All File Changes

v490_preview to v490_preview2 (2025-10-20 to 2025-10-27) v490

• confs/asia.hg.conf
  • lines changed 1, context: html, text, full: html, text
    7ec5fd8d353ae3486915167a5d57c84cb0cb918f Sun Oct 26 01:11:19 2025 -0700
    Installing updated hg.conf files from UCSC servers
• confs/euro.hg.conf
  • lines changed 6, context: html, text, full: html, text
    7ec5fd8d353ae3486915167a5d57c84cb0cb918f Sun Oct 26 01:11:19 2025 -0700
    Installing updated hg.conf files from UCSC servers
• confs/hgwdev.hg.conf
  • lines changed 2, context: html, text, full: html, text
    7ec5fd8d353ae3486915167a5d57c84cb0cb918f Sun Oct 26 01:11:19 2025 -0700
    Installing updated hg.conf files from UCSC servers
• confs/preview.hg.conf
  • lines changed 3, context: html, text, full: html, text
    7ec5fd8d353ae3486915167a5d57c84cb0cb918f Sun Oct 26 01:11:19 2025 -0700
    Installing updated hg.conf files from UCSC servers
• confs/rr.hg.conf
  • lines changed 1, context: html, text, full: html, text
    7ec5fd8d353ae3486915167a5d57c84cb0cb918f Sun Oct 26 01:11:19 2025 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/cgilib/cartEdit9.c
  • lines changed 32, context: html, text, full: html, text
    cf9ef1c37b1056ff1ef009a25d877120054d19d3 Fri Oct 24 14:59:16 2025 -0700
    Add cartEdit 9 that moves ddg2p track to g2p supertrack and encodeCcresCombined into a cCREs supertrack
• src/hg/cgilib/cartRewrite.c
  • lines changed 2, context: html, text, full: html, text
    cf9ef1c37b1056ff1ef009a25d877120054d19d3 Fri Oct 24 14:59:16 2025 -0700
    Add cartEdit 9 that moves ddg2p track to g2p supertrack and encodeCcresCombined into a cCREs supertrack
• src/hg/cgilib/makefile
  • lines changed 2, context: html, text, full: html, text
    cf9ef1c37b1056ff1ef009a25d877120054d19d3 Fri Oct 24 14:59:16 2025 -0700
    Add cartEdit 9 that moves ddg2p track to g2p supertrack and encodeCcresCombined into a cCREs supertrack
• src/hg/hgConvert/hgConvert.c
  • lines changed 4, context: html, text, full: html, text
    6a6e3403ce27f25b3acf514870d466faba3b3b65 Sat Oct 25 14:50:44 2025 -0700
    Adding a beta tag with mouseover and outlink for QuickLift, refs #35609
• src/hg/hgGene/gtex.c
  • lines changed 1, context: html, text, full: html, text
    a3d70754d7f2bd3aa3e2d7caedd53ad74c90f17e Thu Oct 23 14:36:45 2025 -0700
    change in response to code review
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 4, context: html, text, full: html, text
    70696137f1961bee75cc7043ab92ea5c3798219a Tue Oct 21 16:54:09 2025 -0700
    Updating the text to be more general now that the API key is used with the CAPTCHA bypass and not just hubtools, refs #36428
• src/hg/hgMenubar/hgMenubar.c
  • lines changed 9, context: html, text, full: html, text
    19663905eef3c662d647b8da9d30ced044290713 Fri Oct 24 06:33:41 2025 -0700
    making hgMenubar not abort when run outside of an Apache SSI statement, refs #36580
• src/hg/hgTracks/mainMain.c
  • lines changed 3, context: html, text, full: html, text
    1d95bea96bc2a652fe77b22c0639eaa888fe858f Fri Oct 24 05:34:54 2025 -0700
    adding CGI var logging option for hg.conf, refs #36533
• src/hg/htdocs/ENCODE/FAQ/index.html
  • lines changed 8, context: html, text, full: html, text
    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/ENCODE/downloads.html
  • lines changed 95, context: html, text, full: html, text
    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/ENCODE/downloadsMouse.html
  • lines changed 23, context: html, text, full: html, text
    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/ENCODE/newsarch.html
  • lines changed 16, context: html, text, full: html, text
    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/ENCODE/pilot.html
  • lines changed 1, context: html, text, full: html, text
    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/ENCODE/releaseLog.html
  • lines changed 3, context: html, text, full: html, text
    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/ENCODE/search.html
  • lines changed 2, context: html, text, full: html, text
    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/FAQ/FAQblat.html
  • lines changed 8, context: html, text, full: html, text
    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/FAQ/FAQcustom.html
  • lines changed 1, context: html, text, full: html, text
    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/FAQ/FAQdisplay.html
  • lines changed 2, context: html, text, full: html, text
    bf2e5766c27fb8210d2b38bd457dd0b46d7374cb Tue Oct 21 11:08:16 2025 -0700
    Fixing 404 link for the Static Page Cronjob 2025-10-15, no RM
• src/hg/htdocs/FAQ/FAQdownloads.html
  • lines changed 3, context: html, text, full: html, text
    0947fb9b69be138080febf2554d184667045d3a6 Wed Oct 22 11:02:48 2025 -0700
    Clarifying that API key generation is only available on primary website and not mirrors, refs #31058
  • lines changed 36, context: html, text, full: html, text
    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/FAQ/FAQformat.html
  • lines changed 2, context: html, text, full: html, text
    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/FAQ/FAQgenes.html
  • lines changed 7, context: html, text, full: html, text
    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/FAQ/FAQlicense.html
  • lines changed 1, context: html, text, full: html, text
    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/FAQ/FAQlink.html
  • lines changed 4, context: html, text, full: html, text
    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/FAQ/FAQreleases.html
  • lines changed 4, context: html, text, full: html, text
    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/Neandertal/index.html
  • lines changed 197, context: html, text, full: html, text
    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/admin/hgFindSpecHowTo.html
  • lines changed 2, context: html, text, full: html, text
    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/covid19.html
  • lines changed 2, context: html, text, full: html, text
    bf2e5766c27fb8210d2b38bd457dd0b46d7374cb Tue Oct 21 11:08:16 2025 -0700
    Fixing 404 link for the Static Page Cronjob 2025-10-15, no RM
• src/hg/htdocs/ebolaPortal/index.html
  • lines changed 2, context: html, text, full: html, text
    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/goldenPath/datorg.html
  • lines changed 1, context: html, text, full: html, text
    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/goldenPath/gbdDescriptionsOld.html
  • lines changed 10, context: html, text, full: html, text
    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/goldenPath/help/api.html
  • lines changed 27, context: html, text, full: html, text
    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/goldenPath/help/assemblyHubGuidelines.html
  • lines changed 2, context: html, text, full: html, text
    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/goldenPath/help/assemblyHubHelp.html
  • lines changed 2, context: html, text, full: html, text
    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/goldenPath/help/barChart.html
  • lines changed 8, context: html, text, full: html, text
    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/goldenPath/help/bedMethyl.html
  • lines changed 3, context: html, text, full: html, text
    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/goldenPath/help/bigBed.html
  • lines changed 10, context: html, text, full: html, text
    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/goldenPath/help/bigChain.html
  • lines changed 9, context: html, text, full: html, text
    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/goldenPath/help/bigGenePred.html
  • lines changed 11, context: html, text, full: html, text
    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/goldenPath/help/bigLolly.html
  • lines changed 4, context: html, text, full: html, text
    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/goldenPath/help/bigMaf.html
  • lines changed 10, context: html, text, full: html, text
    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/goldenPath/help/bigNarrowPeak.html
  • lines changed 9, context: html, text, full: html, text
    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/goldenPath/help/bigPsl.html
  • lines changed 8, context: html, text, full: html, text
    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/goldenPath/help/bigRmsk.html
  • lines changed 1, context: html, text, full: html, text
    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/goldenPath/help/bigWig.html
  • lines changed 1, context: html, text, full: html, text
    bf2e5766c27fb8210d2b38bd457dd0b46d7374cb Tue Oct 21 11:08:16 2025 -0700
    Fixing 404 link for the Static Page Cronjob 2025-10-15, no RM
  • lines changed 7, context: html, text, full: html, text
    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/goldenPath/help/chain.html
  • lines changed 3, context: html, text, full: html, text
    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/goldenPath/help/cloud.html
  • lines changed 14, context: html, text, full: html, text
    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/goldenPath/help/covidBrowser.html
  • lines changed 1, context: html, text, full: html, text
    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/goldenPath/help/covidBrowserIntro.html
  • lines changed 1, context: html, text, full: html, text
    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/goldenPath/help/customTrackText.html
  • lines changed 3, context: html, text, full: html, text
    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/goldenPath/help/decorator.html
  • lines changed 1, context: html, text, full: html, text
    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/goldenPath/help/ftp.html
  • lines changed 11, context: html, text, full: html, text
    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/goldenPath/help/gbib.html
  • lines changed 12, context: html, text, full: html, text
    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/goldenPath/help/gbic.html
  • lines changed 5, context: html, text, full: html, text
    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/goldenPath/help/hgGeneGraph.html
  • lines changed 5, context: html, text, full: html, text
    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/goldenPath/help/hgSessionHelp.html
  • lines changed 3, context: html, text, full: html, text
    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/goldenPath/help/hgTablesHelp.html
  • lines changed 2, context: html, text, full: html, text
    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 8, context: html, text, full: html, text
    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/goldenPath/help/hgTracksHelp.html
  • lines changed 11, context: html, text, full: html, text
    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/goldenPath/help/hic.html
  • lines changed 2, context: html, text, full: html, text
    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/goldenPath/help/hubBasics.html
  • lines changed 36, context: html, text, full: html, text
    1fd3dd5aea167b70544aa9017846854ce0131f2d Fri Oct 24 16:02:36 2025 -0700
    Small tweaks and improvements to the hub page, refs #28347
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    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
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    f49623d03093fdc8e7f06b65abb0b77efad6a3b9 Sun Oct 26 12:19:55 2025 -0700
    fixed merge conflict.
• src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html
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    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/goldenPath/help/hubQuickStartSearch.html
  • lines changed 8, context: html, text, full: html, text
    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/goldenPath/help/interact.html
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    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/goldenPath/help/mirror.html
  • lines changed 4, context: html, text, full: html, text
    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/goldenPath/help/mirrorManual.html
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    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/goldenPath/help/multiRegionHelp.html
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    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/goldenPath/help/mysql.html
  • lines changed 1, context: html, text, full: html, text
    bf2e5766c27fb8210d2b38bd457dd0b46d7374cb Tue Oct 21 11:08:16 2025 -0700
    Fixing 404 link for the Static Page Cronjob 2025-10-15, no RM
  • lines changed 9, context: html, text, full: html, text
    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/goldenPath/help/net.html
  • lines changed 1, context: html, text, full: html, text
    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/goldenPath/help/publicHubGuidelines.html
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    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/goldenPath/help/sessions.html
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    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
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    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/goldenPath/help/trackDbIndexBb.html
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    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/goldenPath/help/trix.html
  • lines changed 1, context: html, text, full: html, text
    bf2e5766c27fb8210d2b38bd457dd0b46d7374cb Tue Oct 21 11:08:16 2025 -0700
    Fixing 404 link for the Static Page Cronjob 2025-10-15, no RM
  • lines changed 1, context: html, text, full: html, text
    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/goldenPath/help/twoBit.html
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    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/goldenPath/help/vcf.html
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    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/goldenPath/labs.html
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    bf2e5766c27fb8210d2b38bd457dd0b46d7374cb Tue Oct 21 11:08:16 2025 -0700
    Fixing 404 link for the Static Page Cronjob 2025-10-15, no RM
• src/hg/htdocs/goldenPath/mapPlots/RHguide.html
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    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/goldenPath/mapPlots/arch.html
  • lines changed 1, context: html, text, full: html, text
    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/goldenPath/mapPlots/cytoguide.html
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    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/goldenPath/mapPlots/cytoprogram.html
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    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/goldenPath/mapPlots/index.html
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    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/goldenPath/newsarch.html
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    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/goldenPath/releaseLogOld.html
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    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/goldenPath/trackDescriptions/bigRmskTrackDesc.html
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    bf2e5766c27fb8210d2b38bd457dd0b46d7374cb Tue Oct 21 11:08:16 2025 -0700
    Fixing 404 link for the Static Page Cronjob 2025-10-15, no RM
• src/hg/htdocs/gtex.html
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    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/inc/encode.custTracks.topbar.html
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    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/inc/encode.topbar_pilot.html
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    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/inc/gbPageStartHardcoded.html
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    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/inc/globalNavBar.inc
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    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/license/index.html
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    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/robots.rr.txt
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    ca1c644d399c9a9c007d58b1e26c1f94b8f18b22 Fri Oct 24 16:11:30 2025 -0700
    Removing some google user agents for (hopefully) better indexing, this was done by Max in the RR a few weeks ago. And disallowing json output from blat because google doesn't like to hit json, and also removing hgGeneGraph because it fails because of the cart requirement for google. No RM.
• src/hg/htdocs/training/ashg2009/pageAdvTwo.html
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    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/training/ashg2009/sidebar.html
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    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/htdocs/util.html
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    bbabbd5d2566d47d923d51dbe350634783455999 Sun Oct 26 12:14:52 2025 -0700
    change soe to gi, refs #35031
• src/hg/hubApi/findGenome.c
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    e01e278779d39155f4a30916f45faa9828948610 Wed Oct 22 13:18:54 2025 -0700
    turn off the apache log recording for findGenome results no redmine
• src/hg/inc/hgConfig.h
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    1d95bea96bc2a652fe77b22c0639eaa888fe858f Fri Oct 24 05:34:54 2025 -0700
    adding CGI var logging option for hg.conf, refs #36533
• src/hg/lib/cart.c
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    bbdf4db2c3d6c72bc109a9f478870ad711e1a11d Tue Oct 21 09:48:50 2025 -0700
    remove cart visibilities for tracks in hub when disconnecting refs #36536
• src/hg/lib/hgConfig.c
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    1d95bea96bc2a652fe77b22c0639eaa888fe858f Fri Oct 24 05:34:54 2025 -0700
    adding CGI var logging option for hg.conf, refs #36533
• src/hg/lib/wiggleCart.c
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    3a52ad30839586e54377927d8ee87a65d4806a7f Thu Oct 23 21:21:22 2025 -0700
    hubCheck can now scan for and report with text valid values for VIEWLIMIT VIEWLIMITMAX and DEFAULTVIEWLIMIT. fixes #12098
• src/hg/makeDb/doc/evaSnp8.txt
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    3f30aa9effe51ff75c1cfff288ae14cd00e118e0 Tue Oct 21 09:34:02 2025 -0700
    Staging evaSnp8 track, refs #36512
• src/hg/makeDb/doc/mm10.txt
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    41fc9a82e180cd08b149a8b92d7fcc9fb630fec9 Fri Oct 24 13:06:45 2025 -0700
    Adding LiftOver doc, refs #36547
• src/hg/makeDb/scripts/evaSnp/evaSnp8.py
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    3f30aa9effe51ff75c1cfff288ae14cd00e118e0 Tue Oct 21 09:34:02 2025 -0700
    Staging evaSnp8 track, refs #36512
• src/hg/makeDb/trackDb/human/decipher.ra
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    5428fe6145c9d7971704b42e2945fa34978f59c2 Fri Oct 24 10:49:47 2025 -0700
    Accidentally removed the Decipher tracks from hgwdev, refs #36529
• src/hg/makeDb/trackDb/human/g2p.html
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    83cc98681bb258a9eed116893ca85439c0df18f3 Thu Oct 23 16:04:21 2025 -0700
    Moving the DDG2P track into its own container, G2P, refs #36469
• src/hg/makeDb/trackDb/human/g2p.ra
  • lines changed 19, context: html, text, full: html, text
    83cc98681bb258a9eed116893ca85439c0df18f3 Thu Oct 23 16:04:21 2025 -0700
    Moving the DDG2P track into its own container, G2P, refs #36469
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    cf9ef1c37b1056ff1ef009a25d877120054d19d3 Fri Oct 24 14:59:16 2025 -0700
    Add cartEdit 9 that moves ddg2p track to g2p supertrack and encodeCcresCombined into a cCREs supertrack
• src/hg/makeDb/trackDb/human/hg38/knownGene.alpha.ra
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    c2eae1000b4eef5e1b6ca32a5fe0fe0813a04182 Fri Oct 24 16:36:00 2025 -0700
    Upadating the hg38 knownGene alpha.ra V48 to V49, refs #36169
• src/hg/makeDb/trackDb/human/hg38/mane.html
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    a57e95fd50c67dfcb633c5732844d411655b07a0 Fri Oct 24 15:46:37 2025 -0700
    Fixing a singular-plural disconnect that Bob wrote in about, refs #36576
• src/hg/makeDb/trackDb/human/panelApp.ra
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    1dc1b60197136ef89d70326cb8cef0664d028a25 Thu Oct 23 15:13:49 2025 -0700
    Tweaking filters based on feedback from panelApp Aus, refs #36219
• src/hg/makeDb/trackDb/human/spliceImpactSuper.html
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    4ea3d549b2d0aa682aa22e6b31e844fee78d2cfc Tue Oct 21 13:55:33 2025 -0700
    Code review edit, refs #36551
• src/hg/makeDb/trackDb/human/trackDb.ra
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    54832f727c69ed0fbd8dce9d2c5c51d06f249b9b Tue Oct 21 18:15:31 2025 -0700
    Adding linkouts to the HGNC track, refs #36565
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    83cc98681bb258a9eed116893ca85439c0df18f3 Thu Oct 23 16:04:21 2025 -0700
    Moving the DDG2P track into its own container, G2P, refs #36469
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    5428fe6145c9d7971704b42e2945fa34978f59c2 Fri Oct 24 10:49:47 2025 -0700
    Accidentally removed the Decipher tracks from hgwdev, refs #36529
• src/hg/makeDb/trackDb/trackDb.cCREs.alpha.ra
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    cf9ef1c37b1056ff1ef009a25d877120054d19d3 Fri Oct 24 14:59:16 2025 -0700
    Add cartEdit 9 that moves ddg2p track to g2p supertrack and encodeCcresCombined into a cCREs supertrack
• src/hg/utils/automation/HgAutomate.pm
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    2dc78bc27b010545f6af079b46fe1b94b472e90d Mon Oct 27 12:43:42 2025 -0700
    fixup error in help message for fileServer refs #35575
• src/hg/utils/automation/doSameSpeciesLiftOver.pl
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    c71e68a92e5d8d8393e7883f8dee5d9695ae7373 Mon Oct 27 12:45:05 2025 -0700
    ram size only needs to be 3Gb and create the quick.lift files still needs the addQuickLift.py addition refs #35575
• src/hg/utils/automation/makefile
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    a7ecad52c1043982f9fb7818f753fd419d587e51 Mon Oct 27 12:46:14 2025 -0700
    add the addQuickLift.py to the scripts directory refs #35575
• src/hg/utils/hubCheck/hubCheck.c
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    3a52ad30839586e54377927d8ee87a65d4806a7f Thu Oct 23 21:21:22 2025 -0700
    hubCheck can now scan for and report with text valid values for VIEWLIMIT VIEWLIMITMAX and DEFAULTVIEWLIMIT. fixes #12098
• src/hg/utils/otto/genArk/README
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    3eda4bcc9f4d46c9d261f669272765dd7b4e657a Thu Oct 23 12:11:46 2025 -0700
    not new push procedure from hgwdev to only hgwbeta
• src/hg/utils/otto/genArk/alphaBetaPush.pl
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    8d9d8756a819939ab5546289d7722489fbdab44c Tue Oct 21 10:42:12 2025 -0700
    this should only push out to hgwbeta and hgw0, does not need to push to the RR, that is cluster admin territory refs #35575
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    22cbda5e72a0c4429edad0eb3a8545ca0abe1b7c Tue Oct 21 10:59:15 2025 -0700
    obsolete copy of this script refs #35575
• src/hg/utils/otto/genArk/devList.sh
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    3f93380b226036b64a4f43c0cae6701109e04c1d Thu Oct 23 11:56:14 2025 -0700
    sorting the file listings so everything is the same everywhere and making up the push list for admin rsync cron scripts
• src/hg/utils/otto/genArk/gbDbGenArkList.sh
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    3f93380b226036b64a4f43c0cae6701109e04c1d Thu Oct 23 11:56:14 2025 -0700
    sorting the file listings so everything is the same everywhere and making up the push list for admin rsync cron scripts
• src/hg/utils/otto/genArk/pushNewOnes.sh
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    8f6315dbca0175c9de974e7d4a9baa8fb040583e Tue Oct 21 10:38:44 2025 -0700
    this should only push out to hgwbeta, does not need to push to the RR, that is cluster admin territory refs #35575
• src/hg/utils/otto/genArk/pushRR/alphaBetaPush.pl
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    40f327f41b260347654737699c6bd001172a32cd Tue Oct 21 10:56:59 2025 -0700
    this should only push out to hgwbeta and hgw0, does not need to push to the RR, that is cluster admin territory refs #35575
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    17859fc49832ff3dc8144ea2ca5f59250050fb03 Tue Oct 21 14:03:04 2025 -0700
    indicate where these scripts come from in the source tree refs #35575
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    378faee9c90a86c1f2a7dd39cd5e1961a2d10be9 Tue Oct 21 14:09:51 2025 -0700
    eliminate obsolete copies refs #35575
• src/hg/utils/otto/genArk/pushRR/pullHgwdev.sh
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    17859fc49832ff3dc8144ea2ca5f59250050fb03 Tue Oct 21 14:03:04 2025 -0700
    indicate where these scripts come from in the source tree refs #35575
• src/hg/utils/otto/genArk/pushRR/pushRR.sh
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    17859fc49832ff3dc8144ea2ca5f59250050fb03 Tue Oct 21 14:03:04 2025 -0700
    indicate where these scripts come from in the source tree refs #35575
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    4dcf108ba99ec6add9214f7e36b2041b2f950388 Tue Oct 21 14:07:59 2025 -0700
    indicate this is the obsolete copy refs #35575
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    378faee9c90a86c1f2a7dd39cd5e1961a2d10be9 Tue Oct 21 14:09:51 2025 -0700
    eliminate obsolete copies refs #35575
• src/hg/utils/otto/genArk/quickLiftNew.sh
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    3f93380b226036b64a4f43c0cae6701109e04c1d Thu Oct 23 11:56:14 2025 -0700
    sorting the file listings so everything is the same everywhere and making up the push list for admin rsync cron scripts
• src/hg/utils/otto/genArk/quickPush.pl
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    a2224a3ff403b1fb2da3f74dbbf4cb9e39471781 Tue Oct 21 10:43:09 2025 -0700
    this should only push out to hgwbeta and hgw0, does not need to push to the RR, that is cluster admin territory refs #35575
• src/hg/utils/otto/genArk/whatIsNew.sh
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    3f93380b226036b64a4f43c0cae6701109e04c1d Thu Oct 23 11:56:14 2025 -0700
    sorting the file listings so everything is the same everywhere and making up the push list for admin rsync cron scripts
• src/hg/utils/otto/gwas/checkGwas.sh
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    70a0c624de26b19e8f53b2ad429afe617063b4d4 Mon Oct 27 14:40:15 2025 -0700
    Updating the URL to download the GWAS data since the previous URL is now retired, no Redmine.
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    ee617db835fea5844d9fbf28559f3bb515ef75ae Mon Oct 27 15:24:18 2025 -0700
    Unzipping the contents of the gwas catalog before continuing with the script, no Redmine
• src/hg/utils/otto/orphanet/parseOrphadata.py
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    3ff911e2af586e1e45944813cef5138de1421777 Thu Oct 23 14:00:10 2025 -0700
    Updating the URL to the Orphanet data since Ensembl retired the US West server, no Redmine.
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    11594d79515c4bcdec42959a0881d840a26ab908 Thu Oct 23 14:08:20 2025 -0700
    Need 'useast' in the URL, no Redmine
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    0b2258ca5ed205f72a19f77bc3a0bd009a87c117 Thu Oct 23 14:31:54 2025 -0700
    Fixing a bug where the an empty string would break the otto cronjob, no Redmine.
• src/hg/utils/otto/otto.crontab
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    7de6bab0b6434d0bb23ab7e78227063fd4e12af9 Thu Oct 23 12:07:30 2025 -0700
    readjust the timing of the devList.sh script compared to the pushRR.sh script
• src/hg/utils/otto/panelApp/doPanelApp.py
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    f8702ef92125ff1776b67fb09b7917bd346c443e Thu Oct 23 09:03:18 2025 -0700
    PanelApp england began to heavily throttle their API access which was causing this otto to error out because we were not checking that the input was JSON in certain places. Added a new central function with retry logic, and invoked that new function in all previous request locations. Refs otto ML.
• src/inc/cheapcgi.h
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    1d95bea96bc2a652fe77b22c0639eaa888fe858f Fri Oct 24 05:34:54 2025 -0700
    adding CGI var logging option for hg.conf, refs #36533
• src/lib/blastParse.c
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    9ac656e395e77e118215f8836e283ac39a848b70 Tue Oct 21 12:39:31 2025 -0700
    fixed possible reference past end of array from previous change
• src/lib/cheapcgi.c
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    1d95bea96bc2a652fe77b22c0639eaa888fe858f Fri Oct 24 05:34:54 2025 -0700
    adding CGI var logging option for hg.conf, refs #36533
• src/utils/qa/qaTestScript.py
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    e89219a37faa3828eb9fbad7e1ffe578793ebc34 Thu Oct 23 16:41:31 2025 -0700
    Adding more arguments to the headless mode setup, No RM

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• files changed: 156