File Changes for hiram

v461_base to v462_preview (2024-02-19 to 2024-02-26) v462

• src/hg/makeDb/doc/asmHubs/master.run.list
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    ceb56b8ba253193567799661e5bad75c3eb17a3b Tue Feb 20 12:00:26 2024 -0800
    VGP update refs #29545
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    a1f4bdfbe157e1ffa563cb1c17277a8e0f64608a Wed Feb 21 07:55:55 2024 -0800
    continue VGP catch up adding a fish refs #29545
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    1581f886886465a884855e23d36e7ba86b1053e7 Thu Feb 22 11:42:58 2024 -0800
    VGP update adding a refseq replacement for GCA_028389875.1_bPtePen1.pri lesser rhea (bPtePen1 primary hap 2023) refs #29545
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    6a5231ee061fec8de66664cb9194bd4a7f958beb Mon Feb 26 09:29:26 2024 -0800
    catch up VGP assemblies refs #29545
• src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv
  • lines changed 7, context: html, text, full: html, text
    ceb56b8ba253193567799661e5bad75c3eb17a3b Tue Feb 20 12:00:26 2024 -0800
    VGP update refs #29545
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    1581f886886465a884855e23d36e7ba86b1053e7 Thu Feb 22 11:42:58 2024 -0800
    VGP update adding a refseq replacement for GCA_028389875.1_bPtePen1.pri lesser rhea (bPtePen1 primary hap 2023) refs #29545
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    6a5231ee061fec8de66664cb9194bd4a7f958beb Mon Feb 26 09:29:26 2024 -0800
    catch up VGP assemblies refs #29545
• src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    ceb56b8ba253193567799661e5bad75c3eb17a3b Tue Feb 20 12:00:26 2024 -0800
    VGP update refs #29545
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    a1f4bdfbe157e1ffa563cb1c17277a8e0f64608a Wed Feb 21 07:55:55 2024 -0800
    continue VGP catch up adding a fish refs #29545
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
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    6a5231ee061fec8de66664cb9194bd4a7f958beb Mon Feb 26 09:29:26 2024 -0800
    catch up VGP assemblies refs #29545
• src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt
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    8fff54bd94620692c33ca61a765e6c0b6b5f7e2e Mon Feb 19 14:36:52 2024 -0800
    GCA_036323735.1_GRCr8 is now legacy refs #29545
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    db16a92829de8572ec6851100d0c36cbff4b679c Wed Feb 21 13:19:08 2024 -0800
    lesser rhea bird became refseq refs #29545
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    6a5231ee061fec8de66664cb9194bd4a7f958beb Mon Feb 26 09:29:26 2024 -0800
    catch up VGP assemblies refs #29545
• src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    db16a92829de8572ec6851100d0c36cbff4b679c Wed Feb 21 13:19:08 2024 -0800
    lesser rhea bird became refseq refs #29545
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    6a5231ee061fec8de66664cb9194bd4a7f958beb Mon Feb 26 09:29:26 2024 -0800
    catch up VGP assemblies refs #29545
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    ceb56b8ba253193567799661e5bad75c3eb17a3b Tue Feb 20 12:00:26 2024 -0800
    VGP update refs #29545
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    6a5231ee061fec8de66664cb9194bd4a7f958beb Mon Feb 26 09:29:26 2024 -0800
    catch up VGP assemblies refs #29545
• src/hg/makeDb/doc/mm39/chrM.ncbiRefSeq.txt
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    8cf5d04b02f2bacf4fb496891d9cfc3cd99e8df8 Tue Feb 20 10:33:36 2024 -0800
    recover from otto update refs #32902
• src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv
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    bed61f703ece9dceb41a80e602672b1a46cd4dba Tue Feb 20 13:42:26 2024 -0800
    recover a broken assembly refs #29545
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    6a5231ee061fec8de66664cb9194bd4a7f958beb Mon Feb 26 09:29:26 2024 -0800
    catch up VGP assemblies refs #29545
• src/hg/makeDb/doc/vgpAsmHub/vgp.primary.orderList.tsv
  • lines changed 42, context: html, text, full: html, text
    b7834b8f15822ed19ccfd6fb1ac210dd80ac6938 Mon Feb 19 15:38:21 2024 -0800
    update adding about 40 assemblies no redmine
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    907878c0e305c60aa4c3aa34716bf4bcbf3ba1a3 Tue Feb 20 14:18:17 2024 -0800
    catching up 9 assemblies refs #29545
• src/hg/makeDb/doc/vgpAsmHub/vgp.taxId.asmId.class.txt
  • lines changed 4, context: html, text, full: html, text
    79742b17c9cf66a054d07369d0141836ce2752fb Mon Feb 19 15:08:20 2024 -0800
    catching up four assemblies no redmine
  • lines changed 42, context: html, text, full: html, text
    b7834b8f15822ed19ccfd6fb1ac210dd80ac6938 Mon Feb 19 15:38:21 2024 -0800
    update adding about 40 assemblies no redmine
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    907878c0e305c60aa4c3aa34716bf4bcbf3ba1a3 Tue Feb 20 14:18:17 2024 -0800
    catching up 9 assemblies refs #29545
• src/hg/utils/makefile
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    00d972032daa3a173a3142bb4f7923f259caf312 Wed Feb 21 11:56:22 2024 -0800
    add bigChainToChain to userApps build no redmine