v361

Code changes:

• Minor UI change for the Public Sessions and My Sessions interfaces: sort arrows now appear on the left edge of the column heading instead of the right (#20841). Jonathan
• Updating and improving HGMD track (#15536) Max
• A recovery email address for hgLogin (#20888) Max
• Fixed bug: sqlDyStringAppend() is not safe, and it is not needed. Using sqlDyStringPrintf instead. Galt
• Fixed bug in hex encoding for non-ascii high-bit characters. Cast was needed for htmlPrintf functions. Galt
• Adding some needed url-encoding to chromInfoPage links. Galt
• Cleaning up sql for safer usage to avoid injection in CIRM cdw. Galt
• Initial test code for selected facet values and counts. Galt
• Extended the selected facet count algorithm to handle the ignore-null-values option. Galt
• Added pslSomeRecords to userApps delivery (#20215). Hiram
• Improved handling of some uncommon NCBI GGF3 constructs by gff3ToGenePred. Mark
• Allow gff3ToGenePred to skip more types of conversions errors with -warnAndContinue to support other NCBI GFF3 files. Mark
• Work finalizing hgCollection (#11630). Brian
• Polish UI layout and styling of hgCollection and its help doc (#11630). Kate
• hgVai: use PSL+CDS+transcript sequence instead of genePred when possible (currently only RefSeq) to predict consequences and generate HGVS, so we get the correct result even when there is an indel between reference genome and transcript sequence (#20948). Angie
• hgTables: fixed broken intersection with plain VCF custom track. Angie
• joiner lib: restrict routes starting from a table in a genome db to that db even when going through a table (e.g. hgFixed genbank metadata) linked to all genome databases to avoid enormous linked-table lists and slow routing (#20949). Angie
• joinerRoute: new util for examining & debugging all.joiner routing issues. Angie

Data changes:

• Worked up UCSC to RefSeq correspondence list for 171 genome browsers:
  • src/hg/utils/automation/dbAssemblyEquivalents.tab (#20215). Hiram
• all.joiner: apply splitPrefix only to old databases that have split tables so it doesn't slow down newer databases that don't have split tables. Angie
• all.joiner: don't relate seq/extFile to all genbank tables. Angie