Commits for galt

v490_base to v491_preview (2025-11-03 to 2025-11-10) v491

e112c27b7a39c6fd9def5b24ed5015087d057778 Mon Nov 3 16:27:05 2025 -0800

• oops, I accidentally checked in these files, must have missed a -u with git add command so it added everything in the directory. no redmine.
  • src/hg/utils/hubCheck/fooy - lines changed 3331, context: html, text, full: html, text
  • src/hg/utils/hubCheck/fuck - lines changed 152, context: html, text, full: html, text
  • src/hg/utils/hubCheck/hubCheck.c.debugBadFEFFCharsInHubtxtDropBox - lines changed 1326, context: html, text, full: html, text
  • src/hg/utils/hubCheck/hubCheck.c.debugWhyAreSomeSitesSlow - lines changed 1232, context: html, text, full: html, text
  • src/hg/utils/hubCheck/hubCheck.c.rejectedLogLevelAsNotUseful - lines changed 1213, context: html, text, full: html, text
  • src/hg/utils/hubCheck/tracks.tmp - lines changed 26, context: html, text, full: html, text

8f820e5ebdba131bb8dceef34227f326dc892428 Mon Nov 3 23:15:00 2025 -0800

• oops one more unwanted checkin example2.bb.
  • src/hg/utils/hubCheck/example2.bb - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)

f07f43476ae7ac72bdbd83603c63191bb699104a Tue Nov 4 12:05:12 2025 -0800

• Allows local curated genomes by checking for /gbdb/$db. Does not allow those local bigDataUrl directories to be used for custom tracks. Allows those hub URLs with local paths to be loaded in the background for better speed. Allows for vcfTabix etc to work with hs1. Removes need for udc.localDir setting in hg.conf for hgwdev, hgwbeta, RR, and mirrors. Warning do not set udc.localDir= to an empty string since it is completely permissive suffix matches all URLs. fixes #rm34544
  • src/hg/hgTracks/hgTracks.c - lines changed 2, context: html, text, full: html, text
  • src/hg/inc/customFactory.h - lines changed 2, context: html, text, full: html, text
  • src/hg/lib/customFactory.c - lines changed 30, context: html, text, full: html, text

c462aa3843e20d6e149121fd630bb5f8d8023921 Wed Nov 5 17:19:14 2025 -0800

• Need to have customTrack.c clear out this cart variable so it does not hang around and cause problems later. It was causing new autogenerated blat custom tracks to disappear after using hgTrackUi track and submittting. fixes #36660
  • src/hg/lib/customTrack.c - lines changed 2, context: html, text, full: html, text