v317

Code changes:

• Final touches on new CGI, Data Integrator: Fixed pop-up formatting and scrolling behavior; Fixed cart update race condition after changing clade/org/db; Omit BAM and MAF tracks until anno* libs support those types; Print average wiggle value over region instead of comma-sep list; Allow selection of wiggle chrom/start/end columns; Include Tools - Data Integrator in navbar menus on RR too if hgIntegrator exists (#14579). Angie
• Added beta version of keyboard shortcuts (turned off by default, hg.conf:shortcuts=1 to activate) (#15370). Max
• Started work on "Send to" menu (#15113). Max
• Tolerate absence of big genbank tables on mirrors. Max
• Added option to always show errAbort messages (hg.conf:showEarlyErrors=1) even if no http header has been printed yet (#15332). Max
• Fixed GBiB so that it does not overwrite local hg.conf file (#15382). Max
• Fixed filtering on chromosomes in chains (#15143). Brian
• Printed GENCODE ID on knownGene page (#14639). Brian
• Ensured that chromosomes are sorted by case in bedToBigBed (#15400). Brian
• Fixed start/stop codon exon number in genePredToGtf (#15216). Brian
• Fixed hideTracks URL to deal with default tracks correctly (#15299). Brian
• Fixed bug that happened when turning off splice variants in UCSC Genes (#15399). Brian
• Changed the common.mk to auto-detect hgwdev's installation of node.js tools. Angie
• Changed name of expData to expMatrixToJson. Chris
• Changed name of errCheck.sh errCheck (.sh is unnecessary). Chris
• Added error checking to tagStormToJson program. Chris
• Added link to details page to other genome assembly on snake tracks that are not assembly hubs. Mark
• Support setting transMap track default item labeling in trackDb (#15440). Mark
• Fixed race condition on hgsql purging temporary files that caused errors when multiple hgsql commands were run at the same time. Mark
• Added trackHander attribute to mouse GENCODE trackDb entries. This removed the requirement to have code explicitly match versioned table names (#14781). Mark
• Implemented Track Hub spec versioning mechanism. This includes new options to hubCheck utility. A draft version1 spec is available on genome-preview. Finalization of version1 is underway (#10015). Kate
• Added support for +/- All buttons for sub-track selection on track configuration pages (allowing use without matrix) (#14732). Kate

Data changes:

• Released UCSC Genes update for mouse, mm10 (#15145). Matt, Brian
• Created Augustus Gene track for all assemblies (#13088). Hiram
• Created Microsatelite track for all assemblies (#15398). Hiram