v304

Code changes:

• Added code to distinguish IE-pre-version-11 from IE-post-11 and went through all IE special cases in our JS code to determine if post11 worked with/without special case. This fixed drop-down checklist and a couple of minor CSS issues where post11 performs like other browsers (#13422). Tim
• Going from fauxVis to the drop-down select in one click causes IE11 to hang. This fix requires IE11 users to perform 2 clicks to set sub-track visibility. (#13678). Tim
• Added code to 'spectrum' (aka 'useScore') actually work on any pair of color/altColor settings (#10939). Tim
• Added support to Table Browser: export to GenomeSpace (#12559). Galt
• Added support for track hubs with "." in the name (#12453). Brian
• Fixed bug where Table Browser crashed when track hub composites had type bigBed (#13769). Brian
• Allow dash in GFF3 tags (#13673). Brian
• Write list of visible tracks to Apache error_log (#13626). Brian
• Fix hubCheck to be smarter about not checking "type" field if no bigDataUrl. Brian
• Added note to the Gene Haplotype Alleles section of gene details page: "Note the association of SNP alleles within a haplotype is statistically imputed rather than directly observed in most cases". Jim
• Added functionality to bigWigCorrelate so that it can work on a whole list rather than just a pair of bigWigs. Jim
• Added warning to hgTracks when udcTimeout variable is present, and provided link to remove from cart to enhance performance (#13675). Brian
• Extended regulation cluster tools to incorporate metadata into DNase clusters (#13490). Kate
• Implemented initial version of data loader for GTEX (hgGtex) (#13504). Kate
• Added functionality to SNP display in hgTracks: option to show organism's alleles even when ortho alleles are not available; by default, show alleles on + strand or if user clicks 'reverse', all on - strand (with option to revert to showing dbSNP's strand) (#13694). Angie
• Added functionality to details page for VCF data: if haplotype clustering is not enabled, don't show 'sorting order' option; show Hardy-Weinberg only when explicitly enabled since it's usually N/A. Angie
• Added jsMakeSetClearContainer/jsEndContainer to wrap set and clear buttons around a list of checkboxes without inlining JS in HTML (used in hgVai, applicable elsewhere). Angie
• Moved JS functions out of C code / inline script in HTML into JS file. Angie
• Finished work on the new repeat masker display (#9741). Hiram

Data changes:

• Ongoing work for conservation track for dm6 (#13461). Chin
• Added CCDS track to hg38. Brian
• Added Retroposed Genes V5 track for mm10 (#3867). Rachel
• Started work on NCBI Ends track for mm10 (#10083). Steve
• Started working on proteomics track (Peptide Atlas) to hg19. Kate
• Expanded ENCODE Regulation DNase clusters track schema to include metadata (support for Variant Integrator tool) (#13490). Kate
• Initial work on gene expression from RNA-seq in 2921 samples (53 tissues) for GTEx (#13504). Kate
• Created liftOver from papAnu2 to hg19 (#13695). Hiram
• Completed work on NCBI Ends track for hg38 (#13713). Hiram
• Built Ensembl Genes v76 for papAnu2 (#13774). Hiram