All File Changes

v485_preview to v485_preview2 (2025-07-07 to 2025-07-14) v485

• confs/asia.hg.conf
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    aadf58f610aec3ed523daff5909e2b11de1007cc Sun Jul 13 01:11:17 2025 -0700
    Installing updated hg.conf files from UCSC servers
• confs/euro.hg.conf
  • lines changed 10, context: html, text, full: html, text
    aadf58f610aec3ed523daff5909e2b11de1007cc Sun Jul 13 01:11:17 2025 -0700
    Installing updated hg.conf files from UCSC servers
• confs/hgwdev.hg.conf
  • lines changed 1, context: html, text, full: html, text
    aadf58f610aec3ed523daff5909e2b11de1007cc Sun Jul 13 01:11:17 2025 -0700
    Installing updated hg.conf files from UCSC servers
• confs/rr.hg.conf
  • lines changed 10, context: html, text, full: html, text
    aadf58f610aec3ed523daff5909e2b11de1007cc Sun Jul 13 01:11:17 2025 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/hgConvert/hgConvert.c
  • lines changed 4, context: html, text, full: html, text
    ae09c0590da3e36fdf30c30fcec71c6aa3374663 Tue Jul 8 16:32:42 2025 -0700
    fix bugs in quickLift refs #35609
• src/hg/hgGene/rnaStructure.c
  • lines changed 8, context: html, text, full: html, text
    ae09c0590da3e36fdf30c30fcec71c6aa3374663 Tue Jul 8 16:32:42 2025 -0700
    fix bugs in quickLift refs #35609
• src/hg/hgTracks/bedTrack.c
  • lines changed 1, context: html, text, full: html, text
    f577b4c8199360dac5b955dfc4ede99d57c2946f Wed Jul 9 16:57:59 2025 -0700
    ongoing work on quickLift, including displaying mismatches
• src/hg/hgTracks/imageV2.c
  • lines changed 15, context: html, text, full: html, text
    ae09c0590da3e36fdf30c30fcec71c6aa3374663 Tue Jul 8 16:32:42 2025 -0700
    fix bugs in quickLift refs #35609
• src/hg/hgTracks/quickLift.c
  • lines changed 75, context: html, text, full: html, text
    f577b4c8199360dac5b955dfc4ede99d57c2946f Wed Jul 9 16:57:59 2025 -0700
    ongoing work on quickLift, including displaying mismatches
  • lines changed 2, context: html, text, full: html, text
    7e309c4dfe387978e9abdddeca1b52a015091572 Wed Jul 9 17:46:54 2025 -0700
    oops.. remove unused variables
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    1a436460e21282899ff825bab22f137123564e68 Wed Jul 9 18:08:06 2025 -0700
    a fix for quickLift mismatches on the negative strand
• src/hg/hgTracks/simpleTracks.c
  • lines changed 10, context: html, text, full: html, text
    a36c9987016c287c78be72b3087a0b42ae875112 Wed Jul 9 12:15:27 2025 -0700
    Updating bigMethyl mouseOver, refs #33504
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    f577b4c8199360dac5b955dfc4ede99d57c2946f Wed Jul 9 16:57:59 2025 -0700
    ongoing work on quickLift, including displaying mismatches
• src/hg/hgc/hgc.c
  • lines changed 1, context: html, text, full: html, text
    ae09c0590da3e36fdf30c30fcec71c6aa3374663 Tue Jul 8 16:32:42 2025 -0700
    fix bugs in quickLift refs #35609
• src/hg/htdocs/FAQ/FAQformat.html
  • lines changed 1, context: html, text, full: html, text
    2bc4d4c29bb6270454b0945bb475f1b78bea0e08 Thu Jul 10 15:43:34 2025 -0700
    some boiler plate for bedMethyl doc
• src/hg/htdocs/goldenPath/help/api.html
  • lines changed 1, context: html, text, full: html, text
    9a051963c7dc7cafea316417701cae4570aff029 Sun Jul 13 13:07:07 2025 -0700
    templates for bedMethyl and bigMethyl
• src/hg/htdocs/goldenPath/help/bedMethyl.html
  • lines changed 13, context: html, text, full: html, text
    2bc4d4c29bb6270454b0945bb475f1b78bea0e08 Thu Jul 10 15:43:34 2025 -0700
    some boiler plate for bedMethyl doc
  • lines changed 32, context: html, text, full: html, text
    9a051963c7dc7cafea316417701cae4570aff029 Sun Jul 13 13:07:07 2025 -0700
    templates for bedMethyl and bigMethyl
• src/hg/htdocs/goldenPath/help/bigMethyl.html
  • lines changed 81, context: html, text, full: html, text
    94c8445567840aa5b08fd090a7f51508bd15b89f Sun Jul 13 12:18:03 2025 -0700
    adding bigMethyl.html so it will install
  • lines changed 42, context: html, text, full: html, text
    9a051963c7dc7cafea316417701cae4570aff029 Sun Jul 13 13:07:07 2025 -0700
    templates for bedMethyl and bigMethyl
• src/hg/htdocs/goldenPath/help/customTrackText.html
  • lines changed 11, context: html, text, full: html, text
    2bc4d4c29bb6270454b0945bb475f1b78bea0e08 Thu Jul 10 15:43:34 2025 -0700
    some boiler plate for bedMethyl doc
  • lines changed 3, context: html, text, full: html, text
    9a051963c7dc7cafea316417701cae4570aff029 Sun Jul 13 13:07:07 2025 -0700
    templates for bedMethyl and bigMethyl
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 9, context: html, text, full: html, text
    9a051963c7dc7cafea316417701cae4570aff029 Sun Jul 13 13:07:07 2025 -0700
    templates for bedMethyl and bigMethyl
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 16, context: html, text, full: html, text
    9a051963c7dc7cafea316417701cae4570aff029 Sun Jul 13 13:07:07 2025 -0700
    templates for bedMethyl and bigMethyl
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 30, context: html, text, full: html, text
    2f270790e0c543b935be5159bf78c1209a5469bd Mon Jul 7 14:27:44 2025 -0700
    Announcing 25 year anniversary, refs #35980
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    8a54e2bef64ddd7eab88d9e4a73b4fb7e331358c Mon Jul 7 14:29:09 2025 -0700
    Small tweak to be more correct, refs #35980
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    e9e65457cccbb63368ae37dd7bebf88921322f2c Wed Jul 9 15:59:35 2025 -0700
    Announcing the Unusually conserved regions track for hg38, refs #35703
• src/hg/htdocs/images/ucscGenomeBrowser2003Database.png
  • lines changed 0, context: html, text, full: html, text
    2f270790e0c543b935be5159bf78c1209a5469bd Mon Jul 7 14:27:44 2025 -0700
    Announcing 25 year anniversary, refs #35980
• src/hg/htdocs/indexMeetings.html
  • lines changed 27, context: html, text, full: html, text
    728ca2baa55ce625bf92f99cad76dbc3aceab839 Wed Jul 9 17:17:12 2025 -0700
    Removing past meetings.
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    2f270790e0c543b935be5159bf78c1209a5469bd Mon Jul 7 14:27:44 2025 -0700
    Announcing 25 year anniversary, refs #35980
  • lines changed 12, context: html, text, full: html, text
    e9e65457cccbb63368ae37dd7bebf88921322f2c Wed Jul 9 15:59:35 2025 -0700
    Announcing the Unusually conserved regions track for hg38, refs #35703
• src/hg/htdocs/style/HGStyle.css
  • lines changed 1, context: html, text, full: html, text
    ae09c0590da3e36fdf30c30fcec71c6aa3374663 Tue Jul 8 16:32:42 2025 -0700
    fix bugs in quickLift refs #35609
• src/hg/lib/cart.c
  • lines changed 17, context: html, text, full: html, text
    f95037b8f6bb5cad8f0cbd16067e4ebc8cdecaf9 Mon Jul 14 12:00:52 2025 -0700
    fixing captcha problem, refs #36057
  • lines changed 4, context: html, text, full: html, text
    094f9edadee0dd672aa86803ccb559acd45af58e Mon Jul 14 12:18:56 2025 -0700
    supressing captcha on hgRenderTracks, refs #36077
• src/hg/lib/hubConnect.c
  • lines changed 6, context: html, text, full: html, text
    ae09c0590da3e36fdf30c30fcec71c6aa3374663 Tue Jul 8 16:32:42 2025 -0700
    fix bugs in quickLift refs #35609
  • lines changed 13, context: html, text, full: html, text
    f577b4c8199360dac5b955dfc4ede99d57c2946f Wed Jul 9 16:57:59 2025 -0700
    ongoing work on quickLift, including displaying mismatches
• src/hg/lib/trackHub.c
  • lines changed 3, context: html, text, full: html, text
    ae09c0590da3e36fdf30c30fcec71c6aa3374663 Tue Jul 8 16:32:42 2025 -0700
    fix bugs in quickLift refs #35609
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 2, context: html, text, full: html, text
    cdafac821e20bbd8258e0184345859afabd8a01e Tue Jul 8 17:32:28 2025 -0700
    added a couple per user request refs #29545
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    d8d88a23df90e51d5867456a4ba8b78fedeec011 Tue Jul 8 22:21:00 2025 -0700
    adding a couple per user request refs #29545
• src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    d8d88a23df90e51d5867456a4ba8b78fedeec011 Tue Jul 8 22:21:00 2025 -0700
    adding a couple per user request refs #29545
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    cdafac821e20bbd8258e0184345859afabd8a01e Tue Jul 8 17:32:28 2025 -0700
    added a couple per user request refs #29545
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    d8d88a23df90e51d5867456a4ba8b78fedeec011 Tue Jul 8 22:21:00 2025 -0700
    adding a couple per user request refs #29545
• src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    cdafac821e20bbd8258e0184345859afabd8a01e Tue Jul 8 17:32:28 2025 -0700
    added a couple per user request refs #29545
• src/hg/makeDb/trackDb/human/hg19/gencodePfam.html
  • lines changed 69, context: html, text, full: html, text
    306e80a01217beb1baf7bc65a59cf3c70cabf334 Wed Jul 9 18:08:43 2025 -0700
    Updating track to reflect that it is now built from GENCODE, not UCSC Genes, refs #25918
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 5, context: html, text, full: html, text
    306e80a01217beb1baf7bc65a59cf3c70cabf334 Wed Jul 9 18:08:43 2025 -0700
    Updating track to reflect that it is now built from GENCODE, not UCSC Genes, refs #25918
• src/hg/makeDb/trackDb/human/hg38/unusualcons.ra
  • lines changed 1, context: html, text, full: html, text
    e9e65457cccbb63368ae37dd7bebf88921322f2c Wed Jul 9 15:59:35 2025 -0700
    Announcing the Unusually conserved regions track for hg38, refs #35703
• src/hg/makeDb/trackDb/mouse/mm10/gencodePfam.html
  • lines changed 69, context: html, text, full: html, text
    306e80a01217beb1baf7bc65a59cf3c70cabf334 Wed Jul 9 18:08:43 2025 -0700
    Updating track to reflect that it is now built from GENCODE, not UCSC Genes, refs #25918
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
  • lines changed 5, context: html, text, full: html, text
    306e80a01217beb1baf7bc65a59cf3c70cabf334 Wed Jul 9 18:08:43 2025 -0700
    Updating track to reflect that it is now built from GENCODE, not UCSC Genes, refs #25918
• src/hg/makeDb/trackDb/mouse/mm39/gencodePfam.html
  • lines changed 69, context: html, text, full: html, text
    306e80a01217beb1baf7bc65a59cf3c70cabf334 Wed Jul 9 18:08:43 2025 -0700
    Updating track to reflect that it is now built from GENCODE, not UCSC Genes, refs #25918
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.ra
  • lines changed 5, context: html, text, full: html, text
    306e80a01217beb1baf7bc65a59cf3c70cabf334 Wed Jul 9 18:08:43 2025 -0700
    Updating track to reflect that it is now built from GENCODE, not UCSC Genes, refs #25918
• src/utils/qa/weeklybld/buildEnv.csh
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    59d416d9454418fc77cf501adf583d8681d00e06 Mon Jul 14 12:47:43 2025 -0700
    v485 preview2, refs #36036

• lines changed: 810
• files changed: 51