v474

Code changes:

• Added setColorWith to allow wiggles to be colored by a bigBed (#26932). Brian
• Allow people to select Exit Mult-region on the pop-up box (#29452). Galt
• Better error messages if an assembly hub db isn't found for some reason (#34611). Brian
• Added a cart rewrite to support moving decipher tracks into a supertrack (#34702). Brian
• More work on adding support for non-ASCII characters in hgTracks and PDF (#34782). Brian
• Fixed a subtle drawing bug in zoomed-in bigWigs (#34746). Brian
• More fixes for hideOthers, make sure that tracks that are on by default are really hidden (#27890). Max
• Hide legend if all gnomad pli tracks are hidden (#26169). Max
• Suppressed unnecessary error log messages due to loading a hic file with an invalid normalization type (#34394). Jonathan
• Add in GENCODE hgc gene and transcript name display in table, as check for HGCN is missing miRNAs not in HGNC but in mirBASE. Mark
• Fixed an issue in loading expRatio data when the number of experiments exceeded the number of exons; such files should now be able to be loaded and processed (e.g. for conversion to bigBed) (#12101). Jonathan
• Making sure that hgGeneGraph is not spawning more and more dot programs. This came up because on Nov 14 today, a lot of stuck dot programs were running on the RR. The root problem may have been something else, but this should make hgGeneGraph a little less problematic in the future. Also, we can use hg.conf now to constrain dot programs more. Max
• Rework the use of /scratch/tmp /data/tmp and /dev/shm temporary filesystems in the automated pipelines to accommodate new cluster machines (#34685). Hiram
• Fixup security points in the assembly request CGI script that is sending emails (#32596). Hiram
• hgPhyloPlace: add option for subtree JSON files to persist instead of being cleared after 2 days. Angie

Data changes:

• Updating VGP collection of assemblies in preparation for multiple alignment (#34370). Hiram
• Improvements to wuhCor1 big tree build process. Angie.
• Continuous GenArk updates and liftOver file generation (#29545). Hiram