Commits for hiram

v504_preview2 to v504_base (2026-09-14 to 2026-09-21) v504

a7c29f7591b74b35abfa8e3cafc2ad95fa5efcf2 Mon Sep 14 13:46:37 2026 -0700

• VGP additions refs #29545
  • src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv - lines changed 19, context: html, text, full: html, text
  • src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv - lines changed 7, context: html, text, full: html, text

773127a4d26eba2c59c1321044eb58624921373e Mon Sep 14 13:57:30 2026 -0700

• gcOnFly subtracks one counted track refs #29545
  • src/hg/makeDb/doc/asmHubs/verifyOnDownload.sh - lines changed 4, context: html, text, full: html, text

6c7924c5ec8a6511cbfd6895de5894579b228c4a Wed Sep 16 10:18:08 2026 -0700

• better names on the zebrafish assemblty GRCz12ab refs #38365
  • src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv - lines changed 2, context: html, text, full: html, text

6d7fcf6b8743d4b47014eaba4b156b63830bebcb Wed Sep 16 11:53:43 2026 -0700

• eliminate the duplicated dbDb hub genark assemblies and adjust static priorities refs #38365
  • src/hg/hubApi/assemblyList.py - lines changed 56, context: html, text, full: html, text

9bc69ab9197db8f1bfaa54682159c39ef366fb06 Wed Sep 16 16:15:22 2026 -0700

• VGP updates continued refs #29545
  • src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv - lines changed 11, context: html, text, full: html, text
  • src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv - lines changed 12, context: html, text, full: html, text
  • src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv - lines changed 5, context: html, text, full: html, text

3c7dea1af68a9671ba48c550be453845827e115d Wed Sep 16 16:44:17 2026 -0700

• gracefully manage bad response from login status refs #38365
  • src/hg/js/liftRequest.js - lines changed 40, context: html, text, full: html, text

08be525807ff3b3caf1233b9af15b010b950052b Wed Sep 16 16:53:43 2026 -0700

• gracefully manage bad response from api search requests refs #38365
  • src/hg/js/liftRequest.js - lines changed 13, context: html, text, full: html, text

92ba8f72d864456a8a026f52bf90b9e0560b5482 Thu Sep 17 09:33:04 2026 -0700

• provide access to the alpha.hub.txt versions for the group index pages on genome-test refs #35415
  • src/hg/makeDb/doc/asmHubs/asmHubs.mk - lines changed 1, context: html, text, full: html, text

dda07606495066058a431b1ec5924e6d829b9562 Thu Sep 17 11:59:59 2026 -0700

• otto script to detect recursive directory loops no redmine
  • src/hg/utils/otto/genArk/loopDetect.sh - lines changed 51, context: html, text, full: html, text

59737e5bedffc697d6f783c71b56ba711aac7deb Thu Sep 17 12:02:08 2026 -0700

• adding loopDetect.sh no redmine
  • src/hg/utils/otto/genArk/whatIsNew.sh - lines changed 7, context: html, text, full: html, text

2da75463c55d14a61c509128ba82733f39e0c784 Thu Sep 17 12:04:16 2026 -0700

• correctly detect count difference in dev,beta and hgw1 listings no redmine
  • src/hg/utils/otto/genArk/whatIsNew.sh - lines changed 2, context: html, text, full: html, text

1b6caec24e9f9acb5aa00306e6019787856a5b33 Thu Sep 17 12:17:08 2026 -0700

• special case genark hub attach when on hgwdev - use the alpha.hub.txt instead of the hub.txt refs #35415
  • src/hg/hgGateway/hgGateway.c - lines changed 17, context: html, text, full: html, text

0bd10926c28816bcae4e9949cc514899996f2e98 Thu Sep 17 13:09:12 2026 -0700

• corrected marmoset common name and fix errors found by claude in birds.orderList.tsv no redmine
  • src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv - lines changed 3, context: html, text, full: html, text

9efe3bfe8af965d5e183e05615bc337035d8b283 Fri Sep 18 13:45:24 2026 -0700

• consider NCBI refSeq "reference" status in the priorities and fix the error prone manual maintained topPriorities list refs #38365
  • src/hg/hubApi/assemblyList.py - lines changed 205, context: html, text, full: html, text

d362457564bc038b9ecf253a0e6ff1f86222e0fa Sat Sep 19 08:45:09 2026 -0700

• toolsets updated to fix memory leak in chainAntiRepeat refs #31811
  • src/hg/utils/automation/kegAlign.json.ga - lines changed 161, context: html, text, full: html, text

a0bd274a58c1772ff05b975dacbb9e30d910aa5b Sat Sep 19 09:49:23 2026 -0700

• upgrade a zebrafish GCA to GCF refs #38365
  • src/hg/hubApi/assemblyList.py - lines changed 1, context: html, text, full: html, text

52235246a8825164a1d74e753e839d7a392a84bb Sat Sep 19 10:13:31 2026 -0700

• VGP updates refs #29545
  • src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv - lines changed 3, context: html, text, full: html, text

32fbe1660c603d64e8210df9cc041ecb8feb3f38 Mon Sep 21 09:07:43 2026 -0700

• protect against a NULL cart from API search functions refs #38393
  • src/hg/cgilib/cartJson.c - lines changed 3, context: html, text, full: html, text