v352

Code changes:

• Fixed handling of upstream/downstream and introns in HGVS n. notation (#19702). Angie
• Fixed handling of unaligned transcript sequence for HGVS n., c. (#19711). Angie
• Improvement to hgHubConnect to be a bit faster when the server has information about many hubs (#19699). Jonathan
• Fix for hgHubConnect to no longer try to return results for hubs that aren't on the server, but were listed in the search text file (#13625). Jonathan
• Fix for a Table browser bug that was preventing bigWig files without a SQL table from working properly (#19701). Chris E.
• Enhancements to GBiB and GBiC update/install scripts (#19587). Chris L.
• Removed old confusing "ASH: " prefixes from a few error messages. Angie
• Added hgVai warning about incomplete (position-only) HGVS terms instead of crashing (#19702 note-15). Angie
• Fix for a bug with label display of split codons in pack mode (#19634). Kate
• Fix for bedClip command to add -truncate option, which fixes default behavior of dropping items that overrun the ends of chromosome. Instead of dropping the items, they will be adjusted to match the ends of the chromosomes (#19514). Hiram
• Added new debugging log option to gfServer. Jim
• GBIB/GBIC support for gene interactions tool/track (#19745). Max
• CIRM: adding missing https username/password download instructions. Max
• CIRM/HCA: Added support for arrays to tagStorm schemas. Jim
• CIRM/HCA: Made a program that turns a tagStorm schema into a JSON schema. Jim

Data changes:

• Initial work on new GTEx eQTL SNP tracks (#15646). Kate
• Work adding QA requests to the COSMIC V81 track (#14461). Chris E.
• snp150 for hg19, hg38; Ortho Alleles assemblies updated panTro4 -> 5 and rheMac3 -> 8 (#19202). Angie
• Ongoing work on CRISPR tracks (#19514). Hiram
• Updating description.html pages for many assemblies (#19704). Donna