Commits for hiram

v459_preview to v459_preview2 (2023-12-18 to 2024-01-02) v459

aaf71829f6044d4d4fc9d3e9276326878ad16ef0 Mon Dec 18 12:27:44 2023 -0800

• adding two per user request GCA_002220415.3_Triticum_4.0 bread wheat and GCA_027939395.1_ASM2793939v1 human gammaherpesvirus 8 refs #29545
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/viralAsmHub/viral.orderList.tsv - lines changed 14, context: html, text, full: html, text

33deddb49d40819644e5de797cbc217b89b9dc9d Mon Dec 18 14:46:37 2023 -0800

• make the chromInfo table header remain visible during scrolling, much more convenient. no redmine
  • src/hg/hgTracks/hgTracks.c - lines changed 2, context: html, text, full: html, text

6941f6952496d6520dcba4bdb4e1898bb9190325 Wed Dec 20 09:02:31 2023 -0800

• the style border 1px loses the border lines between the columns no redemine
  • src/hg/makeDb/doc/asmHubs/mkAsmStats.pl - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/asmHubs/mkHubIndex.pl - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/asmHubs/trackData.pl - lines changed 1, context: html, text, full: html, text

53671a3d9ee162968ba83068a7771f0216b6a640 Wed Dec 20 15:17:54 2023 -0800

• adding one of the new assemblies for house mouse
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv - lines changed 2, context: html, text, full: html, text

2aa9aef96f234227b5020ff71ef3d8aad27f4fdb Thu Dec 21 11:54:30 2023 -0800

• rearrange 90-way sGroups into subPopulations and correct spelling of Vietnam refs #32285
  • src/hg/makeDb/trackDb/human/hg38/hprcChainNet.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/trackDb.hprc90way.ra - lines changed 15, context: html, text, full: html, text

bfe25cef4aaec5d42f2c4ce71897b70011e0ea42 Thu Dec 21 12:01:22 2023 -0800

• adding new sGroup_ definitions for HPRC 90-way groups refs #32285
  • src/hg/makeDb/trackDb/tagTypes.tab - lines changed 14, context: html, text, full: html, text

04386d851146a423a65dfde5fb2c141bf48e08f0 Thu Dec 21 14:22:16 2023 -0800

• there is no phyloP track for this alignment refs #32285
  • src/hg/makeDb/trackDb/human/hg38/trackDb.hprc90way.ra - lines changed 31, context: html, text, full: html, text

4c928d18e8664613560f90cc593a76127edf40de Fri Dec 22 13:31:58 2023 -0800

• update to bring in new mouse strain assemblies refs #29545
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 18, context: html, text, full: html, text
  • src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv - lines changed 15, 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 1, context: html, text, full: html, text

bb1cac0fc3afcb9446ca0b6b877e8856c748648c Fri Dec 22 14:05:34 2023 -0800

• GCA_001624675.1_NOD_ShiLtJ_v1 has moved to legacy refs #29545
  • src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv - lines changed 1, context: html, text, full: html, text

24f9b3dcfeb38241531404d1ae549c58848ed0f1 Fri Dec 22 14:42:03 2023 -0800

• add Ehrlichia chaffeensis str. (Arkansas 2006) bacteria per user request refs #29545
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/bacteriaAsmHub/bacteria.orderList.tsv - lines changed 1, context: html, text, full: html, text

9b374bee5ec4240f3e95f1cf6167230682fa5940 Fri Dec 22 21:34:59 2023 -0800

• accomodate previous versions of ensGene track no redmine
  • src/hg/utils/automation/asmHubTrackDb.sh - lines changed 19, context: html, text, full: html, text

46776f7940c88ca220483c69dd6a9389c6f529e4 Tue Dec 26 10:53:18 2023 -0800

• update to bring in the two new HG002 assemblies GCA_018852605.2_ASM1885260v2 and GCA_018852615.2_ASM1885261v2 refs #29545
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv - lines changed 4, context: html, text, full: html, text

dd3c511964c88b9d5873890c7b661d6af8d52044 Tue Dec 26 12:09:21 2023 -0800

• correct clade for GCA_018852605.1_HG002.alt.pat.f1_v2 refs #29545
  • src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)

cc4c6b10e07399a96a261bd5912e1a96bf432011 Wed Dec 27 09:48:37 2023 -0800

• update VGP listings refs #29545
  • src/hg/makeDb/doc/vgpAsmHub/vgp.legacy.orderList.tsv - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/vgpAsmHub/vgp.primary.orderList.tsv - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/doc/vgpAsmHub/vgp.taxId.asmId.class.txt - lines changed 4, context: html, text, full: html, text

436b3823058d69b5f9437933718f7b461d37e7e2 Wed Dec 27 11:25:59 2023 -0800

• needs an install rule refs #32821
  • src/hg/utils/hubCheck/makefile - lines changed 7, context: html, text, full: html, text

035d05236c501fde6032a288aba49bbc1423614a Wed Dec 27 17:12:22 2023 -0800

• VGP update refs #29545
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv - lines changed 3, context: html, text, full: html, text

968cb710e3fb2ba7e3697161aae71112666f063c Wed Dec 27 18:18:17 2023 -0800

• VGP update before primary alternate rearragement refs #29545
  • src/hg/makeDb/doc/vgpAsmHub/vgp.legacy.orderList.tsv - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/vgpAsmHub/vgp.primary.orderList.tsv - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/doc/vgpAsmHub/vgp.taxId.asmId.class.txt - lines changed 10, context: html, text, full: html, text

962ed173ca9633aa00aeb8b19a6a8f3d51397b76 Wed Dec 27 18:34:29 2023 -0800

• move GCA_004365275.1_TupTan_v1_BIUU to legacy refs #29545
  • src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv - lines changed 1, context: html, text, full: html, text

75ec54ad980f7e19a154aa28252485f5b28ac8c2 Wed Dec 27 19:40:17 2023 -0800

• adding 41 VGP assemblies refs #29545
  • src/hg/makeDb/doc/vgpAsmHub/vgp.primary.orderList.tsv - lines changed 132, context: html, text, full: html, text
  • src/hg/makeDb/doc/vgpAsmHub/vgp.taxId.asmId.class.txt - lines changed 47, context: html, text, full: html, text

2b8abc091c74e7db658b36d307fc822e7cf0037d Thu Dec 28 10:11:44 2023 -0800

• bring the VGP alternates up to date refs #29545
  • src/hg/makeDb/doc/vgpAsmHub/vgp.alternate.orderList.tsv - lines changed 66, context: html, text, full: html, text
  • src/hg/makeDb/doc/vgpAsmHub/vgp.taxId.asmId.class.txt - lines changed 16, context: html, text, full: html, text

40e734def00da5af71758c6fca89faf781ca8cca Thu Dec 28 11:41:22 2023 -0800

• reset alternates to primaries and primaries to alternates per Erich's list refs #29545
  • src/hg/makeDb/doc/vgpAsmHub/vgp.alternate.orderList.tsv - lines changed 27, context: html, text, full: html, text
  • src/hg/makeDb/doc/vgpAsmHub/vgp.primary.orderList.tsv - lines changed 27, context: html, text, full: html, text