Commits for hiram

v489_preview2 to v489_base (2025-10-06 to 2025-10-13) v489

7fbaf4ec666799c553411e1a8c5ae1edeeafa9ba Wed Oct 8 09:08:13 2025 -0700

• RefSeq update and user requests refs #29545
  • src/hg/makeDb/doc/archaeaAsmHub/archaea.orderList.tsv - lines changed 22, context: html, text, full: html, text
  • src/hg/makeDb/doc/bacteriaAsmHub/bacteria.orderList.tsv - lines changed 90, context: html, text, full: html, text
  • src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/doc/viralAsmHub/viral.orderList.tsv - lines changed 16, context: html, text, full: html, text

1246c62aed3a510683ecb63c27e11ff1fe623140 Wed Oct 8 13:49:50 2025 -0700

• some archaea have slipped to 9 tracks refs #29545
  • src/hg/makeDb/doc/asmHubs/verifyOnDownload.sh - lines changed 1, context: html, text, full: html, text

89a11d909c69766605ea99e1fa2d7e55e2ed6429 Wed Oct 8 16:10:33 2025 -0700

• adding the listing of /gbdb/database/quickLift files refs #34917
  • src/hg/utils/otto/genArk/devList.sh - lines changed 15, context: html, text, full: html, text

96ca3838eddeed315b292153e9c00a176ee3481f Wed Oct 8 16:14:43 2025 -0700

• cron script running on RR machines to make file comparisons for pushing refs #34917
  • src/hg/utils/otto/genArk/gbDbGenArkList.sh - lines changed 31, context: html, text, full: html, text

7176aa3eb099704a9b1372bdc27930f172567d13 Wed Oct 8 16:22:01 2025 -0700

• adding the listing of /gbdb/database/quickLift files refs #34917
  • src/hg/utils/otto/genArk/gbDbGenArkList.sh - lines changed 18, context: html, text, full: html, text

0b85dd107323ffc1151a8162a845a0ae37e389d8 Thu Oct 9 11:46:25 2025 -0700

• remove stray g character that upset a file name refs #34917
  • src/hg/utils/otto/genArk/gbDbGenArkList.sh - lines changed 1, context: html, text, full: html, text

36af765196a9d28d87fa6b67045f9fc30dee13bd Fri Oct 10 15:24:36 2025 -0700

• correctly identify haplotype for stray HPRC assemblies refs #35415
  • src/hg/makeDb/doc/hprcAsmHub/hprc.orderList.tsv - lines changed 20, context: html, text, full: html, text
  • src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv - lines changed 20, context: html, text, full: html, text

076b4ef96b9fc40127c3577cb030585709bf5715 Mon Oct 13 11:10:43 2025 -0700

• adding hprcV2 type of alias refs #36461
  • src/hg/utils/automation/aliasTextToBed.pl - lines changed 1, context: html, text, full: html, text

26db090072511b54c477fb9824d24aaeae349a13 Mon Oct 13 12:38:56 2025 -0700

• document chromAlias procedure refs #36461
  • src/hg/makeDb/doc/asmHubs/README.chromAlias.txt - lines changed 82, context: html, text, full: html, text

e69d556b5fda919a0e8e2e31d18d01c8e20d57ba Mon Oct 13 12:39:36 2025 -0700

• document chromAlias procedure refs #36461
  • src/hg/makeDb/doc/asmHubs/README.chromAlias.txt - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)