v339

Code changes:

• The CGI phyloGif renamed to phylPng since Gif palettes are no longer available (#18104). Galt
• Fixes for bugs related to LRG hgTracks code and data (#13359) & DGV data (#17351). Angie
• Adding infrastructure to allow chrom names from NCBI RefSeq/Genbank and Ensembl to work in the 'position' box (#18027). Hiram
• Preventing a network error in Firefox and Safari while saving the state of the hidden highlight popup; it now waits for the ajax update to finish before submitting the form (#18702). Galt
• Fix for textarea XSS problem in hgVai. Added functions to allow encoded html outputs of large but indeterminate size. Fixed XSS problems in VisiGene and phyloGif (#17782). Galt
• Enhance of hubCheck to check bigPsl files. Mark
• Added a method for knownGene track to be supported through bigGenePred format (#15259). Brian
• Optimized codon drawing in hgTracks to not request sequence unless it needs it. Brian
• Optimization to not check if map boxes are overlapping. Brian
• Make the switch to MAF summary mode be settable by a conf or cart variable. Brian
• CIRM: improvements to cdwCleanMetaData (#17918), cdwWebBrowse (#17918), and cdwSummary. Chris
• CIRM: Additions to stem cell hub: new diseases to controlled vocabulary, better help page with text and images from Clay, renaming body_part tag to more generic sample_label tag, and new utility to scrub a dataset as opposed to just scrubbing single files. Jim.
• Patched out: Added encoding of item names when generating URLs in hgcAnchorSomewhere. This prevents item names with CGI-unsafe characters from being incorrectly encoded, which was happening with PSLs, but could happen in other structures. Mark

Data changes:

• Change UCSC mouse genes build to now have BioCyc links to mouse pathways instead of human (#15315). Jonathan
• Work on CRISPR tracks (#17235). Max
• Improved gorilla/gorGor5 gold/gap description pages to represent the new sequencing assembly technology (#17580). Hiram
• Updating documentation for webBlat docs (#18091). Galt.
• Built bigGenePred's for knownGene tracks for mm9, mm10, hg18, hg19,and hg38 (#15259). Brian
• Pfam in RefSeq track for dm6. Brian