- v411 Preview 1 - 15 Feb 2021
- v411 Preview2 - 22 Feb 2021
- v411 Final - 1 Mar 2021
Code changes:
- New JSON output for hgBlat (#27010). Max
- Add a "More Results" button to get non short-circuit results from hgFind (#26960). Brian
- Add facet counts to hgTrackUi facets, both in the dropdown and in the selected facets list (#25321). Galt
- Implement faceted selection of bars for barChart tracks, activated by a new barChartFacets tag in trackDb in combination with a tab-sep-file referenced in barChartStats (#26769). Jim
- Add ability to add a trixSearch path to findSpecs (#26960). Brian
- Clean up incFiles.txt in trackDb cache when trackDb.txt file no longer includes files. Brian
- Remove "Query Sequence" link for blat custom tracks since there might be multiple sequences. Brian
- Fix maxWindowToDraw to not crash on wiggles (#27085). Brian
- Add API support for tables that use other names for 'chrom' column, e.g. 'tname' in PSL (#25840). Hiram
- Fix error in old encode trackDb regarding default facet selections (#25321). Galt
- Fix existing bug causing "ASSERT: matChkBoxNormalize() called for dim ABC!". This problem happened for old-style abc dimensions that were neither XY matrix nor filterComposite facets (#25012). Galt
- Fix gff3ToGenePred -refseqHacks to not SEGV on a CDS without a Name parameter. Mark
- Add FreeType fonts to GBiB (#27075). Brian
- Add GTF support for chromToUcsc (#26959). Max
- Fix fetchChromSizes for hg19-hg38 patch levels. Max
- Fix bugs and limitations in liftOver (#27023). Galt
- Increase max fields from 64 to 2048.
- Check that required first 3 fields are present and consistent with no silent truncation.
- hgPhyloPlace. Angie
- Support upload of hundreds of sequences: lengthen timeout, skip verbose output if <100 seqs.
- Add downloadable TSV summary files for samples and Spike protein mutations.
- Add config file for QC green/yellow/red thresholds instead of hardcoding.
- Add usher -K comprehensive subtree output.
- Add support for reading tree description from file for otto-update.
- Forwards compatibility: skip over unrecognized fields in protobuf.
- If usher's output includes clade and lineage assignments, include those in summary table.
Data changes:
- (New) SARS-Cov-2 'Variants of Concern' track, now released (#26876). Kate
- (New) TargetScan MicroRNA Target Sites track for hg19. Ready for QA (#26287). Kate, Brittney
- (New) CADD track for hg19, hg38. Now released (#18492). Max
- (Update) SARS-Cov-2 'Spike Mutations' track, now released (#27025). Kate
- (Update) SARS-Cov-2 browser track menu and defaults. Kate
- Add a new search rule for Gencode V36 that uses a culled list for the trix and does a short circuit search on it (#26919). Brian
- Updates to nightly build scripts for public tree for hgPhyloPlace/usher: 'matUtils annotate' Nextstrain clades. Angie
Doc changes:
- (gbib.html) New defaultCart feature for GBiB (#26938). Lou
- (bigMaf.html) Clarify and expand bigMaf examples (#27009). BrianL
- (covid19.html) Update and add news items and new tracks to COVID-19 resources page. Kate