All File Changes

v493_base to v494_preview (2026-01-26 to 2026-02-12) v494

• confs/hgwbeta.hg.conf
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    90224975823519f4e4ecc686d523d57d425baacc Sun Feb 1 01:11:19 2026 -0800
    Installing updated hg.conf files from UCSC servers
• docs/tutorials/customTrackTutorial.md
  • lines changed 201, context: html, text, full: html, text
    3724caa503e2454ffd577edc5a173279924107f5 Fri Jan 30 15:51:30 2026 -0800
    Staging the custom track markdown tutorial, refs #34354
• docs/tutorials/index.md
  • lines changed 15, context: html, text, full: html, text
    3724caa503e2454ffd577edc5a173279924107f5 Fri Jan 30 15:51:30 2026 -0800
    Staging the custom track markdown tutorial, refs #34354
• src/hg/cgilib/cartJson.c
  • lines changed 7, context: html, text, full: html, text
    47ea57080b515e5dad5f658c58feb8944a7e7d61 Thu Jan 29 15:30:26 2026 -0800
    Replace clade/assembly dropdowns with a search bar on most CGIs. Add a recents list to hgGateway and to the species bar and to the 'Genomes' dropdown menu. Track recently selected species in localStorage. Add toGenome and fromGenome arguemnts to hubApi/liftOver in order to find appropriate liftover assemblies, refs #36232
• src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html
  • lines changed 96, context: html, text, full: html, text
    16ae9a2464995949ec09f739683d0b09282a379d Mon Jan 26 13:27:34 2026 -0800
    Stripping timeline chart down to just submission milestones for clarity
  • lines changed 32, context: html, text, full: html, text
    dd088815ca2f10cdc5a4e580c4d12683ec5de43f Mon Jan 26 14:12:32 2026 -0800
    Revamping MiNND milestones to reference spreadsheet blocks: ADGC2_M_28, refers to column M, row 28
  • lines changed 16, context: html, text, full: html, text
    e4b550095f70e0d9b828dccaa740f9a49ecc3e15 Mon Jan 26 14:27:52 2026 -0800
    Cutting Grant Year 2 off milestone, revamping Broads to have Spreadsheet mapping ADGC4_Aim3_year4_item2 -> ADGC4_Aim3_year4_D_16
  • lines changed 21, context: html, text, full: html, text
    e812d974b9e776635398a985fc2c9b96ef477a0e Tue Jan 27 13:12:50 2026 -0800
    Adding a color key, and using 'light blue' = active for milestones with some data, but not all data/metadata
  • lines changed 2, context: html, text, full: html, text
    2aa441358c7c1e09562465dca61c0e0d64667b9f Wed Jan 28 16:03:48 2026 -0800
    Adding ADGC6 active milestone change
• src/hg/hgBlat/hgBlat.c
  • lines changed 25, context: html, text, full: html, text
    47ea57080b515e5dad5f658c58feb8944a7e7d61 Thu Jan 29 15:30:26 2026 -0800
    Replace clade/assembly dropdowns with a search bar on most CGIs. Add a recents list to hgGateway and to the species bar and to the 'Genomes' dropdown menu. Track recently selected species in localStorage. Add toGenome and fromGenome arguemnts to hubApi/liftOver in order to find appropriate liftover assemblies, refs #36232
• src/hg/hgCollection/hgCollection.c
  • lines changed 5, context: html, text, full: html, text
    65bf003397e55927776facd7654de161ea8c1e20 Fri Jan 30 15:59:33 2026 -0800
    Downloading our major CDNs and changing their references to all be local, there are some more corner cases that were low priority as discussed in the ticket. This work is done to improve performance, expecially for overseas users. Refs #33998
• src/hg/hgConvert/hgConvert.c
  • lines changed 136, context: html, text, full: html, text
    47ea57080b515e5dad5f658c58feb8944a7e7d61 Thu Jan 29 15:30:26 2026 -0800
    Replace clade/assembly dropdowns with a search bar on most CGIs. Add a recents list to hgGateway and to the species bar and to the 'Genomes' dropdown menu. Track recently selected species in localStorage. Add toGenome and fromGenome arguemnts to hubApi/liftOver in order to find appropriate liftover assemblies, refs #36232
• src/hg/hgCustom/hgCustom.c
  • lines changed 46, context: html, text, full: html, text
    47ea57080b515e5dad5f658c58feb8944a7e7d61 Thu Jan 29 15:30:26 2026 -0800
    Replace clade/assembly dropdowns with a search bar on most CGIs. Add a recents list to hgGateway and to the species bar and to the 'Genomes' dropdown menu. Track recently selected species in localStorage. Add toGenome and fromGenome arguemnts to hubApi/liftOver in order to find appropriate liftover assemblies, refs #36232
• src/hg/hgGateway/hgGateway.html
  • lines changed 18, context: html, text, full: html, text
    47ea57080b515e5dad5f658c58feb8944a7e7d61 Thu Jan 29 15:30:26 2026 -0800
    Replace clade/assembly dropdowns with a search bar on most CGIs. Add a recents list to hgGateway and to the species bar and to the 'Genomes' dropdown menu. Track recently selected species in localStorage. Add toGenome and fromGenome arguemnts to hubApi/liftOver in order to find appropriate liftover assemblies, refs #36232
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 5, context: html, text, full: html, text
    65bf003397e55927776facd7654de161ea8c1e20 Fri Jan 30 15:59:33 2026 -0800
    Downloading our major CDNs and changing their references to all be local, there are some more corner cases that were low priority as discussed in the ticket. This work is done to improve performance, expecially for overseas users. Refs #33998
• src/hg/hgHubConnect/trackHubWizard.c
  • lines changed 13, context: html, text, full: html, text
    65bf003397e55927776facd7654de161ea8c1e20 Fri Jan 30 15:59:33 2026 -0800
    Downloading our major CDNs and changing their references to all be local, there are some more corner cases that were low priority as discussed in the ticket. This work is done to improve performance, expecially for overseas users. Refs #33998
• src/hg/hgIntegrator/hgIntegrator.c
  • lines changed 1, context: html, text, full: html, text
    47ea57080b515e5dad5f658c58feb8944a7e7d61 Thu Jan 29 15:30:26 2026 -0800
    Replace clade/assembly dropdowns with a search bar on most CGIs. Add a recents list to hgGateway and to the species bar and to the 'Genomes' dropdown menu. Track recently selected species in localStorage. Add toGenome and fromGenome arguemnts to hubApi/liftOver in order to find appropriate liftover assemblies, refs #36232
• src/hg/hgLiftOver/hgLiftOver.c
  • lines changed 43, context: html, text, full: html, text
    47ea57080b515e5dad5f658c58feb8944a7e7d61 Thu Jan 29 15:30:26 2026 -0800
    Replace clade/assembly dropdowns with a search bar on most CGIs. Add a recents list to hgGateway and to the species bar and to the 'Genomes' dropdown menu. Track recently selected species in localStorage. Add toGenome and fromGenome arguemnts to hubApi/liftOver in order to find appropriate liftover assemblies, refs #36232
• src/hg/hgMenubar/hgMenubar.c
  • lines changed 3, context: html, text, full: html, text
    47ea57080b515e5dad5f658c58feb8944a7e7d61 Thu Jan 29 15:30:26 2026 -0800
    Replace clade/assembly dropdowns with a search bar on most CGIs. Add a recents list to hgGateway and to the species bar and to the 'Genomes' dropdown menu. Track recently selected species in localStorage. Add toGenome and fromGenome arguemnts to hubApi/liftOver in order to find appropriate liftover assemblies, refs #36232
• src/hg/hgPcr/hgPcr.c
  • lines changed 22, context: html, text, full: html, text
    47ea57080b515e5dad5f658c58feb8944a7e7d61 Thu Jan 29 15:30:26 2026 -0800
    Replace clade/assembly dropdowns with a search bar on most CGIs. Add a recents list to hgGateway and to the species bar and to the 'Genomes' dropdown menu. Track recently selected species in localStorage. Add toGenome and fromGenome arguemnts to hubApi/liftOver in order to find appropriate liftover assemblies, refs #36232
• src/hg/hgSearch/hgSearch.c
  • lines changed 6, context: html, text, full: html, text
    47ea57080b515e5dad5f658c58feb8944a7e7d61 Thu Jan 29 15:30:26 2026 -0800
    Replace clade/assembly dropdowns with a search bar on most CGIs. Add a recents list to hgGateway and to the species bar and to the 'Genomes' dropdown menu. Track recently selected species in localStorage. Add toGenome and fromGenome arguemnts to hubApi/liftOver in order to find appropriate liftover assemblies, refs #36232
  • lines changed 2, context: html, text, full: html, text
    65bf003397e55927776facd7654de161ea8c1e20 Fri Jan 30 15:59:33 2026 -0800
    Downloading our major CDNs and changing their references to all be local, there are some more corner cases that were low priority as discussed in the ticket. This work is done to improve performance, expecially for overseas users. Refs #33998
• src/hg/hgTables/mainPage.c
  • lines changed 68, context: html, text, full: html, text
    47ea57080b515e5dad5f658c58feb8944a7e7d61 Thu Jan 29 15:30:26 2026 -0800
    Replace clade/assembly dropdowns with a search bar on most CGIs. Add a recents list to hgGateway and to the species bar and to the 'Genomes' dropdown menu. Track recently selected species in localStorage. Add toGenome and fromGenome arguemnts to hubApi/liftOver in order to find appropriate liftover assemblies, refs #36232
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 72, context: html, text, full: html, text
    ce138738e24cb6e84502440b79490c412f6786f8 Tue Jan 27 03:13:16 2026 -0800
    Reapply "changing superTrack TrackUi quite a bit. This reverts commit e6ee88658405177aee46ddb8902ae93aee5b1378.
  • lines changed 98, context: html, text, full: html, text
    ac48943c159a91ae0ba861823d9962e7e92efa1b Wed Jan 28 01:06:25 2026 -0800
    First pass at having the facetedComposite UI correctly recognize subtracks that are on by default, refs #36320
  • lines changed 72, context: html, text, full: html, text
    55df1a106590a6c9fd7e3cca90fa6bbad8eb50c4 Thu Jan 29 05:26:21 2026 -0800
    Revert "Reapply "changing superTrack TrackUi quite a bit." This reverts commit ce138738e24cb6e84502440b79490c412f6786f8.
• src/hg/hgTracks/bigBedTrack.c
  • lines changed 1, context: html, text, full: html, text
    2f41bf5c522766d4bb5bb9f94e2942f7612406de Sat Jan 31 10:27:35 2026 -0800
    special case bigBed loader to only load a bed6 if asked to load a bed7 for backwards compatibility
• src/hg/hgTracks/hgTracks.c
  • lines changed 1, context: html, text, full: html, text
    ce138738e24cb6e84502440b79490c412f6786f8 Tue Jan 27 03:13:16 2026 -0800
    Reapply "changing superTrack TrackUi quite a bit. This reverts commit e6ee88658405177aee46ddb8902ae93aee5b1378.
  • lines changed 1, context: html, text, full: html, text
    55df1a106590a6c9fd7e3cca90fa6bbad8eb50c4 Thu Jan 29 05:26:21 2026 -0800
    Revert "Reapply "changing superTrack TrackUi quite a bit." This reverts commit ce138738e24cb6e84502440b79490c412f6786f8.
• src/hg/hgTracks/mainMain.c
  • lines changed 1, context: html, text, full: html, text
    65bf003397e55927776facd7654de161ea8c1e20 Fri Jan 30 15:59:33 2026 -0800
    Downloading our major CDNs and changing their references to all be local, there are some more corner cases that were low priority as discussed in the ticket. This work is done to improve performance, expecially for overseas users. Refs #33998
• src/hg/hgTracks/simpleTracks.c
  • lines changed 12, context: html, text, full: html, text
    e745ccb794a88cf79f4e63a375a3eeb93e918563 Mon Jan 26 10:15:44 2026 -0800
    move code to reverse exonFrames to calcLiftOverGenePred() so it will work with the liftOver tool
• src/hg/hgVai/hgVai.c
  • lines changed 61, context: html, text, full: html, text
    47ea57080b515e5dad5f658c58feb8944a7e7d61 Thu Jan 29 15:30:26 2026 -0800
    Replace clade/assembly dropdowns with a search bar on most CGIs. Add a recents list to hgGateway and to the species bar and to the 'Genomes' dropdown menu. Track recently selected species in localStorage. Add toGenome and fromGenome arguemnts to hubApi/liftOver in order to find appropriate liftover assemblies, refs #36232
• src/hg/htdocs/cite.html
  • lines changed 1, context: html, text, full: html, text
    c7eebb45ae05223d9f771acbb6abcbe061c4d6b6 Wed Jan 28 14:45:46 2026 -0800
    changing the word Archive in reference to GenArk to become Repository refs #37027
• src/hg/htdocs/contribTracks.html
  • lines changed 139, context: html, text, full: html, text
    451babbb2d02e1d3803422f96a054f96ad5ad78c Wed Jan 28 14:28:04 2026 -0800
    initial ontent to describe contributed track procedure refs #34706
• src/hg/htdocs/fonts/fontawesome-webfont.eot
  • lines changed 0, context: html, text, full: html, text
    65bf003397e55927776facd7654de161ea8c1e20 Fri Jan 30 15:59:33 2026 -0800
    Downloading our major CDNs and changing their references to all be local, there are some more corner cases that were low priority as discussed in the ticket. This work is done to improve performance, expecially for overseas users. Refs #33998
• src/hg/htdocs/fonts/fontawesome-webfont.svg
  • lines changed 655, context: html, text, full: html, text
    65bf003397e55927776facd7654de161ea8c1e20 Fri Jan 30 15:59:33 2026 -0800
    Downloading our major CDNs and changing their references to all be local, there are some more corner cases that were low priority as discussed in the ticket. This work is done to improve performance, expecially for overseas users. Refs #33998
• src/hg/htdocs/fonts/fontawesome-webfont.ttf
  • lines changed 0, context: html, text, full: html, text
    65bf003397e55927776facd7654de161ea8c1e20 Fri Jan 30 15:59:33 2026 -0800
    Downloading our major CDNs and changing their references to all be local, there are some more corner cases that were low priority as discussed in the ticket. This work is done to improve performance, expecially for overseas users. Refs #33998
• src/hg/htdocs/fonts/fontawesome-webfont.woff
  • lines changed 0, context: html, text, full: html, text
    65bf003397e55927776facd7654de161ea8c1e20 Fri Jan 30 15:59:33 2026 -0800
    Downloading our major CDNs and changing their references to all be local, there are some more corner cases that were low priority as discussed in the ticket. This work is done to improve performance, expecially for overseas users. Refs #33998
• src/hg/htdocs/fonts/fontawesome-webfont.woff2
  • lines changed 0, context: html, text, full: html, text
    65bf003397e55927776facd7654de161ea8c1e20 Fri Jan 30 15:59:33 2026 -0800
    Downloading our major CDNs and changing their references to all be local, there are some more corner cases that were low priority as discussed in the ticket. This work is done to improve performance, expecially for overseas users. Refs #33998
• src/hg/htdocs/goldenPath/help/decorator.html
  • lines changed 7, context: html, text, full: html, text
    4209b0dccb1b07beb7d690859c46c5b68fbe0b0e Sat Jan 31 12:49:32 2026 -0800
    Making edits from Bob's feedback, refs #32818
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 1, context: html, text, full: html, text
    05b5f7747fd2a6dd056109f0dd37df88b2819540 Wed Jan 28 08:57:08 2026 -0800
    adding closing p tag based on CR, refs #37023
• src/hg/htdocs/goldenPath/mapPlots/RHguide.html
  • lines changed 1, context: html, text, full: html, text
    c7eebb45ae05223d9f771acbb6abcbe061c4d6b6 Wed Jan 28 14:45:46 2026 -0800
    changing the word Archive in reference to GenArk to become Repository refs #37027
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 4, context: html, text, full: html, text
    c7eebb45ae05223d9f771acbb6abcbe061c4d6b6 Wed Jan 28 14:45:46 2026 -0800
    changing the word Archive in reference to GenArk to become Repository refs #37027
  • lines changed 102, context: html, text, full: html, text
    c5ff7a18c40453535ec9514b16da3d2f39a9a0cc Fri Jan 30 16:18:23 2026 -0800
    Moving the Hub Space announcement to the top for next week's release, refs #36290
  • lines changed 25, context: html, text, full: html, text
    3e2267a6e80290cc0ea3cab62f017e83897f58e1 Fri Jan 30 17:05:31 2026 -0800
    Staging the visible track groups announcement for the release next week, refs #36609
• src/hg/htdocs/images/newsArchImages/visibleTracks.png
  • lines changed 0, context: html, text, full: html, text
    1198e35a9106aa82703f8c3b3f306a44bc7e8aa8 Fri Jan 30 17:02:14 2026 -0800
    Adding the news image for the Visible features track, no Redmine
• src/hg/htdocs/inc/gbPageIncludeStart.html
  • lines changed 1, context: html, text, full: html, text
    65bf003397e55927776facd7654de161ea8c1e20 Fri Jan 30 15:59:33 2026 -0800
    Downloading our major CDNs and changing their references to all be local, there are some more corner cases that were low priority as discussed in the ticket. This work is done to improve performance, expecially for overseas users. Refs #33998
• src/hg/htdocs/inc/gbPageStart.html
  • lines changed 9, context: html, text, full: html, text
    65bf003397e55927776facd7654de161ea8c1e20 Fri Jan 30 15:59:33 2026 -0800
    Downloading our major CDNs and changing their references to all be local, there are some more corner cases that were low priority as discussed in the ticket. This work is done to improve performance, expecially for overseas users. Refs #33998
• src/hg/htdocs/inc/gbPageStartHardcoded.html
  • lines changed 1, context: html, text, full: html, text
    c7eebb45ae05223d9f771acbb6abcbe061c4d6b6 Wed Jan 28 14:45:46 2026 -0800
    changing the word Archive in reference to GenArk to become Repository refs #37027
  • lines changed 9, context: html, text, full: html, text
    65bf003397e55927776facd7654de161ea8c1e20 Fri Jan 30 15:59:33 2026 -0800
    Downloading our major CDNs and changing their references to all be local, there are some more corner cases that were low priority as discussed in the ticket. This work is done to improve performance, expecially for overseas users. Refs #33998
• src/hg/htdocs/inc/globalNavBar.inc
  • lines changed 1, context: html, text, full: html, text
    c7eebb45ae05223d9f771acbb6abcbe061c4d6b6 Wed Jan 28 14:45:46 2026 -0800
    changing the word Archive in reference to GenArk to become Repository refs #37027
  • lines changed 6, context: html, text, full: html, text
    47ea57080b515e5dad5f658c58feb8944a7e7d61 Thu Jan 29 15:30:26 2026 -0800
    Replace clade/assembly dropdowns with a search bar on most CGIs. Add a recents list to hgGateway and to the species bar and to the 'Genomes' dropdown menu. Track recently selected species in localStorage. Add toGenome and fromGenome arguemnts to hubApi/liftOver in order to find appropriate liftover assemblies, refs #36232
• src/hg/htdocs/inc/hgSearch.html
  • lines changed 72, context: html, text, full: html, text
    47ea57080b515e5dad5f658c58feb8944a7e7d61 Thu Jan 29 15:30:26 2026 -0800
    Replace clade/assembly dropdowns with a search bar on most CGIs. Add a recents list to hgGateway and to the species bar and to the 'Genomes' dropdown menu. Track recently selected species in localStorage. Add toGenome and fromGenome arguemnts to hubApi/liftOver in order to find appropriate liftover assemblies, refs #36232
• src/hg/htdocs/liftRequest.html
  • lines changed 69, context: html, text, full: html, text
    dbbf12ecd3916a4105cd9191f328a5318ad30a40 Mon Jan 26 13:12:12 2026 -0800
    move the text to after the entry form refs #31811
• src/hg/htdocs/style/HGStyle.css
  • lines changed 58, context: html, text, full: html, text
    ce138738e24cb6e84502440b79490c412f6786f8 Tue Jan 27 03:13:16 2026 -0800
    Reapply "changing superTrack TrackUi quite a bit. This reverts commit e6ee88658405177aee46ddb8902ae93aee5b1378.
  • lines changed 58, context: html, text, full: html, text
    55df1a106590a6c9fd7e3cca90fa6bbad8eb50c4 Thu Jan 29 05:26:21 2026 -0800
    Revert "Reapply "changing superTrack TrackUi quite a bit." This reverts commit ce138738e24cb6e84502440b79490c412f6786f8.
  • lines changed 44, context: html, text, full: html, text
    47ea57080b515e5dad5f658c58feb8944a7e7d61 Thu Jan 29 15:30:26 2026 -0800
    Replace clade/assembly dropdowns with a search bar on most CGIs. Add a recents list to hgGateway and to the species bar and to the 'Genomes' dropdown menu. Track recently selected species in localStorage. Add toGenome and fromGenome arguemnts to hubApi/liftOver in order to find appropriate liftover assemblies, refs #36232
• src/hg/htdocs/style/dataTables-1.10.12.min.css
  • lines changed 1, context: html, text, full: html, text
    65bf003397e55927776facd7654de161ea8c1e20 Fri Jan 30 15:59:33 2026 -0800
    Downloading our major CDNs and changing their references to all be local, there are some more corner cases that were low priority as discussed in the ticket. This work is done to improve performance, expecially for overseas users. Refs #33998
• src/hg/htdocs/style/dataTables-1.13.6.min.css
  • lines changed 1, context: html, text, full: html, text
    65bf003397e55927776facd7654de161ea8c1e20 Fri Jan 30 15:59:33 2026 -0800
    Downloading our major CDNs and changing their references to all be local, there are some more corner cases that were low priority as discussed in the ticket. This work is done to improve performance, expecially for overseas users. Refs #33998
• src/hg/htdocs/style/dataTables-2.2.2.min.css
  • lines changed 1, context: html, text, full: html, text
    65bf003397e55927776facd7654de161ea8c1e20 Fri Jan 30 15:59:33 2026 -0800
    Downloading our major CDNs and changing their references to all be local, there are some more corner cases that were low priority as discussed in the ticket. This work is done to improve performance, expecially for overseas users. Refs #33998
• src/hg/htdocs/style/dataTables.buttons-3.2.2.min.css
  • lines changed 1, context: html, text, full: html, text
    65bf003397e55927776facd7654de161ea8c1e20 Fri Jan 30 15:59:33 2026 -0800
    Downloading our major CDNs and changing their references to all be local, there are some more corner cases that were low priority as discussed in the ticket. This work is done to improve performance, expecially for overseas users. Refs #33998
• src/hg/htdocs/style/dataTables.select-1.7.0.min.css
  • lines changed 1, context: html, text, full: html, text
    65bf003397e55927776facd7654de161ea8c1e20 Fri Jan 30 15:59:33 2026 -0800
    Downloading our major CDNs and changing their references to all be local, there are some more corner cases that were low priority as discussed in the ticket. This work is done to improve performance, expecially for overseas users. Refs #33998
• src/hg/htdocs/style/dataTables.select-3.0.0.min.css
  • lines changed 1, context: html, text, full: html, text
    65bf003397e55927776facd7654de161ea8c1e20 Fri Jan 30 15:59:33 2026 -0800
    Downloading our major CDNs and changing their references to all be local, there are some more corner cases that were low priority as discussed in the ticket. This work is done to improve performance, expecially for overseas users. Refs #33998
• src/hg/htdocs/style/jWest.css
  • lines changed 63, context: html, text, full: html, text
    47ea57080b515e5dad5f658c58feb8944a7e7d61 Thu Jan 29 15:30:26 2026 -0800
    Replace clade/assembly dropdowns with a search bar on most CGIs. Add a recents list to hgGateway and to the species bar and to the 'Genomes' dropdown menu. Track recently selected species in localStorage. Add toGenome and fromGenome arguemnts to hubApi/liftOver in order to find appropriate liftover assemblies, refs #36232
• src/hg/htdocs/style/jstree-3.3.7.min.css
  • lines changed 1, context: html, text, full: html, text
    65bf003397e55927776facd7654de161ea8c1e20 Fri Jan 30 15:59:33 2026 -0800
    Downloading our major CDNs and changing their references to all be local, there are some more corner cases that were low priority as discussed in the ticket. This work is done to improve performance, expecially for overseas users. Refs #33998
• src/hg/htdocs/style/jstree-default/32px.png
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    65bf003397e55927776facd7654de161ea8c1e20 Fri Jan 30 15:59:33 2026 -0800
    Downloading our major CDNs and changing their references to all be local, there are some more corner cases that were low priority as discussed in the ticket. This work is done to improve performance, expecially for overseas users. Refs #33998
• src/hg/htdocs/style/jstree-default/40px.png
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    65bf003397e55927776facd7654de161ea8c1e20 Fri Jan 30 15:59:33 2026 -0800
    Downloading our major CDNs and changing their references to all be local, there are some more corner cases that were low priority as discussed in the ticket. This work is done to improve performance, expecially for overseas users. Refs #33998
• src/hg/htdocs/style/jstree-default/throbber.gif
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    65bf003397e55927776facd7654de161ea8c1e20 Fri Jan 30 15:59:33 2026 -0800
    Downloading our major CDNs and changing their references to all be local, there are some more corner cases that were low priority as discussed in the ticket. This work is done to improve performance, expecially for overseas users. Refs #33998
• src/hg/htdocs/style/liftRequest.css
  • lines changed 1, context: html, text, full: html, text
    2e9c4eff496dbe6ad794e5a3cfdcb88d1f761590 Mon Jan 26 13:13:49 2026 -0800
    the page can be 800px wide refs #31811
• src/hg/htdocs/style/makefile
  • lines changed 5, context: html, text, full: html, text
    65bf003397e55927776facd7654de161ea8c1e20 Fri Jan 30 15:59:33 2026 -0800
    Downloading our major CDNs and changing their references to all be local, there are some more corner cases that were low priority as discussed in the ticket. This work is done to improve performance, expecially for overseas users. Refs #33998
• src/hg/htdocs/style/nice_menu.css
  • lines changed 7, context: html, text, full: html, text
    47ea57080b515e5dad5f658c58feb8944a7e7d61 Thu Jan 29 15:30:26 2026 -0800
    Replace clade/assembly dropdowns with a search bar on most CGIs. Add a recents list to hgGateway and to the species bar and to the 'Genomes' dropdown menu. Track recently selected species in localStorage. Add toGenome and fromGenome arguemnts to hubApi/liftOver in order to find appropriate liftover assemblies, refs #36232
• src/hg/hubApi/dataApi.h
  • lines changed 1, context: html, text, full: html, text
    47ea57080b515e5dad5f658c58feb8944a7e7d61 Thu Jan 29 15:30:26 2026 -0800
    Replace clade/assembly dropdowns with a search bar on most CGIs. Add a recents list to hgGateway and to the species bar and to the 'Genomes' dropdown menu. Track recently selected species in localStorage. Add toGenome and fromGenome arguemnts to hubApi/liftOver in order to find appropriate liftover assemblies, refs #36232
• src/hg/hubApi/findGenome.c
  • lines changed 37, context: html, text, full: html, text
    47ea57080b515e5dad5f658c58feb8944a7e7d61 Thu Jan 29 15:30:26 2026 -0800
    Replace clade/assembly dropdowns with a search bar on most CGIs. Add a recents list to hgGateway and to the species bar and to the 'Genomes' dropdown menu. Track recently selected species in localStorage. Add toGenome and fromGenome arguemnts to hubApi/liftOver in order to find appropriate liftover assemblies, refs #36232
  • lines changed 1, context: html, text, full: html, text
    cc2d4c0b2e4f8fad66d253ec539f7313eaafe5bb Fri Jan 30 18:24:11 2026 -0800
    restore missing line refs #36232
• src/hg/hubApi/hubApi.c
  • lines changed 1, context: html, text, full: html, text
    47ea57080b515e5dad5f658c58feb8944a7e7d61 Thu Jan 29 15:30:26 2026 -0800
    Replace clade/assembly dropdowns with a search bar on most CGIs. Add a recents list to hgGateway and to the species bar and to the 'Genomes' dropdown menu. Track recently selected species in localStorage. Add toGenome and fromGenome arguemnts to hubApi/liftOver in order to find appropriate liftover assemblies, refs #36232
• src/hg/hubApi/liftOver.c
  • lines changed 23, context: html, text, full: html, text
    47ea57080b515e5dad5f658c58feb8944a7e7d61 Thu Jan 29 15:30:26 2026 -0800
    Replace clade/assembly dropdowns with a search bar on most CGIs. Add a recents list to hgGateway and to the species bar and to the 'Genomes' dropdown menu. Track recently selected species in localStorage. Add toGenome and fromGenome arguemnts to hubApi/liftOver in order to find appropriate liftover assemblies, refs #36232
• src/hg/hubApi/tests/expected/test14.gz
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    0be1ae24d41681d9d49d8646aa67b53a8ef2f689 Thu Jan 29 16:38:24 2026 -0800
    Updating tests to remove the hub_ underscore that no longer shows up, and fix the order items are returned from these calls, no RM.
• src/hg/hubApi/tests/expected/test15.gz
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    0be1ae24d41681d9d49d8646aa67b53a8ef2f689 Thu Jan 29 16:38:24 2026 -0800
    Updating tests to remove the hub_ underscore that no longer shows up, and fix the order items are returned from these calls, no RM.
• src/hg/hubApi/tests/expected/test16.gz
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    0be1ae24d41681d9d49d8646aa67b53a8ef2f689 Thu Jan 29 16:38:24 2026 -0800
    Updating tests to remove the hub_ underscore that no longer shows up, and fix the order items are returned from these calls, no RM.
• src/hg/hubApi/tests/makefile
  • lines changed 3, context: html, text, full: html, text
    0be1ae24d41681d9d49d8646aa67b53a8ef2f689 Thu Jan 29 16:38:24 2026 -0800
    Updating tests to remove the hub_ underscore that no longer shows up, and fix the order items are returned from these calls, no RM.
• src/hg/inc/cart.h
  • lines changed 3, context: html, text, full: html, text
    ef2161f0d3079bf41b553ccb01b8e54a35f0be6f Wed Jan 28 01:02:42 2026 -0800
    Adding a cart function to see if any variables matching a wildcard are set, refs #36320
• src/hg/inc/genePred.h
  • lines changed 4, context: html, text, full: html, text
    e745ccb794a88cf79f4e63a375a3eeb93e918563 Mon Jan 26 10:15:44 2026 -0800
    move code to reverse exonFrames to calcLiftOverGenePred() so it will work with the liftOver tool
• src/hg/inc/hui.h
  • lines changed 4, context: html, text, full: html, text
    ce138738e24cb6e84502440b79490c412f6786f8 Tue Jan 27 03:13:16 2026 -0800
    Reapply "changing superTrack TrackUi quite a bit. This reverts commit e6ee88658405177aee46ddb8902ae93aee5b1378.
  • lines changed 4, context: html, text, full: html, text
    55df1a106590a6c9fd7e3cca90fa6bbad8eb50c4 Thu Jan 29 05:26:21 2026 -0800
    Revert "Reapply "changing superTrack TrackUi quite a bit." This reverts commit ce138738e24cb6e84502440b79490c412f6786f8.
• src/hg/inc/jsHelper.h
  • lines changed 3, context: html, text, full: html, text
    47ea57080b515e5dad5f658c58feb8944a7e7d61 Thu Jan 29 15:30:26 2026 -0800
    Replace clade/assembly dropdowns with a search bar on most CGIs. Add a recents list to hgGateway and to the species bar and to the 'Genomes' dropdown menu. Track recently selected species in localStorage. Add toGenome and fromGenome arguemnts to hubApi/liftOver in order to find appropriate liftover assemblies, refs #36232
• src/hg/inc/web.h
  • lines changed 23, context: html, text, full: html, text
    47ea57080b515e5dad5f658c58feb8944a7e7d61 Thu Jan 29 15:30:26 2026 -0800
    Replace clade/assembly dropdowns with a search bar on most CGIs. Add a recents list to hgGateway and to the species bar and to the 'Genomes' dropdown menu. Track recently selected species in localStorage. Add toGenome and fromGenome arguemnts to hubApi/liftOver in order to find appropriate liftover assemblies, refs #36232
• src/hg/js/assemblySearch.js
  • lines changed 1, context: html, text, full: html, text
    7e0265c006a53ca478096ed136cc07712fb593e1 Fri Jan 30 16:52:23 2026 -0800
    beware, returned json data can now include a key "liftable" and it can have the value "null" refs #36232
• src/hg/js/autocompleteCat.js
  • lines changed 87, context: html, text, full: html, text
    47ea57080b515e5dad5f658c58feb8944a7e7d61 Thu Jan 29 15:30:26 2026 -0800
    Replace clade/assembly dropdowns with a search bar on most CGIs. Add a recents list to hgGateway and to the species bar and to the 'Genomes' dropdown menu. Track recently selected species in localStorage. Add toGenome and fromGenome arguemnts to hubApi/liftOver in order to find appropriate liftover assemblies, refs #36232
• src/hg/js/external/bootstrap-3.3.7.min.js
  • lines changed 0, context: html, text, full: html, text
    65bf003397e55927776facd7654de161ea8c1e20 Fri Jan 30 15:59:33 2026 -0800
    Downloading our major CDNs and changing their references to all be local, there are some more corner cases that were low priority as discussed in the ticket. This work is done to improve performance, expecially for overseas users. Refs #33998
• src/hg/js/external/dataTables-1.10.12.min.js
  • lines changed 0, context: html, text, full: html, text
    65bf003397e55927776facd7654de161ea8c1e20 Fri Jan 30 15:59:33 2026 -0800
    Downloading our major CDNs and changing their references to all be local, there are some more corner cases that were low priority as discussed in the ticket. This work is done to improve performance, expecially for overseas users. Refs #33998
• src/hg/js/external/dataTables-1.13.6.min.js
  • lines changed 0, context: html, text, full: html, text
    65bf003397e55927776facd7654de161ea8c1e20 Fri Jan 30 15:59:33 2026 -0800
    Downloading our major CDNs and changing their references to all be local, there are some more corner cases that were low priority as discussed in the ticket. This work is done to improve performance, expecially for overseas users. Refs #33998
• src/hg/js/external/dataTables-2.2.2.min.js
  • lines changed 0, context: html, text, full: html, text
    65bf003397e55927776facd7654de161ea8c1e20 Fri Jan 30 15:59:33 2026 -0800
    Downloading our major CDNs and changing their references to all be local, there are some more corner cases that were low priority as discussed in the ticket. This work is done to improve performance, expecially for overseas users. Refs #33998
• src/hg/js/external/dataTables.buttons-3.2.2.min.js
  • lines changed 0, context: html, text, full: html, text
    65bf003397e55927776facd7654de161ea8c1e20 Fri Jan 30 15:59:33 2026 -0800
    Downloading our major CDNs and changing their references to all be local, there are some more corner cases that were low priority as discussed in the ticket. This work is done to improve performance, expecially for overseas users. Refs #33998
• src/hg/js/external/dataTables.select-1.7.0.min.js
  • lines changed 0, context: html, text, full: html, text
    65bf003397e55927776facd7654de161ea8c1e20 Fri Jan 30 15:59:33 2026 -0800
    Downloading our major CDNs and changing their references to all be local, there are some more corner cases that were low priority as discussed in the ticket. This work is done to improve performance, expecially for overseas users. Refs #33998
• src/hg/js/external/dataTables.select-3.0.0.min.js
  • lines changed 0, context: html, text, full: html, text
    65bf003397e55927776facd7654de161ea8c1e20 Fri Jan 30 15:59:33 2026 -0800
    Downloading our major CDNs and changing their references to all be local, there are some more corner cases that were low priority as discussed in the ticket. This work is done to improve performance, expecially for overseas users. Refs #33998
• src/hg/js/external/jstree-3.3.7.min.js
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    65bf003397e55927776facd7654de161ea8c1e20 Fri Jan 30 15:59:33 2026 -0800
    Downloading our major CDNs and changing their references to all be local, there are some more corner cases that were low priority as discussed in the ticket. This work is done to improve performance, expecially for overseas users. Refs #33998
• src/hg/js/external/makefile
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    65bf003397e55927776facd7654de161ea8c1e20 Fri Jan 30 15:59:33 2026 -0800
    Downloading our major CDNs and changing their references to all be local, there are some more corner cases that were low priority as discussed in the ticket. This work is done to improve performance, expecially for overseas users. Refs #33998
• src/hg/js/facetedComposite.js
  • lines changed 4, context: html, text, full: html, text
    65bf003397e55927776facd7654de161ea8c1e20 Fri Jan 30 15:59:33 2026 -0800
    Downloading our major CDNs and changing their references to all be local, there are some more corner cases that were low priority as discussed in the ticket. This work is done to improve performance, expecially for overseas users. Refs #33998
• src/hg/js/hgGateway.js
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    47ea57080b515e5dad5f658c58feb8944a7e7d61 Thu Jan 29 15:30:26 2026 -0800
    Replace clade/assembly dropdowns with a search bar on most CGIs. Add a recents list to hgGateway and to the species bar and to the 'Genomes' dropdown menu. Track recently selected species in localStorage. Add toGenome and fromGenome arguemnts to hubApi/liftOver in order to find appropriate liftover assemblies, refs #36232
• src/hg/js/hgMyData.js
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    b99f96b3ed42f3644a19890bbb259ab1ca005008 Tue Jan 27 11:16:35 2026 -0800
    HubSpace: when viewing one specific hub directory and then clicking the upload button, make the default choice for the hub name be the on that is being viewed, refs #36830
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    47ea57080b515e5dad5f658c58feb8944a7e7d61 Thu Jan 29 15:30:26 2026 -0800
    Replace clade/assembly dropdowns with a search bar on most CGIs. Add a recents list to hgGateway and to the species bar and to the 'Genomes' dropdown menu. Track recently selected species in localStorage. Add toGenome and fromGenome arguemnts to hubApi/liftOver in order to find appropriate liftover assemblies, refs #36232
• src/hg/js/hgSearch.js
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    47ea57080b515e5dad5f658c58feb8944a7e7d61 Thu Jan 29 15:30:26 2026 -0800
    Replace clade/assembly dropdowns with a search bar on most CGIs. Add a recents list to hgGateway and to the species bar and to the 'Genomes' dropdown menu. Track recently selected species in localStorage. Add toGenome and fromGenome arguemnts to hubApi/liftOver in order to find appropriate liftover assemblies, refs #36232
• src/hg/js/model/hgIntegrator/hgIntegratorModel.js
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    47ea57080b515e5dad5f658c58feb8944a7e7d61 Thu Jan 29 15:30:26 2026 -0800
    Replace clade/assembly dropdowns with a search bar on most CGIs. Add a recents list to hgGateway and to the species bar and to the 'Genomes' dropdown menu. Track recently selected species in localStorage. Add toGenome and fromGenome arguemnts to hubApi/liftOver in order to find appropriate liftover assemblies, refs #36232
• src/hg/js/model/lib/CladeOrgDbMixin.js
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    47ea57080b515e5dad5f658c58feb8944a7e7d61 Thu Jan 29 15:30:26 2026 -0800
    Replace clade/assembly dropdowns with a search bar on most CGIs. Add a recents list to hgGateway and to the species bar and to the 'Genomes' dropdown menu. Track recently selected species in localStorage. Add toGenome and fromGenome arguemnts to hubApi/liftOver in order to find appropriate liftover assemblies, refs #36232
• src/hg/js/react/lib/CladeOrgDb.jsx
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    47ea57080b515e5dad5f658c58feb8944a7e7d61 Thu Jan 29 15:30:26 2026 -0800
    Replace clade/assembly dropdowns with a search bar on most CGIs. Add a recents list to hgGateway and to the species bar and to the 'Genomes' dropdown menu. Track recently selected species in localStorage. Add toGenome and fromGenome arguemnts to hubApi/liftOver in order to find appropriate liftover assemblies, refs #36232
• src/hg/js/react/lib/PositionSearch.jsx
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    47ea57080b515e5dad5f658c58feb8944a7e7d61 Thu Jan 29 15:30:26 2026 -0800
    Replace clade/assembly dropdowns with a search bar on most CGIs. Add a recents list to hgGateway and to the species bar and to the 'Genomes' dropdown menu. Track recently selected species in localStorage. Add toGenome and fromGenome arguemnts to hubApi/liftOver in order to find appropriate liftover assemblies, refs #36232
• src/hg/js/react/lib/SpeciesSearch.jsx
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    47ea57080b515e5dad5f658c58feb8944a7e7d61 Thu Jan 29 15:30:26 2026 -0800
    Replace clade/assembly dropdowns with a search bar on most CGIs. Add a recents list to hgGateway and to the species bar and to the 'Genomes' dropdown menu. Track recently selected species in localStorage. Add toGenome and fromGenome arguemnts to hubApi/liftOver in order to find appropriate liftover assemblies, refs #36232
• src/hg/js/react/lib/TextInput.jsx
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    47ea57080b515e5dad5f658c58feb8944a7e7d61 Thu Jan 29 15:30:26 2026 -0800
    Replace clade/assembly dropdowns with a search bar on most CGIs. Add a recents list to hgGateway and to the species bar and to the 'Genomes' dropdown menu. Track recently selected species in localStorage. Add toGenome and fromGenome arguemnts to hubApi/liftOver in order to find appropriate liftover assemblies, refs #36232
• src/hg/js/react/lib/makefile
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    47ea57080b515e5dad5f658c58feb8944a7e7d61 Thu Jan 29 15:30:26 2026 -0800
    Replace clade/assembly dropdowns with a search bar on most CGIs. Add a recents list to hgGateway and to the species bar and to the 'Genomes' dropdown menu. Track recently selected species in localStorage. Add toGenome and fromGenome arguemnts to hubApi/liftOver in order to find appropriate liftover assemblies, refs #36232
• src/hg/js/utils.js
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    ce138738e24cb6e84502440b79490c412f6786f8 Tue Jan 27 03:13:16 2026 -0800
    Reapply "changing superTrack TrackUi quite a bit. This reverts commit e6ee88658405177aee46ddb8902ae93aee5b1378.
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    55df1a106590a6c9fd7e3cca90fa6bbad8eb50c4 Thu Jan 29 05:26:21 2026 -0800
    Revert "Reapply "changing superTrack TrackUi quite a bit." This reverts commit ce138738e24cb6e84502440b79490c412f6786f8.
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    47ea57080b515e5dad5f658c58feb8944a7e7d61 Thu Jan 29 15:30:26 2026 -0800
    Replace clade/assembly dropdowns with a search bar on most CGIs. Add a recents list to hgGateway and to the species bar and to the 'Genomes' dropdown menu. Track recently selected species in localStorage. Add toGenome and fromGenome arguemnts to hubApi/liftOver in order to find appropriate liftover assemblies, refs #36232
• src/hg/lib/cart.c
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    ef2161f0d3079bf41b553ccb01b8e54a35f0be6f Wed Jan 28 01:02:42 2026 -0800
    Adding a cart function to see if any variables matching a wildcard are set, refs #36320
• src/hg/lib/gbHeader.h
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    65bf003397e55927776facd7654de161ea8c1e20 Fri Jan 30 15:59:33 2026 -0800
    Downloading our major CDNs and changing their references to all be local, there are some more corner cases that were low priority as discussed in the ticket. This work is done to improve performance, expecially for overseas users. Refs #33998
• src/hg/lib/genePred.c
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    e745ccb794a88cf79f4e63a375a3eeb93e918563 Mon Jan 26 10:15:44 2026 -0800
    move code to reverse exonFrames to calcLiftOverGenePred() so it will work with the liftOver tool
• src/hg/lib/hui.c
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    ce138738e24cb6e84502440b79490c412f6786f8 Tue Jan 27 03:13:16 2026 -0800
    Reapply "changing superTrack TrackUi quite a bit. This reverts commit e6ee88658405177aee46ddb8902ae93aee5b1378.
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    55df1a106590a6c9fd7e3cca90fa6bbad8eb50c4 Thu Jan 29 05:26:21 2026 -0800
    Revert "Reapply "changing superTrack TrackUi quite a bit." This reverts commit ce138738e24cb6e84502440b79490c412f6786f8.
• src/hg/lib/jWestHeader.html
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    65bf003397e55927776facd7654de161ea8c1e20 Fri Jan 30 15:59:33 2026 -0800
    Downloading our major CDNs and changing their references to all be local, there are some more corner cases that were low priority as discussed in the ticket. This work is done to improve performance, expecially for overseas users. Refs #33998
• src/hg/lib/jsHelper.c
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    47ea57080b515e5dad5f658c58feb8944a7e7d61 Thu Jan 29 15:30:26 2026 -0800
    Replace clade/assembly dropdowns with a search bar on most CGIs. Add a recents list to hgGateway and to the species bar and to the 'Genomes' dropdown menu. Track recently selected species in localStorage. Add toGenome and fromGenome arguemnts to hubApi/liftOver in order to find appropriate liftover assemblies, refs #36232
  • lines changed 9, context: html, text, full: html, text
    65bf003397e55927776facd7654de161ea8c1e20 Fri Jan 30 15:59:33 2026 -0800
    Downloading our major CDNs and changing their references to all be local, there are some more corner cases that were low priority as discussed in the ticket. This work is done to improve performance, expecially for overseas users. Refs #33998
• src/hg/lib/liftOver.c
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    e745ccb794a88cf79f4e63a375a3eeb93e918563 Mon Jan 26 10:15:44 2026 -0800
    move code to reverse exonFrames to calcLiftOverGenePred() so it will work with the liftOver tool
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    6f2d511f5f6898ff2b48e78c8fa1dee9ac716957 Sun Feb 1 13:29:00 2026 -0800
    move a line of code to prevent printing out a bad genePred no RM
• src/hg/lib/tablesTables.c
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    65bf003397e55927776facd7654de161ea8c1e20 Fri Jan 30 15:59:33 2026 -0800
    Downloading our major CDNs and changing their references to all be local, there are some more corner cases that were low priority as discussed in the ticket. This work is done to improve performance, expecially for overseas users. Refs #33998
• src/hg/lib/web.c
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    47ea57080b515e5dad5f658c58feb8944a7e7d61 Thu Jan 29 15:30:26 2026 -0800
    Replace clade/assembly dropdowns with a search bar on most CGIs. Add a recents list to hgGateway and to the species bar and to the 'Genomes' dropdown menu. Track recently selected species in localStorage. Add toGenome and fromGenome arguemnts to hubApi/liftOver in order to find appropriate liftover assemblies, refs #36232
• src/hg/makeDb/doc/asmHubs/hgdownload.index.html
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    c7eebb45ae05223d9f771acbb6abcbe061c4d6b6 Wed Jan 28 14:45:46 2026 -0800
    changing the word Archive in reference to GenArk to become Repository refs #37027
• src/hg/makeDb/doc/asmHubs/hubIndex.pl
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    c7eebb45ae05223d9f771acbb6abcbe061c4d6b6 Wed Jan 28 14:45:46 2026 -0800
    changing the word Archive in reference to GenArk to become Repository refs #37027
• src/hg/makeDb/doc/asmHubs/sendToHgdownload.sh
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    016fa3f6098cb4f75109efbd048b0327e411e8e4 Wed Jan 28 10:19:59 2026 -0800
    protect the md5sum.txt file do not delete it do not overwrite it
• src/hg/makeDb/doc/hg19.txt
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    fc0444e2770896dfa3e5d4c60b3ef4d506036183 Thu Jan 29 11:41:50 2026 -0800
    Updating the makedoc about the change in the script, which automatically detects and uses the most recent ncbiRefSeq patch version available, refs #36779
• src/hg/makeDb/doc/hg38/gnomad.txt
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    13dc32436ac510521c3366ea68973d3ec4940937 Wed Jan 28 04:48:20 2026 -0800
    adding gnomad3 coverage track, refs #37036
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    7094f49ccc894883750c839779223e4039e0bd16 Thu Jan 29 14:58:17 2026 -0800
    adding gnomad coverage track, refs #37036
• src/hg/makeDb/doc/hg38/hgmd.txt
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    fc0444e2770896dfa3e5d4c60b3ef4d506036183 Thu Jan 29 11:41:50 2026 -0800
    Updating the makedoc about the change in the script, which automatically detects and uses the most recent ncbiRefSeq patch version available, refs #36779
• src/hg/makeDb/doc/hg38/varFreqs.txt
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    5059707121527ccfa37fba0e1bc2617ab15d34b2 Tue Jan 27 08:39:05 2026 -0800
    converting NCBI ALFA to VCF format, necessary for varFreqs merge, refs #36642
• src/hg/makeDb/scripts/alfa_to_vcf.py
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    5059707121527ccfa37fba0e1bc2617ab15d34b2 Tue Jan 27 08:39:05 2026 -0800
    converting NCBI ALFA to VCF format, necessary for varFreqs merge, refs #36642
• src/hg/makeDb/scripts/gnomadCovToBw.py
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    13dc32436ac510521c3366ea68973d3ec4940937 Wed Jan 28 04:48:20 2026 -0800
    adding gnomad3 coverage track, refs #37036
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    6413446eff01d749cfd23e206d4d3da059902759 Fri Jan 30 04:49:02 2026 -0800
    fixing a bug in the gnomad converter and track docs update for the varFreqs track, refs #36642
• src/hg/makeDb/scripts/hgmd/process_hgmd.py
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    a349149ced4bf3e48cc3b36c4308246566ced085 Wed Jan 28 15:42:06 2026 -0800
    Code review edits, #37018
• src/hg/makeDb/trackDb/human/hg38/encode.cCREs.override.ra
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    7e8bb02d95005ad2ed1232915020fe5c5dca5289 Thu Jan 29 18:05:36 2026 -0800
    Adding linkouts to ENCODE3 cCREs, refs #36966
• src/hg/makeDb/trackDb/human/hg38/gnomad.ra
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    13dc32436ac510521c3366ea68973d3ec4940937 Wed Jan 28 04:48:20 2026 -0800
    adding gnomad3 coverage track, refs #37036
• src/hg/makeDb/trackDb/human/hg38/gnomad3Coverage.html
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    7094f49ccc894883750c839779223e4039e0bd16 Thu Jan 29 14:58:17 2026 -0800
    adding gnomad coverage track, refs #37036
• src/hg/makeDb/trackDb/human/hg38/gnomad4ExomeCoverage.html
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    7094f49ccc894883750c839779223e4039e0bd16 Thu Jan 29 14:58:17 2026 -0800
    adding gnomad coverage track, refs #37036
• src/hg/makeDb/trackDb/human/hg38/gnomadCoverage.ra
  • lines changed 96, context: html, text, full: html, text
    13dc32436ac510521c3366ea68973d3ec4940937 Wed Jan 28 04:48:20 2026 -0800
    adding gnomad3 coverage track, refs #37036
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    408c3224d740fb994ab561553848ea054d1ad4df Wed Jan 28 04:57:41 2026 -0800
    fixing up typos in gnomadCoverage track
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    6e3a0adb1ba12087bcb0b6ab98f6ff45c10b1171 Thu Jan 29 07:02:16 2026 -0800
    change scaling after user feedback, refs #36981
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    7094f49ccc894883750c839779223e4039e0bd16 Thu Jan 29 14:58:17 2026 -0800
    adding gnomad coverage track, refs #37036
• src/hg/makeDb/trackDb/human/hg38/recount3.ra
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    8fef2dc7113f6acef0d561c9b8f840759ba04e65 Fri Jan 30 17:07:15 2026 -0800
    Updates to the recount3 track description page and mouseOver, refs #34886
• src/hg/makeDb/trackDb/human/phasedVars.html
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    2cde81f37e3d36224a25ef83d78ecafa9d7ef8a6 Mon Jan 26 14:25:52 2026 -0800
    Adding the Mexico Biobank publication to the track description page, refs #36259
• src/hg/makeDb/trackDb/human/phasedVars.ra
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    e299f89b6d6d2c61a48c5b97875fc126e89e8143 Mon Jan 26 17:22:30 2026 -0800
    Adding the HTML line so the description page appears when you click onto a child, refs #36259
• src/hg/makeDb/trackDb/human/trackDb.ra
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    ce671b11f7dd46e9f57210e4d0ed4209766a3bd0 Mon Jan 26 12:53:40 2026 -0800
    Staging the Phased Variants track on hgwbeta, refs #36259
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    6bd2108b19a9103c186884726831269110a4c1e5 Mon Jan 26 17:11:03 2026 -0800
    Staging the Mexico Biobank track on the RR, refs #36259
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    a85324e30c8ec35aa47c399a076a7791d496ebfb Wed Jan 28 12:15:15 2026 -0800
    Releasing the variant frequencies track for hg38, refs #36642
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    1e2e0e847517a6e9dbadb146d8ee388c29783360 Thu Jan 29 10:14:28 2026 -0800
    Removing the variant frequencies track from the RR, refs #36642
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    dead8387eb8de7074fcc439ec9c9626d15aeed19 Thu Jan 29 13:18:04 2026 -0800
    Updating shortLabel to HGMD 2025 and editing longLabel, refs #36779
• src/hg/makeDb/trackDb/human/varFreqs.html
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    6ba06b49cf98953915f487b3f9080e4dedd2df60 Tue Jan 27 16:31:41 2026 -0800
    Making each line less than 100 characters. Replacing double quotes, <, and > with the HTML entities. Using HTML characters for special characters. Making a section of the Methods for Sfari Spark to use bullet points, refs #36642
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    7fd4df639618f431e81244f1c0ad911e4dcb0bd5 Wed Jan 28 04:56:31 2026 -0800
    adding Australia Biobank and fixing up NCBI Alfa docs, refs #36642
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    6413446eff01d749cfd23e206d4d3da059902759 Fri Jan 30 04:49:02 2026 -0800
    fixing a bug in the gnomad converter and track docs update for the varFreqs track, refs #36642
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    d4e7e1a69b17ccebfc8b558f220dd0e1cc3ba1d0 Mon Feb 2 06:14:27 2026 -0800
    removing regeneron data after rejection of request, code review feedback, refs #36978
• src/hg/makeDb/trackDb/human/varFreqs.ra
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    5059707121527ccfa37fba0e1bc2617ab15d34b2 Tue Jan 27 08:39:05 2026 -0800
    converting NCBI ALFA to VCF format, necessary for varFreqs merge, refs #36642
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    7fd4df639618f431e81244f1c0ad911e4dcb0bd5 Wed Jan 28 04:56:31 2026 -0800
    adding Australia Biobank and fixing up NCBI Alfa docs, refs #36642
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    ca6e4921ffdc8f3f21c2b7110a9c033ec1ca7721 Thu Jan 29 05:26:03 2026 -0800
    adding australia to varfreqs supertrack, refs #36642
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    d4e7e1a69b17ccebfc8b558f220dd0e1cc3ba1d0 Mon Feb 2 06:14:27 2026 -0800
    removing regeneron data after rejection of request, code review feedback, refs #36978
• src/hg/makeDb/trackDb/mouse/mm10/recount3.ra
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    3584f8e32f692961506b33b82be6aa3ace538e43 Sun Feb 1 21:16:12 2026 -0800
    Updates to the mm10 recount3 mouseOver, refs #34886
• src/hg/makeDb/trackDb/recount3.html
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    8fef2dc7113f6acef0d561c9b8f840759ba04e65 Fri Jan 30 17:07:15 2026 -0800
    Updates to the recount3 track description page and mouseOver, refs #34886
• src/hg/makeDb/trackDb/relatedTracks.ra
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    312e8c2cd86604eee47096184210ceebf44382d4 Mon Jan 26 14:56:22 2026 -0800
    Adding the relatedTrack lines for hg38 between the phased variants and variant frequencies tracks, refs #36259
• src/hg/pyLib/hgLib.py
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    65bf003397e55927776facd7654de161ea8c1e20 Fri Jan 30 15:59:33 2026 -0800
    Downloading our major CDNs and changing their references to all be local, there are some more corner cases that were low priority as discussed in the ticket. This work is done to improve performance, expecially for overseas users. Refs #33998
• src/hg/pyLib/hgLib3.py
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    65bf003397e55927776facd7654de161ea8c1e20 Fri Jan 30 15:59:33 2026 -0800
    Downloading our major CDNs and changing their references to all be local, there are some more corner cases that were low priority as discussed in the ticket. This work is done to improve performance, expecially for overseas users. Refs #33998
• src/inc/cheapcgi.h
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    ce138738e24cb6e84502440b79490c412f6786f8 Tue Jan 27 03:13:16 2026 -0800
    Reapply "changing superTrack TrackUi quite a bit. This reverts commit e6ee88658405177aee46ddb8902ae93aee5b1378.
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    55df1a106590a6c9fd7e3cca90fa6bbad8eb50c4 Thu Jan 29 05:26:21 2026 -0800
    Revert "Reapply "changing superTrack TrackUi quite a bit." This reverts commit ce138738e24cb6e84502440b79490c412f6786f8.
• src/inc/common.h
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    ce138738e24cb6e84502440b79490c412f6786f8 Tue Jan 27 03:13:16 2026 -0800
    Reapply "changing superTrack TrackUi quite a bit. This reverts commit e6ee88658405177aee46ddb8902ae93aee5b1378.
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    55df1a106590a6c9fd7e3cca90fa6bbad8eb50c4 Thu Jan 29 05:26:21 2026 -0800
    Revert "Reapply "changing superTrack TrackUi quite a bit." This reverts commit ce138738e24cb6e84502440b79490c412f6786f8.
• src/inc/common.mk
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    af130dd8140ae4fe925032e9534e4adbb2f9f901 Tue Jan 27 14:30:54 2026 -0800
    Restoring static curl. refs #35988
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    3706eefc49cbc3f21f086939ffa77e9d6e684a25 Tue Jan 27 15:02:05 2026 -0800
    Fix for non-hgwdev curl dynanmic dependency.
• src/inc/hash.h
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    249c4b1aadf33329c352c4127b2bffa62faaf039 Wed Jan 28 00:58:52 2026 -0800
    Added hash function to see if any keys match a wildcard value, refs #36320
• src/lib/cheapcgi.c
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    ce138738e24cb6e84502440b79490c412f6786f8 Tue Jan 27 03:13:16 2026 -0800
    Reapply "changing superTrack TrackUi quite a bit. This reverts commit e6ee88658405177aee46ddb8902ae93aee5b1378.
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    55df1a106590a6c9fd7e3cca90fa6bbad8eb50c4 Thu Jan 29 05:26:21 2026 -0800
    Revert "Reapply "changing superTrack TrackUi quite a bit." This reverts commit ce138738e24cb6e84502440b79490c412f6786f8.
• src/lib/common.c
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    ce138738e24cb6e84502440b79490c412f6786f8 Tue Jan 27 03:13:16 2026 -0800
    Reapply "changing superTrack TrackUi quite a bit. This reverts commit e6ee88658405177aee46ddb8902ae93aee5b1378.
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    55df1a106590a6c9fd7e3cca90fa6bbad8eb50c4 Thu Jan 29 05:26:21 2026 -0800
    Revert "Reapply "changing superTrack TrackUi quite a bit." This reverts commit ce138738e24cb6e84502440b79490c412f6786f8.
• src/lib/hash.c
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    249c4b1aadf33329c352c4127b2bffa62faaf039 Wed Jan 28 00:58:52 2026 -0800
    Added hash function to see if any keys match a wildcard value, refs #36320
• src/utils/qa/filterCartDumps.sh
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    6b64c5e8c9b9f5aed293862a54a3d199f210cccd Sun Feb 1 15:44:08 2026 -0800
    Updating the script, increasing the region to 10 Mb, and adding more helpful info to the output, No RM

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