v424

Code changes:

• Checked in Robert Hubley's support for bigRmsk track type (#28466). Brian
• Moved the entire repo to a MIT-by-default license (#27614). Max
• Fixed pipeline library timeout to properly ignore signal() returning non-zero, except in the case of a real error (#28412). Chris
• Checked in first cut of displaying sequence logos based on the reference rather than wiggles at zoomed in levels if a trackDb variable is present (#28499). Brian
• hgHubConnect now properly times out when hubCheck takes too long (#28412). Chris
• Added support for speciesLabels to allow developers to map sequence names to label names in trackDb entries for MAF tracks (#28495). Brian
• bigMaf children of composites can now output MAF format in table browser (#28519). Brian
• Hubs can now be automatically connected in "other browser" link in chain hgc pages (28522). Brian
• Updated common name Microbat for myoLuc2. Future note that changing common names is more trouble than it is worth (#28469). Hiram
• Added -fno-common to library makefiles to fix common extern variable definition errors. Chris
• Created tabJoin utility - a little easier to use on our tab-sep-value tables than the unix join. Jim
• Added "incognito" mode to hgTracks which means the browser ignores cookies (#28520). Max
• Clicking on a public session now opens a new window (#21958). Max
• Major updates to the UniProt otto job, now running on 117 assemblies (#28560). Max
• Fixed hgHubConnect bug where two hubCheck processes would spawn (#28566). Max
• Fixed bug with MSIE detection in jquery that affected the popup dialogue boxes in hgTracks (#28566). Max
• Updated cpgIsland track description page to include the command and how to obtain source (#28401). Hiram
• Reduced size of some image jpg files by removing meta data via 'jhead -purejpg'. Hiram
• Fixed up assembly hub creation procedure to not fail on empty NCBI gene track. Hiram
• Improved processing time for WindowMasker track construction. Hiram
• Improved processing time for cpgIsland track construction. Hiram
• Improved processing time for xenoRefGene track construction. Hiram
• Re-enabled grcIncident otto track construction (#28331). Hiram
• Re-enabled ncbiRefSeq otto track construction (#28331). Hiram
• Ongoing improvements to wuhCor1 big tree build process. Angie
• Added a warn-and-continue option to hgCustom to support https cert verify warnings as well as warnings more generally (#28458). Galt
• Added new features to https like cert verification, error messages that work right with warn and errAbort and our GUI in hgCustom and hgHubConnect and also logging especially for CGIs of problem certs. Also added callback so that we can support multiple levels like warn instead of abort. Cert verify options controlled by env vars and also hg.conf variables [abort|log|warn|none] for CGIs that use the cart. Default is log. Added basic info about the new httpsCertCheck setting to various documents. Added -httpsCertCheck=[abort|warn|none] command-line option to the hubCheck utility (#28332). Galt
• Added domain exceptions whitelist for allowing us to configure a small number of exceptions that are old servers that are still incompatible with openssl. hg.conf setting httpsCertCheckDomainExceptions or env var https_cert_check_domain_exceptions. This setting is not intended to be used for new servers which should just be advised on correct openssl compatibility, which usually means getting their server to output their intermediate certs as well, or even the cert chain which is typically just 3 certs (#28458). Galt
• Added 62 domains with cert issues to https.c domain exceptions whitelist. Also adding a special flag value httpsCertCheckDomainExceptions=noHardwiredExceptions which if present in the hg.conf exceptions list causes the hardwired whitelist in https.c to be ignored. Meanwhile other values in the hg.conf softwired list can be still used. This is very handy for testing purposes (#28458). Galt

Data changes:

• (New) Tabula sapiens track for hg38 (#28320). Jim
• (Update) Variants of Concern track on wuhCor1 now includes Omicron (#28579). Max, Angie
• (Update) Problematic sites track on wuhCor1 updated (#28490). Angie
• (Update) Added bird genome assemblies to VGP collection. Hiram
• (Update) Added bakers yeast SK1 assembly per user request (#28533). Hiram
• (Update) Added Ferret assembly GCF_011764305.1_ASM1176430v1.1 per D. Haussler request and SARS-CoV-2 community. Hiram
• Restored hg19 knownGene to antebellum condition from v422 (#24125). Brian
• Continued updates to hgPhyloPlace. Angie