Commits for hiram

v475_preview2 to v475_base (2024-12-02 to 2024-12-09) v475

d8fa0018fbf6e18abb5e9ba03ef6421fbf5a5693 Mon Dec 2 11:57:34 2024 -0800

• RefSeq update refs #29545
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 38, context: html, text, full: html, text
  • src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/doc/fungiAsmHub/fungi.orderList.tsv - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv - lines changed 12, 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/primatesAsmHub/primates.orderList.tsv - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv - lines changed 4, context: html, text, full: html, text

9c2fdb7758fc65cddfe5db8901ed17295aa6bed1 Tue Dec 3 14:08:47 2024 -0800

• NCBI changing assembly name refs #34370
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv - lines changed 1, context: html, text, full: html, text

f6bb6e1854621da0de056c064007c12381326d13 Wed Dec 4 08:29:59 2024 -0800

• turn of debug flag for release refs #32596
  • src/hg/js/assemblySearch.js - lines changed 1, context: html, text, full: html, text

d3853cf1ab1559c73f28a8bf220aac601c16c015 Wed Dec 4 13:55:17 2024 -0800

• when search matches a dbDb name from the genArk table get that result into the dbDb list for selection refs #34862
  • src/hg/hgGateway/hgGateway.c - lines changed 46, context: html, text, full: html, text

daaa29dc6598c41b9943fe3fdca994ef03186a5c Wed Dec 4 14:43:44 2024 -0800

• special rule to make the jsonData for VGP refs #34370
  • src/hg/makeDb/doc/asmHubs/asmHubs.mk - lines changed 5, context: html, text, full: html, text

8b758f1e95366bca0ee3ad1c0b5584c16647b793 Wed Dec 4 14:46:28 2024 -0800

• update to 2024-11-26 version refs #34370
  • src/hg/makeDb/doc/vgpAsmHub/vgp.alternate.orderList.tsv - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/doc/vgpAsmHub/vgp.legacy.orderList.tsv - lines changed 15, context: html, text, full: html, text
  • src/hg/makeDb/doc/vgpAsmHub/vgp.primary.orderList.tsv - lines changed 34, context: html, text, full: html, text
  • src/hg/makeDb/doc/vgpAsmHub/vgp.taxId.asmId.class.txt - lines changed 18, context: html, text, full: html, text

e835cfc40dd1a513deb18042880fa0f6065ae422 Wed Dec 4 15:47:51 2024 -0800

• moving legacy assemblies to correct list refs #34370
  • src/hg/makeDb/doc/vgpAsmHub/vgp.legacy.orderList.tsv - lines changed 46, context: html, text, full: html, text
  • src/hg/makeDb/doc/vgpAsmHub/vgp.primary.orderList.tsv - lines changed 75, context: html, text, full: html, text

34e16a8f5ab2d54f1f49eb488a3bdc4951ba14b5 Thu Dec 5 14:06:59 2024 -0800

• adding a few per user request refs #29545
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/doc/fungiAsmHub/fungi.orderList.tsv - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv - lines changed 2, context: html, text, full: html, text

a8364911e404223901ff4cfb4e8f3f56a0e8552c Fri Dec 6 11:40:39 2024 -0800

• coordinating common names (really should be a separate unique list) refs #34370
  • src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv - lines changed 89, context: html, text, full: html, text
  • src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv - lines changed 56, context: html, text, full: html, text
  • src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv - lines changed 105, context: html, text, full: html, text
  • src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv - lines changed 29, context: html, text, full: html, text
  • src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv - lines changed 29, context: html, text, full: html, text

65a6374199c998a2303c455630bb45add3dd3147 Fri Dec 6 12:18:15 2024 -0800

• update per BRC request refs #34337
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/doc/bacteriaAsmHub/bacteria.orderList.tsv - lines changed 3, context: html, text, full: html, text

63b8ad4bd3b2ec680ea619ef7dd803019cafaed7 Fri Dec 6 12:22:40 2024 -0800

• update per BRC request refs #34337
  • src/hg/makeDb/doc/brcAsmHub/brc.orderList.tsv - lines changed 4, context: html, text, full: html, text

9ba1f19df30d17211ebd94e05d6feb398ebc56a9 Mon Dec 9 09:33:28 2024 -0800

• updated per comments from QA refs #32596
  • src/hg/htdocs/assemblySearch.html - lines changed 10, context: html, text, full: html, text
  • src/hg/js/assemblySearch.js - lines changed 17, context: html, text, full: html, text