JBrowse 1.16.11

Minor improvements

• Add optional track label field for RegexSequenceSearch (issue #1553,
  @cmdcolin, @Rhinogradentia)

• Bump @gmod/tabix for textdecoder speedup for very large tabix files
  (@arpanda, @cmdcolin, pull #1569)

• Increase GFF3Tabix chunkSizeLimit to avoid it being hit on relatively small
  files

Bug fixes

• Bump @gmod/cram for fix for ultra long reads (GMOD/cram-js#84)

• Fix issue that some users were seeing with "Commit hash required" when
  running setup.sh. Thanks to @GFJHogue and @hans-vg for reporting (issue #1555)

• Bump @gmod/bam which fixes some unsigned BAM tags being reported with a
  negative number

• Bump @gmod/bam and @gmod/tabix for some fixes with reg2bins and chunk
  merging for large chromosomes e.g. wheat. Thanks to @jrobinso for reporting
  (GMOD/tabix-js#118)

JBrowse 1.16.10

Minor improvements

• Added an optimization for BAM that helps for long reads especially
  (@cmdcolin)

• Added generation of the MD tag if none is specified in BAM (issue
  #1022, @cmdcolin)

• Added customRefRename and replaceRefRename global configs for
  extending and replacing ref renaming functionality respectively.
  Ref renaming helps things like chrM and chrMT to be loaded onto the
  same chromosome in jbrowse (@cmdcolin, pull #1506)

• Added support for a -f option for setup.sh. This option causes
  setup to skip installing perl prerequisites and setting up
  sample data. It is primarily intended to support faster builds
  in a Docker context. (@scottcain)

Bug fixes

• Fix the display of mismatches from hard clipped BAM sequences (pull #1513)

• Fix ability to use tracks from Open track dialog in combination tracks.
  Thanks to Sonny Arora for the repo (pull #1536)

• Fix mismatch/SNP calculation for reads with multiple skips, e.g. Iso-Seq
  (@cmdcolin)

JBrowse 1.16.9

Minor improvements

• Added a 'Reset to defaults' menu item, which addresses a long standing
  issue. Thanks to a user with a very long github name for their
  contribution (pull #1496, issue #764).

• Disable coordinate indicator on tab switch, thanks @lukaw3d (pull #1497)

• Small optimization bumping @gmod/bam from version 1.0.35->1.0.36 (@cmdcolin)

• Add ability to include/hide variant filters instead of just hide
  (@cmdcolin, issue #1478)

• Add ability to color by TS tag. The useXS config now applies to XS and
  TS, and the useTS tag only applies to the lower-case ts tag used by
  minimap2 (pull #1493, @cmdcolin)

Bug fixes

• Fixed a race condition in the http-range-fetcher module that caused
  "Error: "failed to retrieve file size"" messages when many tracks
  were opened at once. Thanks to @russellmyers for the bug report!
  (issue #1473)

• Fixed error with exporting highlighted regions with Save track data,
  thanks to @lipan6461188 for reporting (issue #1488)

• Fixed ability to have custom mouseovers on features that have no
  default mouseover e.g. features with no name or ID. Thanks to
  @scottcain for reporting (pull #1487)

• Fixed the response for requests to HTTP 403 errors. Thanks to
  @ilaydabozan for reporting (issue #1490)

• When there is only a single coordinate column in a tabix file, there
  is now improved performance since the overlap checking code was
  incorrect before in @gmod/tabix (@cmdcolin)

• Fix usage of bigwig "scoreType":"maxScore" config for bigwig tracks
  (@cmdcolin, issue #1380)

• Fix a crash related to NCList histogram when a featureScale is applied
  (issue #1327)

• Make it so that VCF tracks don't require CORS headers for Content-Range
  (@cmdcolin)

JBrowse 1.16.8

Bug fixes

• Fixed an regression that made corrupted features around bgzip block
  boundaries. Related to @gmod/tabix 1.2.0->1.3.2 fileOffset based feature ID.
  Bug affected JBrowse 1.16.7 (issue #1464)

JBrowse 1.16.7

Minor improvements

• Add name regularization for refseqs named MtDNA (pull #1408,
  @scottcain, @cmdcolin)

• Improved performance of startup time with large tracklists (pull #1412,
  @cmdcolin)

• Improve consistency of scrolling behavior across browsers using
  normalize-wheel npm package (@cmdcolin, @scottcain, pull #1429)

• Add trackMetadata->sortFacets boolean flag which can be set to false
  to disable sorting the facet categories in the left hand column of the
  faceted track selector. Thanks to Val Wood for championing this issue
  for pombase! (@cmdcolin)

• Add relativeUrl to trackMetadata config so that URLs relative to the
  data directory can be specified (the standard url config is relative
  to the jbrowse root). Thanks to @loraine-gueguen for the report
  (issue #1457)

Bug fixes

• Fix bug that has existed since 1.16.0 (since the introduction of @gmod/bam)
  that caused some BAM tags to be missed.

• Added a fix for a performance regularization for large tracklists that
  contain a lot of data. Thanks to @scottcain for reporting (#pull #1412,
  @cmdcolin)

• Fixed ability to access remote data directories in desktop app
  (issue #1413)

• Fixed ability to open FASTA files with the .fasta extension in the
  desktop app. Thanks to @iankorf for reporting (issue #1415, pull #1426,
  @cmdcolin)

• Fixed generate-names.pl to not overwrite the name store class (@Bjoernsen,
  issue #1297, pull #1423)

• Fixed some documentation for Content-Range CORs headers and
  renderAlignment configs (@cmdcolin)

• Fixed rendering of CRAM hard clipping, which would display mismatches
  incorrectly (@cmdcolin, pull #1440, issue #1438)

• Fixed issue where some BAM features were given the incorrect feature ID
  across blocks (@cmdcolin, GMOD/bam-js#36)

• Removed monkey patching from the dropdown refseq box, thanks to @lukaw3d
  for finding and fixing (@lukaw3d, pull #1439)

• Added fix for bigbed files with large headers, e.g. large autoSql schema
  (@cmdcolin)

• Make VCF based features have distinct file IDs for similar overlapping features
  with same ID, ALT, REF, etc. Thanks @scottcain for the report (@cmdcolin)

JBrowse 1.16.6

Minor improvements

• Add name regularization for drosophila style chromsome naming so that
  2L maps to chr2L and vice versa (@scottcain)

• Add ability to index names in a BEDTabix file, enabled by default.
  Thanks to @billzt for the idea and implementation (pull #1393)

Bug fixes

• Fix the side scrolling on Mac misbehaving and triggering the browser's
  back action (a bug that existed only in 1.16.5). Thanks to @nathandunn
  for debugging (issue #1397)

JBrowse 1.16.5

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 (pull #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, pull #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 (pull #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)

JBrowse 1.16.4

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!
  (pull #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 (pull #1343, pull #1340)

• Updated jbrowse.org website to run entirely off amazon S3 (pull #1347,
  pull #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 (pull #1341)

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

JBrowse 1.16.3

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)

JBrowse 1.16.2

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)