointing this out.
Fixed a bug with GFF3 and Sequin Table export of GFF3 alternate_allele attributes. Thanks to Jillian Rowe for pointing this out (issue #256).
Fixed some hard-coded image paths that were not respecting the setting of the browserRoot configuration variable. Thanks to Harry Yoo for pointing this out (issue #258).
Fixed a bug in which running biodb-to-json.pl with no arguments caused it to crash instead of producing help output. Thanks to GitHub user sreyesch for pointing this out (issue #257).
Fixed a bug in which some browsers report that src/dijit/_editor/nls/commands.js is missing. Thanks to Steffi Geisen for pointing this out.

Release 1.9.3 2013-05-09 12:42:39 EST5EDT

Fixed a bug in VCF backend that prevented display of VCF features containing lines in which the ALT column was '.' or not provided. Thanks to Ignazio Carbone for pointing this out.
Fixed a display bug in faceted track selector in which selected facets that have no available matches were squashed to the left side.
Fixed issue with HTMLVariants track type not being available for selection from the File->Open dialog.

Release 1.9.2 2013-05-02 13:30:12 EST5EDT

Fixed bug in which JBrowse could not properly display all data in BAM files with reference sequence name sections bigger than 64KB. Thanks to GitHub user lfgu for pointing this out (issue #245).
Made REST feature store backend less sensitive more tolerant of stringification of start, end, strand, and score in feature JSON. Thanks to Matt Bomhoff for pointing this out.
Fixed bug in which URLs for plugin resources were not assembled relative to the browserRoot config variable. Thanks to Matt Bomhoff for pointing this out.
Fixed bug in which missing fields in a VCF variant's genotype prevented display of a variant's details. Thanks to Jillian Rowe for pointing this out.
Fixed some minor issues related to the handling of empty BigWig files. Thanks to Nathan Boley for pointing this out (issue #252).
The trackSelector.type global config variable can now contain fully-qualified class names, so plugins can contain their own tracklist classes. Thanks to Matt Bomhoff for pointing this out.
Moved the "Select tracks" tab used to open the faceted track selector downward, so that it does not block access to the left side of the reference sequence overview.

Release 1.9.1 2013-04-25 12:02:25 EST5EDT

Significant speed and memory optimizations in BAM data backend (issue #242).
Significant speed and memory optimizations in VCF data backend.
JBrowse now attempts to smooth over mismatches in the naming of reference sequences between various datasets. For instance, if a BAM file contains reference sequences named like "chrom1", and the canonical reference sequences used in a JBrowse installation are named like "chr1", JBrowse will recognize these two names as equivalent for the purposes of displaying the BAM data. This behavior can be disabled by setting the global configuration variable exactReferenceSequenceNames to true. (issue #239).
Removed support for track blockDisplayTimeout configuration variable. It never worked very well, and the problem it was meant to address (delays caused by large data) are better mitigated by maxHeight and the faster rendering offered by canvas-based track types.
Fixed a bug that prevented displaying some VCF files. Thanks to Steffi Geisen for pointing this out.
Reduced the default value of maxHeight for canvas-based feature tracks (like Alignments2) from 1000 to 600.
Fixed a bug in the Alignments track type where BAM features with missing mate pairs that are not drawn due to their position above the track's maxHeight caused the track rendering to crash. Thanks to Tristan Lubinski for reporting this.
If no global refSeqOrder is specified in the configuration, the reference sequences are now not sorted. Currently, this means that they will appear in the same order as loaded by prepare-refseqs.pl. Users with a very large number of (more than 10,000) reference sequences may wish to avoid specifying a refSeqOrder, since sorting the reference sequences is done at JBrowse startup time. Thanks to Tristan Lubinski for reporting this.
Fixed bug preventing display of quantitative data from files loaded with flatfile-to-json.pl. Thanks to Gwendoline Andres for pointing this out.
Instead of quantitative (wiggle) tracks throwing an error when they cannot choose a min and max for the display scale, they now just make a guess. While probably wrong, this at least has the track displaying something, and users can then look up how to fix the display scale.
Added support for a chunkSizeLimit configuration variable for BAM and VCF-based tracks, which defaults to 5MB for BAM and 15MB for VCF. When fetching data, if a given region requires fetching a file chunk that is larger than this limit, a 'Too much data' message is displayed. This helps prevent speed and memory problems when displaying deep-coverage BAM tracks and large VCF tracks (issue #242). Thanks to Gustavo Cerquiera (GitHub user cerca11) for pushing for progress on this.
Fixed a regression in which callbacks and interpolations were not evaluated in left-click and right-click menu configurations.
Fixed incorrect display of negative values in log-scale wiggle tracks. Thanks to GitHub user drusch for pointing this out (issue #244).
Fixed more minor errors when running under IE 7.
Fixed "Max height reached" message sometimes being drawn under instead of over HTML-based features.

Release 1.9.0 2013-04-16 18:59:19 EST5EDT

Added a direct-access data backend for reading variation data directly from VCF files that have been compressed with bgzip and indexed with tabix. See the JBrowse Configuration Guide on the GMOD wiki for details about how to add directly-displayed VCF files (issue #211).
Added a new HTMLVariants track type based on HTMLFeatures with a feature-details popup optimized for displaying variant details.
Added a text box at the top of the simple (i.e. the default) track selector that finds tracks in the track list matching the typed text (issue #210).
Added support for autoscale: "local" in Wiggle, FeatureCoverage, and SNPCoverage tracks, which automatically sets the scale of the y-axis based on the range of the data being displayed in the current view. Thanks to Gregor Rot and Raymond Wan for championing the need for this (issue #203).
Added an optional dropdown selector in the menu bar that allows switching between multiple datasets. To enable it, add a datasets array in your JBrowse configuration, and set a dataset_id in each of the trackList.json (or other) files that are optionally loaded by the dataset selector. See the JBrowse Configuration Guide on the GMOD wiki for details (issue #134).
Added a new datastore class, JBrowse/Store/SeqFeature/REST that fetches data from any back end system that implements the simple REST API it uses. See the JBrowse Configuration Guide for details on how to implement its REST API. Thanks to Brett Thomas, Daniel Troesser, and Brad Chapman for pointing out the need for this (issue #227).
By default, JBrowse now continuously updates the browser's URL bar to contain a URL that will show the current JBrowse view directly. This is enabled by default only if JBrowse is running from the default index.html included in the JBrowse distribution.
HTMLFeatures, Alignments, and Alignments2 tracks now accept a maxHeight configuration variable specifying the maximum displayed height of a track in pixels. Features that would cause the track to grow beyond its maximum height will not be drawn (issue #222).
Removed the refSeqDropdown configuration variable; the reference sequence selector is now shown for any number of reference sequences, with its length limited by the refSeqSelectorMaxSize variable (see next item).
Added support for optional refSeqSelectorMaxSize and refSeqOrder global configuration variables that set the maximum length of the reference sequence dropdown selector, and specify the sort order of the reference sequences in that selector, respectively. One instance in which this is particularly useful is in displaying annotations on early-stage, incomplete genomic assemblies: to display the N biggest contigs in the assembly in the reference sequence selector dropdown, one can set refSeqOrder to length descending, and set refSeqSelectorMaxSize to N. Thanks to Ignazio Carbone for pointing out the need for this. (issues #234 and #235).
Fixed some bugs causing memory leaks when scrolling and zooming, especially on tracks with a lot of data like BAM tracks. Thanks to Gustavo Cerquiera for pointing this out (issue #220).
HTMLFeatures tracks now accept style->label and style->description configuration variables variable that can be set to a function callback that returns a string with the feature's label or long description, respectively (issue #9).
Wiggle/XYPlot, Wiggle/Density, and FeatureCoverage tracks now accept function callbacks in their style->pos_color, style->neg_color, style->bg_color, and style->clip_marker_color configuration variables. Function callbacks are passed two arguments: the feature object (with start bp, end bp, and score of the quanititative region being shown, and the track object (which can be used to access track configuration data, along with many other things). (issue #133).
Wiggle/XYPlot tracks now accept an array for their variance_band argument, allowing users to set the position of the variance bands to show (issue #133).
Wiggle/XYPlot tracks now accept a style->variance_band_color configuration variable, allowing users to set the colors of the variance bands. The variance band color should usually be specified with a partial opacity. Default is 'rgba(0,0,0,0.3)', which is black with 30% opacity (issue #133).
Added an "About JBrowse" popup dialog, which supports an aboutThisBrowser configuration stanza containing a title for the main browser window, and a description to be shown in a pop-up dialog when the title is clicked (issue #206).
Where possible (i.e. supported by the data store), JBrowse will now pop up a warning if a local data file is opened that contains no data for the current reference sequence (issue #178).
Fixed bug in which hard- and soft-clipped regions were erroneously counted toward the overall length of a BAM alignment (issue #229).
Fixed bug in which dragging the vertical scroll bar marker on the right side of the track pane did not behave correctly. (Julien Smith-Roberge, issue #223).
Fixed bug in which the navigation location for some reference sequences can get messed up when ref.start != 0, or ref.end != ref.length (issue #215).
Fixed bug in which, when using the dynamic zooming tool (rubber-band zooming), some browsers (particularly Safari) would inaccurately display the locations of HTML-based features and per-basepair colored bars in sequence tracks.
Fixed bug in which navigating via sequence dropdown selection ignores previous location on selected sequence, whereas with navigation text box entering just a sequence name navigates to previous location on that sequence (if visited previously). Thanks to Gregg Helt for implementing this fix (issue #216).
Fixed bug in which the initial default view of a previously unviewed reference sequencestarts at 80% centered view, but any use of reference sequence selection pulldown takes it to 100%. Big thanks to Gregg Helt for implementing this fix (issue #217).
Fixed bug in which iframe popups did not display correctly in Internet Explorer 9. Thanks to Steffi Geisen for pointing this out (issue #233).
Fixed a number of bugs that prevented JBrowse from running in Internet Explorer 7 and 8 (issue #236).
Improved JSON syntax error messages in server-side scripts (issue #214).
Increased the default display timeout (blockDisplayTimeout) on HTML-based features tracks from 5 seconds to 20 seconds.
Added a new-plugin.pl helper script that makes the skeleton of a new JBrowse plugin.
Added an add-json.pl helper script that advanced users can use to set arbitrary value in JSON files from the command line.
Fixed a bug in which the --conf option to prepare-refseqs.pl did not support comments in JSON conf files (issue #213). Thanks to Keiran Raine for pointing this out.
Fixed some missing dojo/dijit nls directories in the non-dev release zipfile.
Fixed a bug with handling of timeout events in HTMLFeatures tracks. Thanks to Matt Henderson of KBase for pointing this out.

Release 1.8.1 2013-02-12 12:56:24 EST5EDT

Added support for cigarAttribute and mdAttributes configuration variables to Alignments and Alignments2 tracks, allowing users to change which feature attribute is used for showing mismatches (issue #200).
Fixed some bugs preventing Alignments and Alignments2 tracks from working with non-BAM data backends.
Added --trackLabel and --key options to prepare-refseqs.pl, allowing users to specify the sequence track's label and title.
Added --seqType option to prepare-refseqs.pl, allowing users to specify the type of sequences being formatted, usually either 'dna', 'rna', or 'protein'. Additionally, if --seqType is something over than DNA (case insensitive), "showReverseStrand" is set to false on the reference sequence track.
prepare-refseqs.pl now calls the track showing the reference sequence "Reference sequence" instead of "DNA".
Added a shareURL configuration option that accepts a JS function to assemble the URL that users will get when clicking the "Share" button or the "Full view" link in embedded mode (issue #198).
Fixed annoying bug in which popup feature detail boxes are initially scrolled all the way to the bottom.

Release 1.8.0 2013-01-31 14:05:27 America/New_York

Added new "File -> Open" function that can display BAM, BigWig, and GFF3 files located on the user's machine, at remote URLs, or a mixture of both. When opening local files, everything is done locally, no data is transferred to the server.
Added a new "SNPCoverage" track type, designed for use with BAM files (but which works with any features that have MD fields), that shows a coverage plot with a graphical representation of SNP distribution, and tables showing frequencies for each SNP.
Added a new "Alignments2" track type, which is a much faster implementation of the "Alignments" track type. It is more suitable for very deep BAM alignments, but has a slightly different configuration scheme.
Added a flexible plugin system whereby external code can be loaded as part of JBrowse. Plugin JavaScript has full access to customize nearly everything in JBrowse. The plugin system is quite new, but many hooks are available that plugins can use to safely modify JBrowse's behavior, and more are on the way. See the JBrowse wiki for details on how to write your own plugins. Thanks to Gregg Helt and the other members of the WebApollo project for helping to drive development of the new plugin system.
JBrowse feature name indexing (generate-names.pl) now uses an all-new hash-based filesystem backend. Although generate-names.pl now takes longer to run, it can handle much larger numbers of names to index, and uses much less RAM to do it. As a side benefit, the JBrowse location box's autocompletion feature is now faster and more reliable. Thanks to Steffi Geisen and Volodymyr Zavidovych for pointing out the issues with name indexing scalability and reliability.
Added support in "HTMLFeatures", "Alignments", and "Alignments2" tracks for a style.featureScale configuration variable, which, if set, specifies a minimum zoom scale (pixels per basepair) for displaying features. If zoomed out more than this (i.e. fewer pixels per bp), either histograms or a "too many features" message will be displayed.
Changed binning algorithm of "FeatureCoverage" tracks when zoomed out. Now calculates the average base coverage in each bin, rather than the absolute number of features that overlap each bin.
"HTMLFeatures" tracks now accept a comma-separated list of field names in their description configuration variable, allowing users to customize which attribute(s) of a feature hold the description.
Added a timeout to HTMLFeatures and Alignments tracks to prevent data-heavy tracks (like BAM tracks with very deep coverage) from freezing or crashing a user's browser.
Improved graphical look of canvas-based tracks during zoom operations. Thanks to Mitch Skinner for implementing this!
Fixed a bug in which the Y-axis scale for feature density histograms in HTMLFeatures tracks was sometimes drawn incorrectly.
Greatly improved speed and responsiveness of BAM data backend.
Fixed yet another bug that prevented display of some types of BAM files.

Release 1.7.6 2013-01-10 01:25:58 America/New_York

Fixed a bug in the BAM direct-access backend that prevented some BAM files from being displayed.

Release 1.7.5 2012-12-12 13:40:12 America/New_York

Fixed a bug in which typing a key that is bound to a global keyboard shortcut (currently only 't' or '?') in the location box would erroneously execute the action for that global shortcut. Thanks to Gregor Rot for pointing this out.
Fixed a bug in which toggling 'Show labels' in the track menu did not re-layout the track on the first toggling.
Make columns in the faceted track selector initially each be an equal percentage of the total width of the grid. Thanks to Steffi Geisen for pointing this out.

Release 1.7.4 2012-12-06 23:08:22 America/New_York

Fixed a bug preventing loading of JBrowse in some browsers. Thanks to Steffi Geisen for pointing this out.
Fixed a bug in the BigWig data backend that prevented some BigWig files with large numbers of reference sequences from displaying. Thanks to Gregg Helt for providing sample data to help isolate this.
Fixed a bug in the BigWig data backend that prevented BigWig files rendering in Safari. Thanks to Gregor Rot for his help in isolating this.
Worked around a bug in Safari 6 (and probably earlier) in which HTTP byte-range requests are erroneously cached. Thanks to Gregor Rot for pointing out the Safari problems.
Fixed some minor styling bugs in the facet menus of the faceted track selector.
Fixed blurry edges of location trapezoid in Firefox (Eric Derohanian).

Release 1.7.3 2012-11-28 23:29:48 America/New_York

Fixed several more bugs in the BAM data backend that prevented display of some BAM files. Thanks to Gleb Kuznetzov for help in isolating these.
Fixed bug in display of faceted track selector in which the facet titles were taking up too much vertical height. Thanks to Steffi Geisen for pointing this out.
"Alignments" tracks now parse an alignment's CIGAR string if it does not have an MD field, and display mismatches and skipped sequence regions (particularly important for RNA-seq alignments). Thanks to Gregg Helt for providing the sample dataset used to test this.
Added support for a showReverseStrand config variable to Sequence track that, if set to false, turns off display of the reverse sequence strand.
"Alignments" tracks now show reads with missing mate pairs with a red crosshatched pattern instead of with a red border.
Added an Apache .htaccess file to the JBrowse root directory that enabled CORS by default for all files under it, if AllowOverride is on.
Fixed bug in which the vertical scroll position can sometimes be set too far down when zooming in and out.
Fixed some bugs in server-side formatting code for feature tracks: data was recorded multiple times in JSON files in some circumstances. Thanks to Volodymyr Zavidovych and Steffi Geisen for pointing this out.

Release 1.7.2 2012-11-09 15:40:06 America/New_York

Fixed more bugs in BAM backends that failed to load some types of BAM files, including BAM files containing no alignments. Thanks to John St. John for his assistance in isolating the problem.

Release 1.7.1 2012-11-07 11:25:39 America/New_York

Fixed bug in which bars below the origin of Wiggle/XYPlot were drawn incorrectly (issue #161). Thanks to GitHub user @makela for pointing this out.
Wiggle/XYPlot tracks now by default draw a horizontal line at the origin, and support a style.origin_color configuration variable to set its color or turn it off.
Fixed bug in BAM backend that caused an infinite loop and/or browser crash with some BAM files. Thanks to Gleb Kuznetzov for pointing this out.

Release 1.7.0 2012-11-05 19:22:17 America/New_York

Added a new direct-access storage driver for BAM files, removing the need for bam-to-json.pl. This new method of BAM access is far superior to the old bam-to-json.pl in nearly every way, except in browser compatibility. Like the BigWig direct access backend added in JBrowse 1.5.0, it is based on code from Thomas Down's Dalliance Genome Explorer, and works in all major browsers except Internet Explorer, because IE lacks support for the necessary web standards. It may work with Internet Explorer 10, but this has not been tested yet.
Added a new Alignments track type designed to work seamlessly with BAM files. This track type shows basepair differences and insertions between aligned reads and the reference, and highlights reads with missing mate-pairs in red.
Added the ability to export track data in FASTA, GFF3, bed, bedGraph, and Wiggle formats (issue #104). To export data, turn on the track of interest, then click on its track label to bring up the track menu, and select "Save track data".
Added a new Wiggle/Density track type, analagous to the GBrowse wiggle_density glyph type. Shows the Wiggle information using varying intensity of color (issue #66). Renamed the Wiggle track to Wiggle/XYPlot, and made the old Wiggle track type an alias to Wiggle/XYPlot.
Both Wiggle/XYPlot and Wiggle/Density now support a style -> bg_color option. Color-density plots blend the pos_color or neg_color into the bg_color in amounts that vary with the wiggle data, and xyplots fill the background color behind all points that have data present, regardless of value. bg_color defaults to off for xy xplots, and semi-transparent gray for density plots. Setting this makes it easier for users to distinguish at a glance between regions with no data, and regions with a value of 0.
Added a new FeatureCoverage track type, which shows a dynamically-computed XY-plot of the depth of coverage of features across a genome. One good use of this track type is to provide a quick coverage plot directly from a BAM file. However, since this track calculates coverage on the fly, it can be slow when used with large regions or very deep coverage. In this case, it is recommended to generate a BigWig file containing the coverage data, and display it with a Wiggle/XYPlot or Wiggle/Density track.
DNA bases are now displayed with color-coded backgrounds, allowing basepair information to be discerned when zoomed somewhat further out, when base letter cannot be drawn. Colors are also designed to match the base-mismatch colors used in Alignment tracks, enabling clearer SNP visualization.
Added a vertical line cursor and labels showing the current basepair position of the mouse when hovering over the scale bar, or when doing a rubber-band zoom (Erik Derohanian) (issue #32).
Added an animation to make it easier to see where in the track selection list a closed track has gone, when using the simple track selector (issue #151).
Information dialog boxes are now easier to dismiss: clicking anywhere outside of them, or pressing any key, will make them go away.
Improvements to feature track configuration:
- Feature tracks no longer use the style.subfeatureScale configuration variable to determine whether to show subfeatures. Instead, subfeatures are shown if the parent feature, when shown on the screen, is wider than style.minSubfeatureWidth, which defaults to 6 pixels.
- Make explicitly-configured track labelScale, histScale, and descriptionScale not be modulated by the feature density: only use the feature density to pick the scale defaults
The default feature-detail dialog box now shows more information, adding:
- the feature's exact length
- full details of its subfeatures
Added a locationBoxLength configuration variable that controls the width of the location box. In addition, the default width of the location box is now also smarter. Instead of a fixed 25 characters, it is calculated to fit the largest location string that is likely to be produced, based on the length of the reference sequences and the length of their names.
Pressing SHIFT+-up/down arrow keys now cause the genome view to zoom in and out. If ALT is added, it zooms further. Thanks to Karsten Hokamp for the excellent suggestion.
Holding SHIFT while scrolling left and right with the arrow keys causes the view to scroll further.
Added a theme configuration variable to allow changing the graphical theme to something different from the default "tundra". However, no other themes are implemented yet.
Greatly sped up rendering of HTML subfeatures by caching the heights of subfeature HTML elements.
Fixed bug in which the genome view executed a double-click zoom when users rapidly clicked on multiple track 'close' buttons.
Fixed bug with the genome view scrolling in response to arrow keys being pressed when typing in the location box.
Fixed bug in which the score display in Wiggle tracks would sometimes flicker when moving the mouse.

Release 1.6.5 2012-10-26 12:10:08 America/New_York

The location box now shows the length of the currently visible region in parentheses. For example: ctgB:1244..3566 (2.32 Kb). Thanks to Karsten Hokamp for the suggestion!
The arrow keys on the keyboard can now be used to pan and scroll around the genome view.
Wiggle track mouseover cursors now display the score with only 6 significant digits, avoiding confusion over approximations introduced by scores being converted to IEEE floating-point numbers (as for BigWig files) and back to text.
The faceted track selector now renders any HTML that may be present in the track metadata by default. To turn this off, it now accepts an escapeHTMLInData option that, if set to true or 1, will not render the HTML, but will instead display the raw code (issue #145).
Upgraded to a more recent version of jszlib, which contains some important bugfixes (issue #157).
Fixed bug dealing with very large regions with the same value in canvas-based Wiggle tracks (also issue #157).
prepare-refseqs.pl now by default uses a more scalable directory structure for storing sequences. This fixes problems some users were experiencing with large numbers of reference sequences (issue #139).
ucsc-to-json.pl now supports a --primaryName option allowing the users to alter which UCSC data field is displayed by JBrowse as the primary name of the features in a track. Also, ucsc-to-json.pl now treats as indexable names all UCSC data columns called "name", "alias", or "id" followed by zero or more digits. Thanks to Steffi Geisen for this suggestion.
Fixed "Duplicate specification" warnings coming from flatfile-to-json.pl and remove-track.pl.
Fixed bugs in which both the first few and the last few bases of a reference sequence were not displaying correctly in a DNA track.

Release 1.6.4 2012-10-16 11:50:44 America/New_York

Improvements to the scalability of generate-names.pl. Many thanks to Steffi Geisen for her ongoing help with this.
- Users can now manually specify which tracks will be indexed to enable autocompletion and searching for their feature names in the JBrowse location box.
- The lazy-trie name indexing structure now correctly handles the case of large numbers of features that may share the same name. Before, it was generating files that were too large for the client to handle.
Fixed off-by-one error in Wiggle track display code: wiggle data was incorrectly displayed shifted one base to the left of its proper position. Thanks to Steffi Geisen for noticing this.
Fixed bug in which the reference-sequence selection box did not automatically update in all situations to reflect the current reference sequence.

Release 1.6.3 2012-09-28 11:33:36 America/New_York

Fixed bug with shift-rubberband-zooming not working on Windows (issue #150) (Erik Derohanian).
Fixed "Can't locate JSON.pm" errors with add-track-json.pl.
Added a reference-sequence-selection dropdown box, similar to the old one, that is on by default if fewer than 30 reference sequences, otherwise it's off unless refSeqDropdown: true is set in the configuration (issue #138).
Fixed bug in which popup dialog boxes showing other websites showed the website in only the top portion of the dialog box. Only present in some browsers (issue #149).
Fix coordinate display bug in feature detail popups. The feature's position was being displayed in interbase coordinates, but should be displayed in 1-based coordinates. Thanks to Steffi Geisen for pointing this out.
Added a style.height option to Wiggle tracks to control the track's height in pixels (issue #131) (Erik Derohanian).
Added support for a style.trackLabelCss configuration variable to allow customizing the appearance of the label for a particular track (issue #4) (Erik Derohanian).

Release 1.6.2 2012-09-10 17:47:43 America/New_York

Fixed feature-layout performance problem when zoomed very far in on features that are much larger than the viewing window.
Added a default menuTemplate to all HTML-based features, so that all HTML features now have a right-click menu by default.
Add css configuration variable that allows users to specify either strings or URLs containing CSS to add.
improved bin/ucsc-to-json.pl error messages
bin/add-track-json.pl now replaces tracks in the target configuration if they have the same label.

Release 1.6.1 2012-08-28 16:50:41 America/New_York

JBrowse now attempts to prevent feature labels being obscured by track labels by keeping the feature labels a bit further away from the left side of the view, if possible.
Fixed bug in which welcome page was not shown when JBrowse has not been configured yet (issue #130).
Fixed bug in which passing tracklist=0 (as when running the browser in embedded mode) caused JBrowse to crash (issue #132).
Added dependency on Bio::GFF3::LowLevel::Parser 1.4, which has an important bugfix related to multi-location features (issue #109). Thanks to Victor Poten for help in isolating this problem.

Release 1.6.0 2012-08-25 18:04:44 America/New_York

Added description capabilities to HTML-based features, similar to GBrowse's descriptions. If zoomed in far enough (as defined by style.descriptionScale), adds a second line of text below the feature's label that shows the content's of the featur's Note or description attribute (issue #67).
Give prepare-refseqs.pl the capability to load reference sequences from embedded FASTA sections in GFF3 files (issue #128).
Configuration files can now recursively include eachother, and tracks sections are merged intelligently.
Made sequence tracks not disappear when zoomed out too far to see base pairs. Instead, sequence tracks simply display lines suggesting that DNA would be visible at higher magnification. (issue #124).
Double-clicking track labels in the simple track selector now turns the track on (issue #123).
Fixed bug in BigWig tracks that use the "scale": "log" option: did not render properly when the wiggle data included 0's. This was due to the fact that the origin was being mapped to Infinity. Thanks to the Mockler Lab for the fix! (issue #127).
Fixed bug in NCList binary search code in which zero-length features at node boundaries would not be found (fix by Ed Lee).
Fixed bug in which dragging the scroll bar on the simple track selector can sometimes cause a drag-and-drop to erroneously begin (issue #89).
Fixed some bugs in the layout of HTML-based features in which features in different blocks would overlap in some circumstances. Under the hood, replaced the contour-based layout engine with a simpler, not-much-slower implementation that is more correct in the general case (issue #122).
Fixed a bug with vertical centering of strand arrows and other sub-elements of HTML-based features.

Release 1.5.0 2012-08-13 15:37:27 America/New_York

Added a direct-access storage driver for BigWig data files, based on code from the Dalliance Genome Explorer by Thomas Down. BigWig file access is supported now by the current versions of all major browsers except Internet Explorer (which is expected to work when version 10 is released along with Windows 8).
Added a canvas-based wiggle track implementation for quantitative data that, when used with the new BigWig storage backend, removes the need to pre-generate rendered images of wiggle data. Its display is also highly configurable, with configuration options modeled on the GBrowse wiggle_xyplot glyph type (i.e. Bio::Graphics::Glyph::wiggle_xyplot).
Added highly configurable behavior for left-clicking and right-clicking features in HTML-based feature tracks. If a menuTemplate option is specified in the track configuration, right-clicking a feature brings up a context menu, the items in which can be configured to do nearly anything, but that are easy to configure for the very common use case of wanting to display content from a certain URL. Feature left-clicks are also configurable using the same mechanism. Thanks to Alexie Papanicolaou and Temi Varghese for the initial implementation of context menus.
Improved the default HTML feature left-click dialog box. It is now both prettier, and more comprehensive, displaying all available data for the feature.
Added the long-missing ability to render a second line of label text for features containing their description, which is taken from the feature's 'Note' or 'description' attribute, if present. The description is only displayed if the track's description configuration variable is set to a true value, which is the default. There is also a style.maxDescriptionLength value, that can be set to control how long a description can be before it is truncated with ellipses. It defaults to 70 characters.
Added a small helper script, add-track-json.pl that developers and advanced users can use to programmatically add a block of track configuration JSON to an existing JBrowse configuration file.
Improved / fixed vertical alignment of sub-elements of HTML features, including subfeatures and the arrowheads that show strand. All elements in a feature are now vertically centered by default.

Release 1.4.2 2012-07-12 15:38:55 America/New_York

Restore support for histScale, subfeatureScale, and labelScale in --clientConfig and track configuration JSON. Thanks to Hernán Bondino for pointing this out.

Release 1.4.1 2012-07-10 14:58:34 America/New_York

Made displayColumns option for the faceted track selector case-insensitive, and interpret a column name of "Name" as meaning the track's key.
bam-to-json.pl now filters out alignments that are not at least two nucleotides in length. Thanks to Tristan Lubinski for assistance.
Introduced limits on the sizes of cookies that can be set, preventing '400 bad request' errors (issue #113).

Release 1.4.0 2012-06-14 17:43:50 America/New_York

Added a full-featured faceted track selector for users that have many (hundreds or thousands) of tracks. This can be turned on by setting the trackSelectorType config variable to "Faceted". See the JBrowse wiki for more documentation on how to use faceted track selection. (issue #95)
Removed the dropdown selector for reference sequences in favor of making the location box auto-complete reference sequence and feature names. This makes JBrowse much more scalable to large numbers of reference sequences. (fixes issues #3, #60, and #101)
Added a vertical-scrolling marker on the right side of the track pane, making it much easier to discern the vertical position of the track display. (issue #93).
biodb-to-json.pl and flatfile-to-json.pl now load all available feature data: all attributes of features are now encoded in the JSON and are available for use by feature callbacks. (issue #72)
Feature labels now do not scroll off screen if any part of the feature is still visible (fixes issue #62).
Added jbrowse_conf.json, a default JSON-format configuration file, to the JBrowse root directory. Makes it easier to get started with more advanced JBrowse configuration.
JBrowse instances now report usage statistics to the JBrowse developers. This data is very important to the JBrowse project, since it is used to make the case to grant agencies for continuing to fund JBrowse development. No research data is transmitted, the data collected is limited to standard Google Analytics, along with a count of how many tracks the JBrowse instance has, how many reference sequences are present, their average length, and what types of tracks (wiggle, feature, etc) are present. Users can disable usage statistics by setting "suppressUsageStatistics: true" in the JBrowse configuration.

Release 1.3.1 2012-04-19 17:55:44 America/New_York

Fixed memory-management bug that caused way too much RAM to be used by FeatureTrack loading (flatfile, bam, and biodb-to-json.pl) when loading with very large numbers of reference sequences. Big thanks to Tristan Lubinski for help in isolating this.
Fixed some bugs in BAM support section of setup.sh autosetup script, thanks to Tristan Lubinski for help in isolating this as well.
Added an example document with an iframe running JBrowse in embedded mode in docs/examples/embedded_mode.html
flatfile-to-json.pl now loads the 'score' attribute of features in the JSON.

Release 1.3.0 2012-04-13 17:04:30 America/New_York

Added support for "rubberband" dynamic zooming, in which users can click and drag to select a region to zoom to. Dragging on any scale bar, or shift-dragging on the main track pane, triggers a dynamic zoom.
Correcting a long-standing oversight, wiggle data tracks and feature histograms now have numerical y-axis scales that show the numerical values of the data.
Server-side data-formatting scripts now support a --compress option to compress (gzip) feature and sequence data to conserve server disk space. Using this option requires some web server configuration. Under Apache, AllowOverride FileInfo (or AllowOverride All) must be set for the JBrowse data directories in order to use the included .htaccess files, and mod_headers and mod_setenvif must be installed and enabled. Under nginx a configuration snippet like the following should be included in the configuration:

location ~* ".(json|txt)z$" { add_header Content-Encoding gzip; gzip off; types { application/json jsonz; } }
flatfile-to-json.pl: now much faster and more memory-efficient, especially for GFF3 files. Remember that '###' directives are very important to have in large GFF3 files! Also removed nonfunctional --extraData switch.
Added ability to turn off some JBrowse UI panels via URL arguments to the default index.html, or via arguments to the Browser constructor itself. Can dynamically turn off the navigation box, the overview panel, and the track list, respectively. When all of these are off, and if run in an iframe, JBrowse is running in an "embedded mode" that looks similar to the output of GBrowse's gbrowse_img script, with the exception that the view in this case is a fully functioning, scrollable and zoomable JBrowse. See the GMOD wiki (http://gmod.org/wiki/JBrowse) for more on how to set up embedded mode. Thanks to Julie Moon, a co-op student working at OICR, for this work!
Improved graphical look and feel.
Browser support for this release:
- Google Chrome 18 perfect
- Google Chrome 17 perfect
- Mozilla Firefox 11.0 perfect
- Mozilla Firefox 10.1 perfect
- Mozilla Firefox 10.0.2 perfect
- Mozilla Firefox 3.6.28 nonfunctional
- Apple Safari 5.1.5 (Lion) perfect
- Microsoft Internet Explorer 9 perfect
- Microsoft Internet Explorer 8 good
- Microsoft Internet Explorer 7 minor problems
- Microsoft Internet Explorer 6 not tested
- KDE Konqueror 4.7.4 nonfunctional
- KDE Konqueror 4.5.5 nonfunctional
- Opera (all versions) not tested
NOTE: Internet Explorer 6 is no longer supported by JBrowse.
Added an automated-setup script, setup.sh, that tries to install Perl prerequisites, format Volvox example data, and install Wiggle and BAM support (fetching samtools from SVN if necessary) automatically.
Navigating to JBrowse with missing or malformed configuration or data will now bring up an error page with useful messages and links to help documentation, instead of a blank white page.
JBrowse data directories now include an Apache .htaccess in their root directory that, if mod_headers is installed and AllowOverride FileInfo or AllowOverride All is enabled, will emit the proper HTTP headers to allow cross-origin XHR requests for the data.
A new "Help" link in the upper right, or pressing "?" on the keyboard, brings up a "JBrowse Help" dialog box with basic usage information and links to more help information.
Arrowheads indicating strandedness are now drawn inside feature boundaries.
Clicking on the overview bar or the main scale bar now centers the view at the clicked position. In addition, while holding down shift, clicking in the main track panel will also center the view at that position.
Added bin/remove-track.pl, a script to remove a track from a JBrowse data directory. Run bin/remove-track.pl -? to see its documentation.
Added build instrumentation to support a JSDoc-based system of developer API documentation. This documentation is still far from complete.
Ian Davis contributed code to add a view of the reverse strand of the sequence in the DNA track. Thanks Ian!
Fixed bug in which, for some sequence chunk sizes, the DNA bases would display incorrectly.
Added minor gridlines to the main track view.
Fixed a long-standing off-by-one bug where the window could not be scrolled to view the last base in the reference sequence.
Coordinates displayed in the user interface are now 1-based closed coordinates, which are more familiar to most users. Previously, the labels displayed interbase (i.e. 0-based half-open) coordinates.
NON-BACKWARDS-COMPATIBLE improvements to the JSON format used for track configuration, feature data, and image data
- initial support for a new hook system for greater administrator-configurability of feature display
- support for more than one level of subfeatures
Miscellaneous improvements and refactoring of data-formatting Perl code.
More detailed POD-based help documentation on all scripts
--tracklabel options to all scripts replaced with --trackLabel.
New suite of integration tests, and some unit tests, for server-side Perl code.
Beginnings of a suite of Selenium-based integration tests for the front-end JavaScript code.
Support for Apple touch-based devices merged into normal index.html, so that the same link can be used regardless of the browsing platform.
Bug fixed in which non-stranded features do not display properly (a problem with the CSS styles).

========================================================

version 1.2.1, March 2011

Fixed bugs in release 1.2:

problems with BED handling reported by Gregg Helt and Brenton Graveley
performance regression reported by Chris Childers
incorrect handling of names in ucsc-to-json.pl
wig2png slowdown reported by Brenton Graveley

========================================================

version 1.2, Febrary 2011

These notes document changes since release 1.1 in September 2010.

Most of the work in this release went into making JBrowse handle large amounts of feature data better. Before, the amount of memory used when processing BAM files was more than 10 times the size of the file; now, the amount of memory required is fixed.

Other new features in this release:

Import of UCSC database dumps. A ucsc-to-json.pl script is now provided for taking database dumps from UCSC and creating a JBrowse instance using them. The "genePred" and "bed" track types are currently supported; "psl" tracks are not yet supported.
Touch. Juan Aguilar's code for using JBrowse on an iOS device (iPhone, iPod touch, iPad) is now integrated. As of the current release, users wanting to use JBrowse on those devices have to navigate to a separate HTML page (touch.html) rather than the default index.html; i.e. the code does not currently detect touchscreen devices automatically.
Bug fixes. A number of bugs have also been fixed, including one that restricted the placement of the "data" directory, and a bug in wiggle rendering that caused spurious peaks or troughs at tile boundaries.

Known issues/limitations with this release:

Some additional CPAN modules are now required:

PerlIO::gzip Heap::Simple Devel::Size
No JSON-level backward compatibility. If you are upgrading from an older version of JBrowse, you will have to regenerate all the JSON files on your server. This means wiping your jbrowse/data directory and re-running all server scripts (flatfile-to-json, biodb-to-json, wig-to-json, etc.) to regenerate your data from the original FASTA/GFF/BED/WIG files. We apologize for the inconvenience of this, but it is inevitable sometimes; we do aim to minimize the number of releases which are backwardly-incompatible in this way.

========================================================

version 1.1, September 2010.

These notes document JBrowse developments in the period from July 2009 (online publication of the first JBrowse paper in Genome Research, the de facto "version 1.0") up to September 2010 (the first in a planned series of quarterly releases).

New features in this release:

Scalability. JBrowse can now handle very large data tracks, including human EST/SNP tracks, or tracks of next-gen sequence reads. Large datasets are broken into smaller chunks, so there is no loading delay for big tracks.
Extensibility. A Perl module (ImageTrackRenderer.pm) for creating user-drawn image tracks is now available, based on the CPAN GD.pm module. An example program is provided, draw-basepair-track.pl, that uses this module to draw arcs over a sequence representing the base-pairing interactions of RNA secondary structure.
Bug fixes. Numerous display glitches have been fixed, including issues with wide-screen monitors and long mostly-offscreen features.

Known issues/limitations with this release:

No JSON-level backward compatibility. If you are upgrading from an older version of JBrowse, you will have to regenerate all the JSON files on your server. This means wiping your jbrowse/data directory and re-running all server scripts (flatfile-to-json, biodb-to-json, wig-to-json, etc.) to regenerate your data from the original FASTA/GFF/BED/WIG files.
Next-gen sequence display is currently restricted to the co-ordinates of the outermost region to which a single read is mapped. There is no support (yet) for displaying pairing between reads, sequences of reads, alignment of read to reference sequence (e.g. splicing), or mismatches between read and reference.
Processing SAM/BAM next-gen sequence files takes a lot of memory (about 500 megabytes per million features).
Numerical (as opposed to comparative) readout of the data in Wiggle tracks, e.g. via a y-axis label or mouseover popup, is still unsupported.

Please visit the website for contact info

http://jbrowse.org/

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