v447

Code changes:

• Users can now keep multiple isPCR results in one track rather than overwriting the custom track with each new hit (#30925). Chris
• Changed recommended track sets to merge into the current session instead of overwriting it (#28525). Brian
• Longer descriptions are now allowed in .as field labels, separated by | character. Max
• hgTracks searches that go to only one place now correctly set their parent track visibilities on the url (#31090). Chris
• Added a new endpoint to API: /list/files?genome=someGenome to provide a list of download files for the specified genome. TBD: document this feature and add error catching (#23589). Hiram
• Added format=text argument to the API /list/files endpoint to return plain text list of files rather than the standard API JSON (#23589). Hiram
• Added a new "downloadUrl" trackDb statement which adds a download link to the trackUi page (#30904). Max
• Improved code around browser "themes" (=user-selected CSS files) which are now more resilient to crashing if there are missing files (#7867). Max
• Ongoing work on incorporating snake display in the chain and psl support (including big versions)(#30280). Brian
• Cleaned up logoMaf display so it scales to the existing window instead of by the viewing region. Brian
• The DNA retrieval tool would sometimes fail to color bases in exons appropriately if the transcript began outside the window of retrieved DNA. This is now fixed (#31029). Jonathan
• Details pages for Interact tracks could fail to load if the track was set to generate multi-region view links and the file for the track was using chromosome aliases instead of native names. Chromosome aliases are now handled properly in that situation (#31056). Jonathan
• All CGIs now support a secret argument for logging to the Apache error log. utils.js contains an asynchronous function to call the CGI that included it with this argument. Used currently for reporting our javascript run time back to the server (#30591). Chris
• Errors were not being caught when trying to load a hic track with a missing file. Those errors are now caught and reported appropriately (#31071). Jonathan
• Small improvements to bigGuessDb (#30316). Max
• GBiC patch to fix mysql tables that are in a broken state on hgdownload, like GBIB. Max
• Fixed a dump bug in the pipeline library module that could cause second pipeline calls in a process to fail under some circumstances. Mark
• Continuous GenArk process improvements (#29545). Hiram

Data changes:

• Improvements to wuhCor1 big tree build process. Angie.
• Continuous GenArk updates and liftOver files generation. (#29545). Hiram