v493

Code changes:

• New feature: "Visible Tracks" group at the top of the hgTracks group list with the list of currently visible tracks if there are more than 32 tracks displayed (#36609). Chris
• Added a strand filter to the short match track (#36984). Max
• Allow changes to custom track data, even when uploaded via URL (#35492). Max
• Eliminated separate load/draw path for bigBeds with less than 9 fields. Use bigBed header for number of fields ONLY if the number of fields is not specified in trackDb (#36940). Brian
• Improved readability of hub error message on hgTracks (#36916). Max
• The disconnect button now appears in the group blue bar when a hub encounters an error (#36791). Max
• Added hicArcLimit and hicArcLimitEnabled trackDb settings for Hi-C tracks to limit the number of displayed interactions in arc mode. These settings display only the N strongest interactions. This setting is enabled by default for all Hi-C tracks, with a default limit of the top 10000 interactions (#36774). Jonathan
• Tweaked the auto-shading scheme for HI-C tracks when more than 1000 interactions are being displayed - ideally, this should result in fewer interactions displaying with a fully-saturated color (#36774). Jonathan
• Hubspace: users can overwrite uploaded files and delete hub.txt files without deleting all other files in the hub. warn users about certain actions. Don't add auto-generated trackDb stanzas if the user is uploading a hub.txt and the bigDataUrl for a track in the hub.txt is part of the current upload (hacky reliance on scanning the file, not true trackDb parsing (#36830). Chris
• Enabled filters in hgTrackUi for bigBed3 and bigBed4 (#28501). Brian
• Creation of a new page to automate chain file requests/delivery (#31811). Hiram
• Fixed hubUrl retry button url encoding. Chris
• Fixed hubUrl encoding in hubSpace UI (#36936). Chris
• Made grey bar icons and hgc popups on by default (#36953). Chris
• Made trackHubsCanAddGroups the default setting (#36955). Brian
• Encode IDs used by jsOnEventById to prevent cases where IDs contain parentheses, quotes, etc. Now IDs can be used more safely in selectors too (#36841).
• Whitelist GenArk in localUrl paths in isValidBigDataUrl() in customFactory.c (#34544). Galt
• Added support for vai.pl to accept a GenArk assembly accession as db, and for hgVai to accept a geneTrack without the hub_number_ prefix when db is a hub (#36534). Angie
• Moved parsePosition and parseRange routines into common.c. Added callback routines for -bed and -positions shared library bigBedCmdSupport and refactored the utilities to use them. -bed and -positions input are sorted automatically by chrom, start (#28109). Galt
• Modified pslMap to remotely access chain psl input file if given a URL. Mark
• Added number of aligned bases, alignment span, and strand to pslStats. Mark
• CGIs should report when they fail to connect to a bottleneck server, rather than silently dying (#36992). Jonathan
• Incorporated changes from Andrew Smith to tidy up the new facetedComposite UI for composite tracks (#36320). Jonathan
• Fixed the problem with liftOver with genePreds when the result ends up on a different strand and the exonFrames need to be reversed. Brian
• Hide table browser link on hgTrackUi for superTracks as per MarkD request. Max
• Increased buffer size for VCF INFO field. Max

Data changes:

• Continuous GenArk updates and liftOver file generation (#29545). Hiram