v357

Code changes:

• Making dataVersion in trackDb more consistent (#20419). Max
• Fixed problem causing lost custom trash db records caused by silently returning FALSE from sqlTableExists() when the error has nothing to do with whether the table exists or not. Reported by Hiram when using namedSession cleaner (#20423). Galt
• GBIC pulls from genome-euro mysql instead of ucsc if mirror is closer to europe (#20353). ChrisL
• Update to GTEx eQTL track code and data to address some issues found with filtering and item uniqueness noted by QA after initial release. The schema for the Combined track was extended to include the Ensembl gene ID (for item uniqueness) and additional summary fields (to provide additional mechanisms for filtering via scripting or the Table Browser) (#20236). Kate
• Fixed bug in git-reports caused by parent paths end up not being created when whitespace-only diff occurs. Galt
• Updated links to the CDC HuGE database resources (#20317). Galt
• Removed broken GAD links in hgc (#20317). Galt
• Added pslRc command to reverse-complement a psl file. Mark
• Display Gencode version in all Gencode tracks transcript detail page. Mark
• Fixed missing file extension for tarballs in cdwWebBrowse. Max
• Fixed a bug in QA qaGbTracks script where the program was crashing on the gap table. ChrisL
• Fixed several corner cases in VAI: Angie
  • Insertion into transcript on - strand, after shifting, gets new sequence value on wrong strand in HGVS transcript term (#20327).
  • Insertion at boundary between splice site and splice region is not detected as splice region variant (#20328).
  • Values of {aa,codon}{OId,New} truncated when multi-base substitution straddles codon boundary (#20329).
• Upgrade position/search: added support for LRG genomic and protein terms. Angie
• Fix autocomplete.js: don't reset position/search input at init time if it already has focus (#20433). Angie
• Added HGVS output options to vai.pl Angie
• Ongoing work on hgCollection. Braney
• Moved the cloning of custom tracks to BEFORE loading of track hubs in initialization. Braney
• Fix link out to MGI from hgGene. Braney

Data changes:

• Ensembl gene version 90 - tracks loaded on hgwdev and ready for QA (#20304). Hiram
• Updated chromAlias table for all Ensembl gene track browsers (#20304). Hiram
• Loaded reciprocal best and syntenic chainNet tracks on 27 primate browsers (#20216). Hiram
• Last changes to the uniProt track, after release (#20414). Max
• Tweaking of clinvar data again after some changes on their side (#20268). Max
• New genome browsers ready for QA. Hiram
  1. cebCap1 (#20237).
• Fixed of /gbdb/hg38/ncbiRefSeq/refSeqFuncElemsMm10.bb --> /gbdb/mm10/ncbiRefSeq/refSeqFuncElems.bb (#19638). Angie