JBrowse 1

JBrowse 1.15.4 maintenance release

October 5, 2018

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

Minor improvements

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

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

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

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

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

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

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

Bug fixes

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

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

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

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

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

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

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

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