v434

Code changes:

• Expanding coloring based on query sequence to include chain tracks. Jim
• Making base-by-base alignment display work for bigChains and bigPsls (#29688). Jim
• Making 'View details of parts of alignment within browser window.' link on bigPsl and psl work better when query sequence is big text (#29688). Jim
• Adding 2bit option to baseColorUseSequence tag. Jim
• Making qInserts be rendered as two bases wide rather than always a single pixel line. If zoomed in enough will show size of insert in query as a number in the middle of the box. See also redmine #29642. Also qInserts are drawn after, not before, the red blocks of base mismatches. Jim
• Documenting new otherTwoBitUrl tag and addition to baseColorUseSequence tag (#29642). Jim
• Made cacheTwoBit system - which will cache pieces of two bit files we've read. System has some sense about only loading what it hasn't seen already, and only loading the part it needs to see. Could be improved, but better than storing all of each sequence. Jim
• Updated hubApi expected test output to match current table contents (#29729). Hiram
• Fixed default cart problem with ipNode redirect. Brian
• Made LRG accessions and problematic regions searchable (#29689). Max
• Added message to track long label if either doWiggle or maxWindowCoverage is active (#29715). Max
• bigBed files can include JSON data in an extra field and hgc will build a table from this. Fixed the code that builds the table (#29742). Max
• Added "tableBrowser tbNoGenome" to trackDb, so we can block tracks just in the table browser but not in the API. Some tracks are so big that they time out the table browser when on "entire genome", but the API doesn't time out (#29729). Max
• Continued updates to hgPhyloPlace. Angie

Data changes:

• knownGeneV41 on hg38 and knownGeneVM30 on mm39. Brian
• Brought listings of GenArk assemblies and VGP assemblies up to date so that VGP is now properly a subset of all GenArk assemblies (#29545). Hiram
• Ongoing improvements to wuhCor1 big tree build process. Angie