- v398 Preview 1 - 27 Apr 2020
- v398 Preview 2 - 4 May 2020
- v398 Final - 11 May 2020
Code changes:
- Add right click/hgTrackUi option to merge bigBed items that span the window into a single item (#25133). Chris
- Changes for Hide Empty Subtracks feature, minor UI improvements (#23365). Kate
- Add note to track label when Hide Empty Subtracks feature is on.
- Add "info icon" with explanatory text on mouseover forHide Empty Subtracks feature, next to UI control was a question mark.
- Make phyloTree use UDC (lineFileUdc) to support remote tree files for VCF (#25197). Angie
- Increased default label width to 20 characters from 17. Brian
- Tweaked Short Match track to work with RNA. Brian
- Increased the number of bases that extended DNA color choices will allow from 1 million to 5 million. Brian
- Added a new tool, genbankToBigGenePred, to extract the gene models from Genbank records directly. Max
- Fixed bug in pslScore.pl from user problem report (#25538). Hiram
- Fixed bug in faAlign kent command to allow larger sequences to align. Hiram
- Updated source tree to build correctly on Mac OSX Catalina 10.15. Hiram
- Fixed up assembly hub procedure to use NCBI supplied RepeatMasker result to avoid expensive compute procedure to calculate that locally (#23734). Hiram
- Fix sqlDescribe to use regular DESC command if a table schema does not exist in the tableList table (#25536). Chris
- Color ribosomal shift codons to call attention to them. Brian
- Changed trackDb caching to depend on access times instead of modification times. Brian
- Expanded a HTML header buffer to 8k from 2000. Brian
- Added a flag to bedToBigBed allowing exons to overlap one basepair. Brian
- Fixed bug in VCF display where track visibility was assumed to be valid but wasn't on parallel load. Brian
- Fixing up some text for hgBlat. Only print it for nucleotide search. Galt
- Adding missing canPcr field to blatServers.as. This should have been done long ago by whoever made the change. Galt
Data changes:
- Added makedoc for hg38 vs enhLutNer1 (southern sea otter) lastz alignment (#21152). Jonathan
- Load GTEx V8 Gene Expression track. Ready for QA (#25130). Kate
- Updated COVID-19 landing page with new links and updated transmission graphic (#24217). Kate
- Another round of clinvar improvements suggested by Ana (#24850). Max
- Finish up special regions track (#24245). Max
- Removing more Avada track duplicates (#25433). Max
Coronavirus data by Max:
- wuhCor1 arctic network primers (#25416)
- wuhCor1 T-cell epitopes track (#25458)
- wuhCor1 rfam track (#25463)
- wuhCor1 transcriptome track (#25468)
- wuhCor1 nextstrain frequency (#25481)
- Nextstrain VCF improvements: merge records at same position, add BACKMUTS tag (#25188). Angie
- [hgwdev-only Nextstrain-derived custom tracks and files for David et al.]. Angie
- Added Max's Nextstrain Count (since changed to Frequency) to otto update (#25481). Angie
- Working on updated VGP set of assembly hubs (#23734). Hiram
- New data for Rangan track from Manny in whuCor1 (#25228). Brian
- New NCBI genes with ribosomal frame shit in genePred. Brian
- Tweaked mafSnp tables on wuhCor1 to treat codingVariants that are neither syn or nonsyn as missing. Brian