Commits for hiram

v503_base to v504_preview (2026-08-31 to 2026-09-07) v504

6e9cae86505025606c69d9f06ca08a1426f6eed9 Mon Aug 31 16:52:26 2026 -0700

• VGP update refs @29545
  • src/hg/makeDb/doc/archaeaAsmHub/archaea.orderList.tsv - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv - lines changed 80, context: html, text, full: html, text
  • src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv - lines changed 215, context: html, text, full: html, text
  • src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv - lines changed 54, context: html, text, full: html, text
  • src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv - lines changed 79, context: html, text, full: html, text

bd5952e27a963cccacf526649b5be02b9049e8e0 Tue Sep 1 12:43:00 2026 -0700

• testing the RCPediaVGP_v1 contrib tracks refs #38223
  • src/hg/makeDb/trackDb/betaGenArk.txt - lines changed 1, context: html, text, full: html, text

1ba03723b75a8d501529931b7e80b27ece5c34b1 Tue Sep 1 12:59:41 2026 -0700

• remove the obsolete gcOnTheFlyCoExist flag and hg.conf variable refs #38208
  • src/hg/hgTracks/hgTracks.c - lines changed 7, context: html, text, full: html, text

67731d2ba246fec0ba68843228e1fe7d18afd64c Tue Sep 1 13:35:40 2026 -0700

• enable the gcOnFly track for the GenArk hubs refs #35958
  • src/hg/utils/automation/asmHubGc5Percent.pl - lines changed 20, context: html, text, full: html, text
  • src/hg/utils/automation/asmHubTrackDb.sh - lines changed 37, context: html, text, full: html, text

583e765f8a3035ac100f0e841f29ec8d79fb3633 Wed Sep 2 08:37:53 2026 -0700

• correct bigDataUrl for the gcOnFly.bw file error found by claude review refs #35958
  • src/hg/utils/automation/asmHubTrackDb.sh - lines changed 1, context: html, text, full: html, text

9f4f893d208b9f082b1e64dc4932e8df8afbcb5a Wed Sep 2 08:53:55 2026 -0700

• html and trackDb for RCPediaVGP_v1 contrib tracks refs #38224
  • src/hg/makeDb/trackDb/contrib/RCPediaVGP_v1/RCPediaVGP_v1.html - lines changed 67, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/contrib/RCPediaVGP_v1/RCPediaVGP_v1.trackDb.txt - lines changed 8, context: html, text, full: html, text

cd363560ba2735155c189ac52f636b66d5a3c469 Wed Sep 2 12:16:21 2026 -0700

• correctly use the new indexes on the assemblyList table - this was improved in June but the code here did not match the new indexes - will now be a few ms search on accession names instead of 10s of seconds - no redmine
  • src/hg/hubApi/findGenome.c - lines changed 69, context: html, text, full: html, text

7a185fecc55ea44b360f04d250e64bcbaaf4d53e Wed Sep 2 13:45:33 2026 -0700

• remove references and functions related to the "debug" argument, becomes a harmless no-operation and eliminated potential security loop-holes no redmine
  • src/hg/hubApi/apiUtils.c - lines changed 11, context: html, text, full: html, text
  • src/hg/hubApi/getData.c - lines changed 26, context: html, text, full: html, text
  • src/hg/hubApi/hubApi.c - lines changed 89, context: html, text, full: html, text
  • src/hg/hubApi/list.c - lines changed 1, context: html, text, full: html, text