- v399 Preview 1 - 18 May 2020
- v399 Preview 2 - 25 May 2020
- v399 Final - 1 June 2020
Code changes:
- To make hierarchy more apparent, add supertrack description and track list to top of supertrack member configuration page (#24948). Kate
- New track and display type vcfPhasedTrio (#25585). Christopher
- Fix bug when there are missing fields when loading VCF custom track (#25603). Christopher
- Added parsing of B tag type to BAM display (#25612). Brian
- Added color range to non-synonymous changes in mafSnp display using BLOSUM62 scores. Brian
- gfServer and blat and isPcr extended with new commandline option -noSimpRepMask to help with small genomes. In particular this is motivated by allowing extremely sensitive and short protein and dna queries on Sars-Cov2 (wuhCor1) as well as other microorganisms. (#25477). Galt
- Added All Results checkbox to hgBlat and short paragraph explaining it. Changed it to read tileSize etc from gfserver status so it can use whatever it finds. Instead of limit 20 for dna it now detects mininimum psl matches from genome size. Error messages and warnings should now be complete and correct about suggested and required minimum query lengths (#25477). Galt
- Added -timeout=1 and -host=blat1a options to blatServersCheck utility. Galt
- Remove dependance of hgHubConnect on it's special udcCache (#25574). Christopher
- Fix hgHubConnect to not crash on search if a hub is down (#25574). Christopher
- Modified hgVai code to grok frameshifts, added utility pslRemoveFrameShifts (#25634). Brian
- Continued improvement of assembly hub construction scripts VGP set of assembly hubs ready to release (#23734). Hiram
- Fixed problem in blastz-run-ucsc script to work correctly with ‘dash’ shell in place of bash or sh (#25528). Hiram
- hgc, hgTrackUi for VCF: use 'sample' instead of 'haplotype' for SARS-CoV-2 data (viruses aren't diploid like we are) (#25409). Angie
- hgc for GnomAD, ExAC VCF: use trackDb-driven URLs not hardcoded (#25595). Angie
- tdbQuery: tolerate spaces between release labels like "beta, public" Angie.
- Yet another little converter tool, genbankToBigGenePred (#25114). Max
- Adding a gene-phenotype table to OMIM hgc page and otto jobs (#18419). Max
Data changes:
- 7-way alignment of human coronaviruses on the SARS-CoV-2 browser (#25187). Hiram
- panTro6 <-> ponAbe3 lastz/chain/net constructed per user request (#25581). Hiram
- Added Southern sea otter (enhLutNer1) to the placental chain/net tracks for hg38 and mm10 (#21152). Jonathan
- 1000 Genomes trio track QA ready (#25582). Christopher
- Created track for ENCODE Registry of Candidate cis-Regulatory Elements (cCREs) in human and mouse (hg38, mm10) (#24668). Kate
- Update COVID-19 landing page to include UCSC-authored biorxiv paper,
newer Nextstrain transmission graphic, and new item for GENCODE COVID-19
gene annotation hub (#25217). Kate
- Update hideEmptySubtracks section of Track Database Definition docs (#23365). Kate
- Nextstrain Frequency track (#25481). Angie
- A protease sites track for wuhCor1 (#25192). Max
- A phyloCsf track for wuhCor1 (#25644). Max