File Changes for hiram

v485_preview2 to v485_base (2025-07-14 to 2025-07-21) v485

• src/hg/makeDb/doc/asmHubs/commonNames.py
  • lines changed 2, context: html, text, full: html, text
    a010260c82d5dc73f51bf6e97fe81a24bccd53e2 Sat Jul 19 15:59:50 2025 -0700
    do not need to prefix bacteria with the word "bacteria"
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 62, context: html, text, full: html, text
    2fd4a65a7038c1d266c1eaa68934f6c65e5e34d0 Tue Jul 15 12:38:48 2025 -0700
    RefSeq update adding a number of assemblies refs #29545
  • lines changed 1, context: html, text, full: html, text
    89922ed38bddbfe18b5059fef25367ab0788bd1c Wed Jul 16 19:39:41 2025 -0700
    adding one per user request refs #29545
  • lines changed 5223, context: html, text, full: html, text
    f19415b648e74cdb12d3cba860a82748f49b1018 Sun Jul 20 00:14:08 2025 -0700
    adding all "reference" sequences for RefSeq refs #29545
  • lines changed 1, context: html, text, full: html, text
    1ba5c3f59d5400dd0f46056d82dc33c11696f7e6 Mon Jul 21 12:09:45 2025 -0700
    Plasmodium malariae got on the wrong list moved from bacteria to invertebrate refs @29545
• src/hg/makeDb/doc/asmHubs/sciNameOverride.txt
  • lines changed 4, context: html, text, full: html, text
    f1365818b0bbaf5b2c8ab01b848b26eec33be087 Mon Jul 14 14:19:41 2025 -0700
    Per advice from Francoise, do not override taxId for Bos indicus Bost taurus cross no redmine
• src/hg/makeDb/doc/bacteriaAsmHub/bacteria.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    89922ed38bddbfe18b5059fef25367ab0788bd1c Wed Jul 16 19:39:41 2025 -0700
    adding one per user request refs #29545
  • lines changed 5310, context: html, text, full: html, text
    f19415b648e74cdb12d3cba860a82748f49b1018 Sun Jul 20 00:14:08 2025 -0700
    adding all "reference" sequences for RefSeq refs #29545
  • lines changed 1, context: html, text, full: html, text
    1ba5c3f59d5400dd0f46056d82dc33c11696f7e6 Mon Jul 21 12:09:45 2025 -0700
    Plasmodium malariae got on the wrong list moved from bacteria to invertebrate refs @29545
• src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv
  • lines changed 27, context: html, text, full: html, text
    2fd4a65a7038c1d266c1eaa68934f6c65e5e34d0 Tue Jul 15 12:38:48 2025 -0700
    RefSeq update adding a number of assemblies refs #29545
  • lines changed 1, context: html, text, full: html, text
    f19415b648e74cdb12d3cba860a82748f49b1018 Sun Jul 20 00:14:08 2025 -0700
    adding all "reference" sequences for RefSeq refs #29545
• src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv
  • lines changed 6, context: html, text, full: html, text
    2fd4a65a7038c1d266c1eaa68934f6c65e5e34d0 Tue Jul 15 12:38:48 2025 -0700
    RefSeq update adding a number of assemblies refs #29545
• src/hg/makeDb/doc/fungiAsmHub/fungi.orderList.tsv
  • lines changed 14, context: html, text, full: html, text
    2fd4a65a7038c1d266c1eaa68934f6c65e5e34d0 Tue Jul 15 12:38:48 2025 -0700
    RefSeq update adding a number of assemblies refs #29545
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
  • lines changed 15, context: html, text, full: html, text
    2fd4a65a7038c1d266c1eaa68934f6c65e5e34d0 Tue Jul 15 12:38:48 2025 -0700
    RefSeq update adding a number of assemblies refs #29545
  • lines changed 1, context: html, text, full: html, text
    1ba5c3f59d5400dd0f46056d82dc33c11696f7e6 Mon Jul 21 12:09:45 2025 -0700
    Plasmodium malariae got on the wrong list moved from bacteria to invertebrate refs @29545
• src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt
  • lines changed 2, context: html, text, full: html, text
    74b681671bc11e8cd7c4e5e582080ce28afc7e27 Tue Jul 15 12:44:33 2025 -0700
    RefSeq update adding a number of assemblies refs #29545
• src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    74b681671bc11e8cd7c4e5e582080ce28afc7e27 Tue Jul 15 12:44:33 2025 -0700
    RefSeq update adding a number of assemblies refs #29545
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 24, context: html, text, full: html, text
    2fd4a65a7038c1d266c1eaa68934f6c65e5e34d0 Tue Jul 15 12:38:48 2025 -0700
    RefSeq update adding a number of assemblies refs #29545
• src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv
  • lines changed 17, context: html, text, full: html, text
    2fd4a65a7038c1d266c1eaa68934f6c65e5e34d0 Tue Jul 15 12:38:48 2025 -0700
    RefSeq update adding a number of assemblies refs #29545
  • lines changed 2, context: html, text, full: html, text
    f19415b648e74cdb12d3cba860a82748f49b1018 Sun Jul 20 00:14:08 2025 -0700
    adding all "reference" sequences for RefSeq refs #29545
• src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv
  • lines changed 147, context: html, text, full: html, text
    2fd4a65a7038c1d266c1eaa68934f6c65e5e34d0 Tue Jul 15 12:38:48 2025 -0700
    RefSeq update adding a number of assemblies refs #29545
• src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv
  • lines changed 5, context: html, text, full: html, text
    2fd4a65a7038c1d266c1eaa68934f6c65e5e34d0 Tue Jul 15 12:38:48 2025 -0700
    RefSeq update adding a number of assemblies refs #29545
  • lines changed 4, context: html, text, full: html, text
    f19415b648e74cdb12d3cba860a82748f49b1018 Sun Jul 20 00:14:08 2025 -0700
    adding all "reference" sequences for RefSeq refs #29545
• src/hg/makeDb/doc/viralAsmHub/viral.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    f19415b648e74cdb12d3cba860a82748f49b1018 Sun Jul 20 00:14:08 2025 -0700
    adding all "reference" sequences for RefSeq refs #29545