JBrowse 1

JBrowse 1.16.5 maintenance release

June 12, 2019

I am pleased to announce the release of JBrowse 1.16.5. This includes some name regularization fixes (e.g. when you have chr1 and 1 it tries to map to the same thing), some bigwig fixes, a small speedup for BAM data, and more. Please read the release notes!

Minor improvements

  • Added better error reporting if there is a BAI file for a genome that is longer than 2^29 and requires a CSI index

  • Added default dontRedispatch=chromosome,region which avoids long GFF3Tabix redispatching for common gff3 types that don't need it.

  • Added a hideIframeDialogUrl option to hide the iframe url in a iframeDialog popup. Thanks to @mictadlo for the suggestion (issue #1365)

  • Updated @gmod/tabix and @gmod/bam to unzip bgzf chunks as they are received instead of performing chunk merges. This also allows actual fileOffset to be used as a feature ID instead of CRC32 hash (@cmdcolin)

  • Added regularization of chromosome names using roman numerals, common in both S. cerevisiae and C. elegans genome communities. Thanks to @scottcain for assistance (issue #1376, @cmdcolin)

  • Added ability for vertical scroll events to bubble out of the jbrowse div or iframe, which can be more intuitive in embedded jbrowse's. Otherwise, the GenomeView stopped all vertical scroll events in it's area. If you need the old behavior use alwaysStopScrollBubble. (@cmdcolin, issue #1373)

Bug fixes

  • Fixed a long standing issue with BigWig files not accessing the lowest summary zoom level (e.g. the first one after unzoomed). (@cmdcolin, issue #1359)

  • Fixed a bug with using the scoreType: maxScore configuration on Wiggle tracks failing at non-summary zoom levels. Thanks to @patrickcng90 for reporting

  • Fixed a bug with name regularizing that particularly affected CRAM on mitochondrial chromosomes. Thanks to @sachalau for patience and sample data for debugging this issue! (issue #1367, @cmdcolin)

  • Fixed issue with GFF3/Tabix types colliding their attribute names with the field e.g. if start=0 was in column 9. Thanks to @loraine-gueguen for reporting (issue #1364).

  • Fixed an issue with NeatHTMLFeatures when zoomed out. Thanks to @abretaud for the implementation and fix (issue #1368).

  • Restored ability to access widest zoom level from bigwig. Thanks to @lukaw3d for noticing and debugging (issue #1375, @cmdcolin)

  • Fixed some minor parsing of 'b' type data series in CRAM files, which happens when CRAM is not using reference based compression so it is uncommon (@cmdcolin)

  • Added some more checks for track types for combination tracks (issue #1361)

Recent Posts