v322

Code changes:

• Added chainToPslBasic utility which quickly converts chain files to PSL files without the overhead of computing match and mismatch counts. Mark
• Activated keyboard shortcuts (#15370). Max
• Fixed phyloGif to accept spaces and special characters in tree node labels (#15919). Galt
• Added troubleshooting information to MySQL SSL setup documentation. Galt
• Added utilities to the user apps: hgLoadMaf, hgLoadMafSummary and hgLoadChain (#15955). Hiram
• Changes to Data Integrator: Fixed bug where wiggle db values were overhanging edges of search region (#15952); Fixed bug where it was using out-of-range large-bin items if query limit was hit (affects very large mysql tables like hg19.phastCons100Way (#15953)); Added context-specific Help menu item (git 45a604c). Angie
• Fixed bug in hgTracks: lookupTrackHandler wasn't getting child tracks' trackHandler settings (git 4abb8b25). Angie
• Fixed bug in hgCustom: was using hardcoded default form action instead of cart value (#15517). Angie
• Fixed bug in Table Browser: prevent mysql query for composite track with bigData type (git 9fa9d88). Angie
• Added 'top' target to hg/js makefile to build only top-level *.js (not new React UI stuff (git a86b674)). Angie
• Fixed 'est' vs 'all_est' confusion that caused checkTableCoords error (git d09ea5e9). Angie
• Minor cleanups: add missing clean target to makefile (git e835e6d5), set verbose level to 0 for util messages causing unnecessary stderr output during test (git 3888cc), check existence of file before usage (git fd0cbd09). Angie
• Added -max option to bigWigMerge (#15929). Brian
• Fixed bug in hubPublicCheck in the case of missing descriptionUrl (#15932). Brian
• Do not allow new default tracks to sneak into existing saved sessions; ensure that they maintain exact original track contents (#6551). Brian
• Fixed crash in snake track controls (#15994). Brian
• Added the ability to specify genome within assembly hub on URL. Brian

Data changes:

• Flipped the switch to make GRCh38/hg38 the default human assembly browser.
• Reloaded PeptideAtlas track metadata table (hgFixed.peptideAtlas2014Peptides) to fix bug (hydrophobicity and proteotypic score in wrong columns) (#15998). Kate
• Rebuilt snp144* on hg19 and hg38 after dbSNP provided some missing mappings to alt haplotype sequences (#15493). Angie
• Lifted Coriell deletion/duplication cell line track from hg19 to hg38 (#15534). Chris
• Ongoing work on CIRM data, manifests and programs. Chris, Steve
• Added links from the GENCODE/UCSC Genes detail pages to GTEx (#15649). Kate