- v412 Preview 1 - 8 Mar 2021
- v412 Preview 2 - 15 Mar 2021
- v412 Final - 22 Mar 2021
Code changes:
- Add support for dynamic BLAT servers, which pre-index genomes to files and are run on demand to handle a BLAT request rather than a dedicated server in memory. See http://genomewiki.ucsc.edu/index.php/Running_your_own_gfServer. Mark
- Multi-region feature enhancements, using 'custom regions' mode for sparse tracks. Includes new trackDb setting "multiRegionsBedUrl" (#26385). Kate
- Implement maxWindowCoverage, a trackDb variable to force the browser to put a track into density coverage mode when the size of the window is bigger than N bases (#27079). Brian
- Improvements to hgBlat to tolerate and explain limitations of using dynamic blat servers with the Search All feature, including Search All verbiage and FAQ links (#26658). Galt
- Fixing outlink click tracking with Google Analytics on hgc and hgTrackUi pages to avoid popup blocker on pre-2016 Firefoxes (#21916). Max
- Replaced some lost barChart details, e.g. score, strand (#27149). Kate
- Surface up any warnings or errors that came about from an asynchronous hgTracks update (#26847, #27247). Chris
- Add database-specific hg.conf setting to put up a link on position line for wuhCor1 quick start guide (#27198). Kate
- Remove extra call to free() in pubsTrack.c now that we are using the trackDbCache. Chris
- Ensure consistent treatment of underscores and spaces on hgc boxplots (#27214). Chris
- Fix up relatedTracks section on hgTrackUi/hgc pages to not choke on superTracks, and don't show duplicate tracks (#25721). Chris
- Allow menubar links to hgTracks to use the current web browser window size for hgTracks image width (#26908). Chris
- Right-click label fix for a genes track (#26687). Max
- Change density coverage to count zero width intervals as single base intervals. Brian
- Add support for bigBed into featureBits utility (#14726). Brian
- Allow custom BLAT tracks to be used in DNA extra color/case options (#23045). Brian
- Add link to COVID landing page to coronavirus browser footer text (#27117). Kate
- hgPhyloPlace. Angie
- Offer a zip archive of subtree Newick and JSON files.
- Quick download links near top of page.
- If protobuf has nextclade & pangolin annotations, show in summary table.
- Subtree custom tracks: dense by default.
Data changes:
- (New) knownGeneV36 for hg38 (#26919). Brian
- (New) Swift Primers for SARS-CoV-2 (#27178). Angie
- (New) Initial hg19 release of gene haploinsufficiency predictions from DECIPHER, as described by Huang et al. 2010 ( #25707). Jonathan
- (Update) Table hgFixed.asmEquivalent brought up to date. Hiram
- (Update) Ensembl genes v103 brought up to date for genome browsers and assembly hubs (#27194). Hiram
- (Update) Further updates to hosted assembly hubs (https://hgdownload.soe.ucsc.edu/hubs/). Hiram
- Corrected data error (L452R identifier misspelled) in coronavirus Spike Mutations track. Kate
- Add defaultCart to hgcentral dump for mirror support (#27035). Brian
- hgPhyloPlace tree automation. Angie.
- Run pangolin & nextclade only for new public seqs, not all
- For GenBank sequences: query BioSample only for new seqs, not all
- Public tree: split out by quarter (20Q1, 20Q2, ... 21Q1) for smaller VCFs
- Automate GISAID stuff (pangolin, nextclade, metadata, map to public IDs, tree update)