v333

Code changes:

• Added 'RNA-Seq Expression' section to hgGene, that displays GTEx tissue-specific gene expression in a box-plot graph. Support default collapsed sections of hgGene. Set microarray section to default off (and change label to 'Microarray Expression' (#17244). Kate
• Add measureTiming support to hgGene. Kate
• Add settings to improve display of large composite tracks with metadata (hoverMetadata) and many or fixed track colors (darkerLabels), in support of GTEx Signal Hub (#17314). Kate
• Display metadata on details page directly (don't require click on metadata link) in support of GTEx Signal Hub (#17314). Kate
• Final polish for GBiC product (#14399). Max
• Fixed some minor sql injection in hgTracks and hgc. Galt
• Fixed signal handling in https made compatible with OSX (#17362). Galt
• Restored cytoBand fuzzy search (#17253). Angie
• Changes to new Gateway: Initialize oldVars so position is set correctly when db=... is a CGI param (#17267); Don't crash on missing hub description URL (#17315). Angie
• Fix hgCustom so that it does not crash on empty cart (#16174). Angie
• Fix hgTables crash when intersection settings were carried over from local db to hub. Angie
• Changes to hgSession / hgLogin / cart: if login is enabled, attempt to add a new column keyList to gbMembers and store random keys there, similar to userDb.sessionKey for hguid cookie. If able to add the column, use random keys to verify login (#17327). Angie
• Fix track search for the new mm10 UCSC Genes (#15315). Jonathan
• Started implementing Chromatin interaction display mode; Libified ave program (#15232). Brian
• Use autoscale and maximum mode as defaults for BAM density graphs (#952). Brian
• GenBank changes: default to looking for genbank metadata tables in hgFixed. Brian
• Fixed a bug with stacked wiggles where only one dataset is selected (#17281). Brian
• Support bigPsl, bigChain, and bigMaf as custom tracks. Brian
• Sped up the display of ORegAnno tracks in large regions, now that we load the color table once instead of once per track item (#17278). Jonathan
• Ongoing work on CIRM: cdwSubmit, cdwMakeEnrichments, cdwMakeValidFile, cdwLib, cdwValid: changes to cdwSubmit and adding in a new vocabulary term (#17334); renamed maniMani program (#16113). Chris

Data changes:

• Completed new assembly browser for chicken, galGal5 (#17168). Hiram
• Ongoing work on NCBI RefSeq Gene track for hg38 (#13673). Hiram
• Created GRCh38 patch 7 (#17134). Hiram
• Created GRCm38 patch 4 (#16414). Hiram
• Added 'chainCleaner' code from Michael Hiller to source tree (#17286). Hiram
• Added 145-way multiple alignment on hg38 from Michael Hiller (uses the new 'chainCleaner' procedure) (#17286). Hiram
• Created liftOvers from rn6 and danRer10 to galGal5 and galGal4 (#17015). Hiram
• Created liftOvers for ce8 to ce11. Hiram
• First draft of big* format docs. Brian
• Added some additional clustering for the PFAM track. Brian
• Created public track hub of GTEx Signal Data, hosted on hgdownload (#15647). Kate