v395

Code changes:

• Now hgTables includes related tables for composite tracks (#25015). Angie
• Now hgIntegrator, hgTables prevent warning about invalid group from causing invalid HTTP header for output (#25003) (#25016). Angie
• Now hgCustom does not allow invalid group setting in custom tracks (#25003) (#25016) Angie
• Fixed up some hubCheck UI bugs, and added warns for missing hub and genome description pages (#24958). Christopher
• Fix bug in hgTracks where opening or closing a track group wasn't saved before navigating to hgTrackUi (#22359). Christopher
• Improved assembly hub automatic build scripts (#23891). Hiram
• Argument -chromSizes added to genePredFilter to allow work on assembly hubs without database chromInfo table (#23963). Hiram
• Added options -tab, -fillSpace and -score=N options to genePredToBed to allow conversion of genePred that has spaces in the name field (#23891). Hiram
• Fixed up up usage() message in a number of commands so they will have a single line definition statement as the first line output of the usage message to facilitate packaging of the kent commands in bioconda packages (#25071). Hiram
• Procedures added to automatic build scripts to allow Ensembl gene tracks created on assembly hubs (#24963). Hiram
• Table Browser now correctly provides BED3 when asked to provide hic data in BED format (as opposed to broken BED5) (#24988). Jonathan
• Tools now account for the chromosome name conversions performed by the Juicer toolkit when making .hic files (like 1A vs chr1a) (#25055). Jonathan
• Deleted a bunch of unused HIV/Cancer browser code. Brian
• Now Table Browser will use name index on bigBed's if available. Brian
• Added workaround for problem with %g going into scientific notation too early. Brian
• Now hidden collection multiwigs are not added to list of tracks to display (#25050). Brian

Data changes:

• SARS-CoV-2 genome browser released (#24851). Hiram
• Added clinvarLift track to a few assemblies (#24825). Max
• New gnomAD structural variants track QA ready (#24179). Christopher