JBrowse 1

JBrowse 1.16.4 maintenance release

April 10, 2019

I'm pleased to announce the release of JBrowse 1.16.4. This has a couple of specialized fixes.

One fix provides a better error message if you give improper inputs for tabix or BAI files that actually require CSI indexes. This came up often for people in the wheat genome.

Another helps display multiple transcript features for a gene top level feature from HTMLFeatures

Minor improvements

  • Added indexedFeatures tracklist attribute for GFF3Tabix track types which controls the feature types from a GFF3Tabix file that are indexed. Thanks to @loraine-gueguen for the idea and implementation! (issue #1337, @loraine-guegen)

  • Added inferHTMLSubfeatures which automatically creates multiple mRNA transcripts from a single gene parent feature. Thanks to @abretaud for the idea and implementation! Note that this is enabled by default now (issue #1343, issue #1340)

  • Updated jbrowse.org website to run entirely off amazon S3 (issue #1347, issue #1348)

Bug fixes

  • Added better error reporting to GFF3Tabix tracks for if a parsing error occured. Thanks to @nathanhaigh for reporting (@cmdcolin)

  • Added fix for VCF that don't contain alternative alleles (@cmdcolin)

  • Added better error handling if there is a case where a tabix file is loaded that is on a genome longer than 2^29. CSI indexes are needed for this. Old versions of tabix which hadn't invented CSI would generate invalid tabix indexes in this case. Thanks to Hans Vasquez-Gross for reporting (@cmdcolin)

  • Fixed link in documentation. Thanks @agarciamontoro (issue #1341)

  • Fixed issue with ucsc-to-json.pl creating subfeatures with the wrong strand. Thanks to @sachalau for finding and fixing (issue #1346)

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