v328

Code changes:

• Multi-region display. This feature allows users to "slice" their track viewing experience into a variety of different modes that focus the display on certain features: exon-only, gene-only, or user-defined BED coordinates. Only the portions of track annotations that fall within these displayed regions are shown; extraneous intergenic, intronic and otherwise unwanted regions are hidden from view (#12242, #16666). Galt
  • Turn off chrom ideogram when there is more than one chromosome in the view (#16798). Galt
  • Apply consistent scaling for wig/multiWig/bigWig/bedGraph when auto-scaling is enabled and users are in multi-region view (#16797). Galt
  • Turned off tracks of type vcfTabix when in multi-region mode (#16725). Galt
  • Added order-by clause for Gene Pred tracks in exon/gene multi-region view to aid in navigation (#16708). Galt
  • Disguised position when user checks the checkbox to hide highlighting dialog (#16756). Galt
• Fixed VCF Custom Tracks loading problem over FTP: make lineFile code assume index is .tbi, and not check for .csi (#16761, #16762). Brian
• Fixed bug in VCF handling where files were left open (#16761, #16731). Brian
• Made gff3ToPsl utility smarter about target and query strands (#13673). Brian
• Fixed simpleChain utility to output proper psl insert columns (#13673). Brian
• Fixed bug that occurred when users supplied backwards coordinate range (start > end) which caused both the start and end to be off by 1 (#16721). Galt
• Ongoing work on the CIRM data warehouse, and display. Jim, Chris, Max
• Added the capability to substitute $hgsid from the cart in a help file included by webIncludeHelpFileSubst, for internal links (#16502). Angie
• Ongoing work on GTEx gene expression track: track configuration page including popup version; added tissue selection via sortable table (#15645). Kate
• Fixed a bug in Safari version of popup configuration so newer versions that support image update can use that approach. Kate
• Added ability to request specific version in getRna and generate error if that version isn't available. Mark
• Fixed problem with bigPslToPsl not computing insert counts, which resulted in invalid PSLs. Mark
• Fixed bug with gtfToGenePred logical in included transcript version numbers when available. Mark
• Added -allowMinimalGenes option to gff3ToGenePred to create genePreds when annotation doesn't follow the canonical gene-to-transcripts-to-exons structure. Added to support RefSeq GFF3 files. Mark
• Ongoing work on GBIB: allow R for GTEx tracks; security updates; local track loading (#16616). Max
• Fixed fetchChromSizes utility for Mac OSX 64-bit (#14987, #16763). Hiram
• Ongoing work on supporting CRAM data type (#14717). Brian

Data changes:

• Completed gorilla gorGor4 assembly (#16220). Jonathan
• Finished work on hg38 patch 6 (#16648). Jonathan
• Started building assembly browser for Rhesus - Macaca mulatta, rheMac8 (#16744). Hiram
• Ongoing work on NCBI RefSeq Gene track (#13673). Hiram, Brian, Max, Mark
• Ongoing work on SNP v142 for mm10 (#15934). Brian