All File Changes

v491_preview2 to v491_base (2025-11-17 to 2025-11-24) v491

• confs/hgwbeta.hg.conf
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    80b6f9d4785e217584338166300f891d44ab6625 Sun Nov 23 01:11:15 2025 -0800
    Installing updated hg.conf files from UCSC servers
• confs/preview.hg.conf
  • lines changed 1, context: html, text, full: html, text
    80b6f9d4785e217584338166300f891d44ab6625 Sun Nov 23 01:11:15 2025 -0800
    Installing updated hg.conf files from UCSC servers
• src/hg/bigCompositeUpdate/README.md
  • lines changed 81, context: html, text, full: html, text
    eef3ac987538affd38eb38ccddf6ce6721f4c6f4 Sun Nov 23 22:03:29 2025 -0800
    Removing bigCompositeUpdate CGI (folded into cartDump), and some kent-ifying of the remaining code. refs #36320
• src/hg/bigCompositeUpdate/bigCompositeUpdate.c
  • lines changed 1, context: html, text, full: html, text
    dbfa5c9cda813297ec034d10037ac91f89ee69d7 Tue Nov 4 21:56:23 2025 -0800
    Removing redundant cart cleanup, refs #36320
  • lines changed 79, context: html, text, full: html, text
    eef3ac987538affd38eb38ccddf6ce6721f4c6f4 Sun Nov 23 22:03:29 2025 -0800
    Removing bigCompositeUpdate CGI (folded into cartDump), and some kent-ifying of the remaining code. refs #36320
• src/hg/bigCompositeUpdate/makefile
  • lines changed 18, context: html, text, full: html, text
    eef3ac987538affd38eb38ccddf6ce6721f4c6f4 Sun Nov 23 22:03:29 2025 -0800
    Removing bigCompositeUpdate CGI (folded into cartDump), and some kent-ifying of the remaining code. refs #36320
• src/hg/cartDump/cartDump.c
  • lines changed 34, context: html, text, full: html, text
    eef3ac987538affd38eb38ccddf6ce6721f4c6f4 Sun Nov 23 22:03:29 2025 -0800
    Removing bigCompositeUpdate CGI (folded into cartDump), and some kent-ifying of the remaining code. refs #36320
• src/hg/hgBlat/hgBlat.c
  • lines changed 10, context: html, text, full: html, text
    faa3f79076ac44a5209f73de8e344ee08880c54b Wed Nov 19 15:38:32 2025 -0800
    Improving the labels around the new rearrangement display check box and mouseover help icon, refs #32857
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 8, context: html, text, full: html, text
    9fd202b891f2e2d5be9cfa807e5d5ba15e7fc02d Fri Nov 21 15:59:50 2025 -0800
    protect the hs1 assembly on the outlinks with db=hs1 instead of genome=hs1 refs #36540
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 4, context: html, text, full: html, text
    c98c3de9ee7469a28f93815b873a1693231791ec Tue Nov 4 21:55:36 2025 -0800
    Fixing dependency on named central database/server in new UI, refs #36320
  • lines changed 91, context: html, text, full: html, text
    eef3ac987538affd38eb38ccddf6ce6721f4c6f4 Sun Nov 23 22:03:29 2025 -0800
    Removing bigCompositeUpdate CGI (folded into cartDump), and some kent-ifying of the remaining code. refs #36320
  • lines changed 76, context: html, text, full: html, text
    e6482750f5f9258ac7578e2f458ef81f634721d2 Sun Nov 23 23:15:11 2025 -0800
    More kent-ifying of the faceted composite code, refs #36320
• src/hg/hgTracks/hgTracks.c
  • lines changed 1, context: html, text, full: html, text
    eef3ac987538affd38eb38ccddf6ce6721f4c6f4 Sun Nov 23 22:03:29 2025 -0800
    Removing bigCompositeUpdate CGI (folded into cartDump), and some kent-ifying of the remaining code. refs #36320
• src/hg/hgTracks/imageV2.c
  • lines changed 5, context: html, text, full: html, text
    3eb95c01ca1df4d988730fc4318a4ad7b4644b9e Sun Nov 23 09:56:48 2025 -0800
    Right-click menu in hgTracks should reflect onlyVisibility settings, refs #36746
• src/hg/hgTracks/simpleTracks.c
  • lines changed 53, context: html, text, full: html, text
    eef3ac987538affd38eb38ccddf6ce6721f4c6f4 Sun Nov 23 22:03:29 2025 -0800
    Removing bigCompositeUpdate CGI (folded into cartDump), and some kent-ifying of the remaining code. refs #36320
• src/hg/hgTracks/wigMafTrack.c
  • lines changed 11, context: html, text, full: html, text
    9dbc95fd97afbb7a278452fb660d7ddc1a28d9c7 Mon Nov 24 09:55:38 2025 -0800
    fix maf frames caching bug #36691
• src/hg/htdocs/allTipsRaw.html
  • lines changed 24, context: html, text, full: html, text
    61241bfbbff01f7888533518b5394984ee64536e Tue Nov 18 12:16:57 2025 -0800
    Adding new tip of the day feature. Only for .ucsc domains, it will display a new tip every weekday on the home page. The script generateTipOfDay.py runs weekdays and overwrites the tipOfDay page using the raw page, saving the used tips in a hash file on the running user (e.g. hive qateam), then recycling the list picking a random tip again once the full list has been run through. This is page and allTips page are autoPushed daily. Refs #19784
• src/hg/htdocs/goldenPath/help/posters.html
  • lines changed 11, context: html, text, full: html, text
    001f48ab4a372d351aa44edb874e0339ecd4d046 Tue Nov 18 16:13:08 2025 -0800
    Adding the ASHG 2020 poster to the poster gallery, refs #36182
• src/hg/htdocs/goldenPath/help/trackDb/trackDbTestBlurbs.html
  • lines changed 37, context: html, text, full: html, text
    d3e54c95d824bfe86f086e130755dd260202f249 Fri Nov 21 10:54:07 2025 -0800
    These files came up in the static doc cron and we decided to drop them, refs #35294
• src/hg/htdocs/goldenPath/statistics/chromocompare.html
  • lines changed 141, context: html, text, full: html, text
    d3e54c95d824bfe86f086e130755dd260202f249 Fri Nov 21 10:54:07 2025 -0800
    These files came up in the static doc cron and we decided to drop them, refs #35294
• src/hg/htdocs/goldenPath/statistics/chromos.html
  • lines changed 141, context: html, text, full: html, text
    d3e54c95d824bfe86f086e130755dd260202f249 Fri Nov 21 10:54:07 2025 -0800
    These files came up in the static doc cron and we decided to drop them, refs #35294
• src/hg/htdocs/goldenPath/statistics/clone-coverage.html
  • lines changed 10, context: html, text, full: html, text
    d3e54c95d824bfe86f086e130755dd260202f249 Fri Nov 21 10:54:07 2025 -0800
    These files came up in the static doc cron and we decided to drop them, refs #35294
• src/hg/htdocs/images/configureOptions.png
  • lines changed 0, context: html, text, full: html, text
    61241bfbbff01f7888533518b5394984ee64536e Tue Nov 18 12:16:57 2025 -0800
    Adding new tip of the day feature. Only for .ucsc domains, it will display a new tip every weekday on the home page. The script generateTipOfDay.py runs weekdays and overwrites the tipOfDay page using the raw page, saving the used tips in a hash file on the running user (e.g. hive qateam), then recycling the list picking a random tip again once the full list has been run through. This is page and allTips page are autoPushed daily. Refs #19784
• src/hg/htdocs/images/didYouKnow.png
  • lines changed 0, context: html, text, full: html, text
    61241bfbbff01f7888533518b5394984ee64536e Tue Nov 18 12:16:57 2025 -0800
    Adding new tip of the day feature. Only for .ucsc domains, it will display a new tip every weekday on the home page. The script generateTipOfDay.py runs weekdays and overwrites the tipOfDay page using the raw page, saving the used tips in a hash file on the running user (e.g. hive qateam), then recycling the list picking a random tip again once the full list has been run through. This is page and allTips page are autoPushed daily. Refs #19784
• src/hg/htdocs/images/downloadCurrentRegion.png
  • lines changed 0, context: html, text, full: html, text
    61241bfbbff01f7888533518b5394984ee64536e Tue Nov 18 12:16:57 2025 -0800
    Adding new tip of the day feature. Only for .ucsc domains, it will display a new tip every weekday on the home page. The script generateTipOfDay.py runs weekdays and overwrites the tipOfDay page using the raw page, saving the used tips in a hash file on the running user (e.g. hive qateam), then recycling the list picking a random tip again once the full list has been run through. This is page and allTips page are autoPushed daily. Refs #19784
• src/hg/htdocs/images/editTitle.png
  • lines changed 0, context: html, text, full: html, text
    61241bfbbff01f7888533518b5394984ee64536e Tue Nov 18 12:16:57 2025 -0800
    Adding new tip of the day feature. Only for .ucsc domains, it will display a new tip every weekday on the home page. The script generateTipOfDay.py runs weekdays and overwrites the tipOfDay page using the raw page, saving the used tips in a hash file on the running user (e.g. hive qateam), then recycling the list picking a random tip again once the full list has been run through. This is page and allTips page are autoPushed daily. Refs #19784
• src/hg/htdocs/images/encode4cCREsBiosampleSpectrum.png
  • lines changed 0, context: html, text, full: html, text
    108195970773b6ad987e5c1f2562fdd4d177c5e1 Mon Nov 17 17:19:00 2025 -0800
    Feedback from Zhiping. Updated the body map image, fixed the priorities so that the biosample signals all show together, and updated the mouseOver and filter based on the new file. Refs #34109
• src/hg/htdocs/images/multiRegionButtonTip.png
  • lines changed 0, context: html, text, full: html, text
    61241bfbbff01f7888533518b5394984ee64536e Tue Nov 18 12:16:57 2025 -0800
    Adding new tip of the day feature. Only for .ucsc domains, it will display a new tip every weekday on the home page. The script generateTipOfDay.py runs weekdays and overwrites the tipOfDay page using the raw page, saving the used tips in a hash file on the running user (e.g. hive qateam), then recycling the list picking a random tip again once the full list has been run through. This is page and allTips page are autoPushed daily. Refs #19784
• src/hg/htdocs/images/recommendedTrackSetMenu.png
  • lines changed 0, context: html, text, full: html, text
    61241bfbbff01f7888533518b5394984ee64536e Tue Nov 18 12:16:57 2025 -0800
    Adding new tip of the day feature. Only for .ucsc domains, it will display a new tip every weekday on the home page. The script generateTipOfDay.py runs weekdays and overwrites the tipOfDay page using the raw page, saving the used tips in a hash file on the running user (e.g. hive qateam), then recycling the list picking a random tip again once the full list has been run through. This is page and allTips page are autoPushed daily. Refs #19784
• src/hg/htdocs/images/rightClickZoom.png
  • lines changed 0, context: html, text, full: html, text
    61241bfbbff01f7888533518b5394984ee64536e Tue Nov 18 12:16:57 2025 -0800
    Adding new tip of the day feature. Only for .ucsc domains, it will display a new tip every weekday on the home page. The script generateTipOfDay.py runs weekdays and overwrites the tipOfDay page using the raw page, saving the used tips in a hash file on the running user (e.g. hive qateam), then recycling the list picking a random tip again once the full list has been run through. This is page and allTips page are autoPushed daily. Refs #19784
• src/hg/htdocs/index.html
  • lines changed 11, context: html, text, full: html, text
    61241bfbbff01f7888533518b5394984ee64536e Tue Nov 18 12:16:57 2025 -0800
    Adding new tip of the day feature. Only for .ucsc domains, it will display a new tip every weekday on the home page. The script generateTipOfDay.py runs weekdays and overwrites the tipOfDay page using the raw page, saving the used tips in a hash file on the running user (e.g. hive qateam), then recycling the list picking a random tip again once the full list has been run through. This is page and allTips page are autoPushed daily. Refs #19784
• src/hg/htdocs/style/facetedComposite.css
  • lines changed 0, context: html, text, full: html, text
    032a28a3e535df744037191c1fed40776b275844 Sun Nov 23 20:06:28 2025 -0800
    Renaming bigComposite to facetedComposite, since big means something special, refs #36320
• src/hg/htdocs/style/makefile
  • lines changed 1, context: html, text, full: html, text
    eef3ac987538affd38eb38ccddf6ce6721f4c6f4 Sun Nov 23 22:03:29 2025 -0800
    Removing bigCompositeUpdate CGI (folded into cartDump), and some kent-ifying of the remaining code. refs #36320
• src/hg/htdocs/testToc.html
  • lines changed 35, context: html, text, full: html, text
    d3e54c95d824bfe86f086e130755dd260202f249 Fri Nov 21 10:54:07 2025 -0800
    These files came up in the static doc cron and we decided to drop them, refs #35294
• src/hg/htdocs/tipOfDay.html
  • lines changed 1, context: html, text, full: html, text
    c1d1bee722a66ed8e53c5afa6e53c3adcd4cd493 Tue Nov 18 20:02:32 2025 -0800
    Temporarily adding this page to git so I can push out the page manually.
• src/hg/inc/trackDb.h
  • lines changed 5, context: html, text, full: html, text
    98d595118a466c5ef78850d88a2e41f06049d548 Wed Nov 19 14:21:02 2025 -0800
    Max prefers to have one shared copy of the routine. This changes does not affect functionality, just moves the routine into the trackDb.c lib file. Feedback from Max code review. refs #28113
  • lines changed 1, context: html, text, full: html, text
    4ae605479b0a70ba1399018687433df8a50ba860 Wed Nov 19 14:24:26 2025 -0800
    updated the code comment for the isCOmplexSetting().
  • lines changed 1, context: html, text, full: html, text
    d4e76665e938408d8decc4beb257809fa6b22c78 Wed Nov 19 14:28:06 2025 -0800
    fixed the code comment terminating characters for the isComplexSetting().
• src/hg/js/bigComposite.js
  • lines changed 13, context: html, text, full: html, text
    dae1e675b0b01daeba5f781b4818ec5a9e372d04 Tue Nov 4 22:17:57 2025 -0800
    Getting javascript for the new container type to pass jslint, refs #36320
• src/hg/js/facetedComposite.js
  • lines changed 0, context: html, text, full: html, text
    032a28a3e535df744037191c1fed40776b275844 Sun Nov 23 20:06:28 2025 -0800
    Renaming bigComposite to facetedComposite, since big means something special, refs #36320
  • lines changed 5, context: html, text, full: html, text
    eef3ac987538affd38eb38ccddf6ce6721f4c6f4 Sun Nov 23 22:03:29 2025 -0800
    Removing bigCompositeUpdate CGI (folded into cartDump), and some kent-ifying of the remaining code. refs #36320
• src/hg/js/hgTracks.js
  • lines changed 7, context: html, text, full: html, text
    9af04e0e3c5af3663149d78b1bdb0581ff0654a5 Tue Nov 18 07:37:22 2025 -0800
    commit ae63ce55185746c5f was a mistake, happened right before the build and was not caught in code review. It includes mostly harmless changes, but one that affects the UI (I had taken back the CSS change before the build). Rather than reverting the entire commit now, I am keeping the patch minimal and only comment out a few javascript lines. refs #36726
  • lines changed 20, context: html, text, full: html, text
    3eb95c01ca1df4d988730fc4318a4ad7b4644b9e Sun Nov 23 09:56:48 2025 -0800
    Right-click menu in hgTracks should reflect onlyVisibility settings, refs #36746
• src/hg/js/jshintrc.json
  • lines changed 1, context: html, text, full: html, text
    dae1e675b0b01daeba5f781b4818ec5a9e372d04 Tue Nov 4 22:17:57 2025 -0800
    Getting javascript for the new container type to pass jslint, refs #36320
• src/hg/js/makefile
  • lines changed 1, context: html, text, full: html, text
    eef3ac987538affd38eb38ccddf6ce6721f4c6f4 Sun Nov 23 22:03:29 2025 -0800
    Removing bigCompositeUpdate CGI (folded into cartDump), and some kent-ifying of the remaining code. refs #36320
• src/hg/js/utils.js
  • lines changed 1, context: html, text, full: html, text
    3a4801b70a7c73d3b0d2a543f641111c346691a0 Fri Nov 21 22:32:01 2025 -0800
    fixing jquery version bug, refs #36743
• src/hg/lib/hdb.c
  • lines changed 2, context: html, text, full: html, text
    75f1385d737808f6df3d81103f5427cf786b9cef Thu Nov 20 10:32:49 2025 -0800
    Fixing issue with apiKeys not validating when the central server is remote, refs #36428
• src/hg/lib/hui.c
  • lines changed 1, context: html, text, full: html, text
    fee89631699bd5bdfb821e27ec3cc386c98628cd Sun Nov 23 21:42:45 2025 -0800
    Setting a url on bed3 tracks shouldn't crash because idInUrl is undefined, no ticket
• src/hg/lib/trackDb.c
  • lines changed 52, context: html, text, full: html, text
    98d595118a466c5ef78850d88a2e41f06049d548 Wed Nov 19 14:21:02 2025 -0800
    Max prefers to have one shared copy of the routine. This changes does not affect functionality, just moves the routine into the trackDb.c lib file. Feedback from Max code review. refs #28113
  • lines changed 1, context: html, text, full: html, text
    4ae605479b0a70ba1399018687433df8a50ba860 Wed Nov 19 14:24:26 2025 -0800
    updated the code comment for the isCOmplexSetting().
  • lines changed 1, context: html, text, full: html, text
    d4e76665e938408d8decc4beb257809fa6b22c78 Wed Nov 19 14:28:06 2025 -0800
    fixed the code comment terminating characters for the isComplexSetting().
• src/hg/makeDb/doc/bacteriaAsmHub/bacteria.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    4637fe065c495e4e12805521872e51dc45880fff Wed Nov 19 15:02:30 2025 -0800
    adding several per user request refs #29545
• src/hg/makeDb/doc/hg38/g2p.txt
  • lines changed 165, context: html, text, full: html, text
    0c05142eca44cb0c609e93edb2bf2b570b2951ad Wed Nov 19 13:32:23 2025 -0800
    Adding the makedoc for the G2P track, refs #36469
• src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    83b077f17c6a2b4a297e48c035b64ac6ecc86b44 Wed Nov 19 14:48:53 2025 -0800
    NCBI assembly name change refs #29545
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    4637fe065c495e4e12805521872e51dc45880fff Wed Nov 19 15:02:30 2025 -0800
    adding several per user request refs #29545
• src/hg/makeDb/doc/viralAsmHub/viral.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    4637fe065c495e4e12805521872e51dc45880fff Wed Nov 19 15:02:30 2025 -0800
    adding several per user request refs #29545
• src/hg/makeDb/trackDb/cpgIslandSuper.html
  • lines changed 1, context: html, text, full: html, text
    62b1428915cc2c8b9acbf46a86c1248833257efe Mon Nov 17 18:50:32 2025 -0800
    changing rest of genome-source references to github, refs #34485
• src/hg/makeDb/trackDb/ebola/eboVir3/cons160way.html
  • lines changed 1, context: html, text, full: html, text
    62b1428915cc2c8b9acbf46a86c1248833257efe Mon Nov 17 18:50:32 2025 -0800
    changing rest of genome-source references to github, refs #34485
• src/hg/makeDb/trackDb/human/clinvar.html
  • lines changed 5, context: html, text, full: html, text
    44943adffb5893ab0843285b1992928de03fa4b8 Thu Nov 20 22:05:10 2025 -0800
    changing the clinvar docs to reflect new update frequency, no redmine
• src/hg/makeDb/trackDb/human/dbSnp152.shared.html
  • lines changed 2, context: html, text, full: html, text
    62b1428915cc2c8b9acbf46a86c1248833257efe Mon Nov 17 18:50:32 2025 -0800
    changing rest of genome-source references to github, refs #34485
• src/hg/makeDb/trackDb/human/dbSnp153Composite.html
  • lines changed 2, context: html, text, full: html, text
    62b1428915cc2c8b9acbf46a86c1248833257efe Mon Nov 17 18:50:32 2025 -0800
    changing rest of genome-source references to github, refs #34485
• src/hg/makeDb/trackDb/human/dbSnp155Composite.html
  • lines changed 2, context: html, text, full: html, text
    62b1428915cc2c8b9acbf46a86c1248833257efe Mon Nov 17 18:50:32 2025 -0800
    changing rest of genome-source references to github, refs #34485
• src/hg/makeDb/trackDb/human/g2p.ra
  • lines changed 1, context: html, text, full: html, text
    653f5468eda92fa79e03ad398d467cc46ecdcdc5 Tue Nov 18 16:10:16 2025 -0800
    Updating the link outs for the G2P track, refs #36469
• src/hg/makeDb/trackDb/human/hg19/gnomad.html
  • lines changed 4, context: html, text, full: html, text
    0b958dd85cc28a958ed324ee77020ab9b7bd36d4 Fri Nov 21 17:46:22 2025 -0800
    Fixed gnomad MPC bullet point in the gnomad.html, made some edits to the gnomadMpc description page, updated the longLabel, and made some edits to the track's mouseover, refs #36531
• src/hg/makeDb/trackDb/human/hg19/gnomadMpc.html
  • lines changed 80, context: html, text, full: html, text
    0b958dd85cc28a958ed324ee77020ab9b7bd36d4 Fri Nov 21 17:46:22 2025 -0800
    Fixed gnomad MPC bullet point in the gnomad.html, made some edits to the gnomadMpc description page, updated the longLabel, and made some edits to the track's mouseover, refs #36531
• src/hg/makeDb/trackDb/human/hg19/trackDb.gnomad.ra
  • lines changed 5, context: html, text, full: html, text
    0b958dd85cc28a958ed324ee77020ab9b7bd36d4 Fri Nov 21 17:46:22 2025 -0800
    Fixed gnomad MPC bullet point in the gnomad.html, made some edits to the gnomadMpc description page, updated the longLabel, and made some edits to the track's mouseover, refs #36531
• src/hg/makeDb/trackDb/human/hg38/altSequence.html
  • lines changed 2, context: html, text, full: html, text
    62b1428915cc2c8b9acbf46a86c1248833257efe Mon Nov 17 18:50:32 2025 -0800
    changing rest of genome-source references to github, refs #34485
• src/hg/makeDb/trackDb/human/hg38/coreCollection.html
  • lines changed 1, context: html, text, full: html, text
    108195970773b6ad987e5c1f2562fdd4d177c5e1 Mon Nov 17 17:19:00 2025 -0800
    Feedback from Zhiping. Updated the body map image, fixed the priorities so that the biosample signals all show together, and updated the mouseOver and filter based on the new file. Refs #34109
• src/hg/makeDb/trackDb/human/hg38/encode.cCREs.override.ra
  • lines changed 1, context: html, text, full: html, text
    108195970773b6ad987e5c1f2562fdd4d177c5e1 Mon Nov 17 17:19:00 2025 -0800
    Feedback from Zhiping. Updated the body map image, fixed the priorities so that the biosample signals all show together, and updated the mouseOver and filter based on the new file. Refs #34109
• src/hg/makeDb/trackDb/human/hg38/encode4.ccres.ra
  • lines changed 850, context: html, text, full: html, text
    108195970773b6ad987e5c1f2562fdd4d177c5e1 Mon Nov 17 17:19:00 2025 -0800
    Feedback from Zhiping. Updated the body map image, fixed the priorities so that the biosample signals all show together, and updated the mouseOver and filter based on the new file. Refs #34109
• src/hg/makeDb/trackDb/human/varFreqs.html
  • lines changed 3, context: html, text, full: html, text
    9b60e5505dd8218f538ce44ca13bd4bd86df1d38 Tue Nov 18 13:22:09 2025 -0800
    Fixing typos found in code review, refs #36722
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    d8bde2e6d8e0100c915d486f9c44beb06f638a18 Thu Nov 20 22:07:13 2025 -0800
    update to varfreqs docs page
• src/hg/makeDb/trackDb/rmsk.html
  • lines changed 1, context: html, text, full: html, text
    62b1428915cc2c8b9acbf46a86c1248833257efe Mon Nov 17 18:50:32 2025 -0800
    changing rest of genome-source references to github, refs #34485
• src/hg/makeDb/trackDb/tagTypes.tab
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    57d9b7d505f03526b2298d3e74a7fe675f25bf93 Sun Nov 23 22:04:03 2025 -0800
    onlyVisibility trackDb setting should be more widely available, refs #36320
• src/hg/makefile
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    eef3ac987538affd38eb38ccddf6ce6721f4c6f4 Sun Nov 23 22:03:29 2025 -0800
    Removing bigCompositeUpdate CGI (folded into cartDump), and some kent-ifying of the remaining code. refs #36320
• src/hg/ratStuff/mafAddIRows/mafAddIRows.c
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    b6f7fd1e76673d2fd96e46ede11a11f421e15675 Sat Nov 22 17:13:04 2025 -0800
    now correctly managing GenArk GCA and GCF assembly names refs #34370
• src/hg/ratStuff/mafSplit/mafSplit.c
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    c31d6f7174025d44270f64f086b06df10b4196a6 Sat Nov 22 17:14:37 2025 -0800
    now correctly managing GenArk GCA and GCF assembly names refs #34370
• src/hg/utils/automation/aws/hubStart.txt
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    62b1428915cc2c8b9acbf46a86c1248833257efe Mon Nov 17 18:50:32 2025 -0800
    changing rest of genome-source references to github, refs #34485
• src/hg/utils/automation/faToHub.sh
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    62b1428915cc2c8b9acbf46a86c1248833257efe Mon Nov 17 18:50:32 2025 -0800
    changing rest of genome-source references to github, refs #34485
• src/hg/utils/automation/genbank/README.txt
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    62b1428915cc2c8b9acbf46a86c1248833257efe Mon Nov 17 18:50:32 2025 -0800
    changing rest of genome-source references to github, refs #34485
• src/hg/utils/automation/openStack/paraHubSetup.sh
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    62b1428915cc2c8b9acbf46a86c1248833257efe Mon Nov 17 18:50:32 2025 -0800
    changing rest of genome-source references to github, refs #34485
• src/hg/utils/hubCheck/hubCheck.c
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    98d595118a466c5ef78850d88a2e41f06049d548 Wed Nov 19 14:21:02 2025 -0800
    Max prefers to have one shared copy of the routine. This changes does not affect functionality, just moves the routine into the trackDb.c lib file. Feedback from Max code review. refs #28113
• src/hg/utils/otto/genArk/liftOverNew.sh
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    ccff28e568396045db4f31d9fa577412b017e837 Wed Nov 19 14:28:51 2025 -0800
    now getting the /gbdb/*/liftOver/ files on the RR push list refs #35575
• src/hg/utils/otto/genArk/whatIsNew.sh
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    ccff28e568396045db4f31d9fa577412b017e837 Wed Nov 19 14:28:51 2025 -0800
    now getting the /gbdb/*/liftOver/ files on the RR push list refs #35575
• src/hg/utils/otto/otto.crontab
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    61241bfbbff01f7888533518b5394984ee64536e Tue Nov 18 12:16:57 2025 -0800
    Adding new tip of the day feature. Only for .ucsc domains, it will display a new tip every weekday on the home page. The script generateTipOfDay.py runs weekdays and overwrites the tipOfDay page using the raw page, saving the used tips in a hash file on the running user (e.g. hive qateam), then recycling the list picking a random tip again once the full list has been run through. This is page and allTips page are autoPushed daily. Refs #19784
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    04dfe89a68c03f92bb7ec2344b5391c0e58be2a4 Wed Nov 19 10:34:30 2025 -0800
    Silencing the cron now that it has run successfully.
• src/hg/utils/tdbQuery/tdbQuery.c
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    98d595118a466c5ef78850d88a2e41f06049d548 Wed Nov 19 14:21:02 2025 -0800
    Max prefers to have one shared copy of the routine. This changes does not affect functionality, just moves the routine into the trackDb.c lib file. Feedback from Max code review. refs #28113
• src/hg/utils/twoBitMask/makefile
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    986f3f122a40cb28b2ac4cc6c51048784a7ea872 Sat Nov 22 15:39:03 2025 -0800
    add test for bigBed input refs #36672
• src/hg/utils/twoBitMask/tests/input/testMask1.bb
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    986f3f122a40cb28b2ac4cc6c51048784a7ea872 Sat Nov 22 15:39:03 2025 -0800
    add test for bigBed input refs #36672
• src/hg/utils/twoBitMask/twoBitMask.c
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    af3fb358fdeee7bf9080bdee719eb0cc1d4b4c72 Sat Nov 22 15:32:57 2025 -0800
    allow input to be a bigBed file refs #36672
• src/lib/htmshell.c
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    eef3ac987538affd38eb38ccddf6ce6721f4c6f4 Sun Nov 23 22:03:29 2025 -0800
    Removing bigCompositeUpdate CGI (folded into cartDump), and some kent-ifying of the remaining code. refs #36320
• src/product/installer/browserSetup.sh
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    62b1428915cc2c8b9acbf46a86c1248833257efe Mon Nov 17 18:50:32 2025 -0800
    changing rest of genome-source references to github, refs #34485
• src/product/scripts/README
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    62b1428915cc2c8b9acbf46a86c1248833257efe Mon Nov 17 18:50:32 2025 -0800
    changing rest of genome-source references to github, refs #34485
• src/product/scripts/README.trashCleaning
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    62b1428915cc2c8b9acbf46a86c1248833257efe Mon Nov 17 18:50:32 2025 -0800
    changing rest of genome-source references to github, refs #34485
• src/product/scripts/kentSrcUpdate.sh
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    62b1428915cc2c8b9acbf46a86c1248833257efe Mon Nov 17 18:50:32 2025 -0800
    changing rest of genome-source references to github, refs #34485
• src/userApps/Makefile
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    62b1428915cc2c8b9acbf46a86c1248833257efe Mon Nov 17 18:50:32 2025 -0800
    changing rest of genome-source references to github, refs #34485
• src/userApps/README
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    62b1428915cc2c8b9acbf46a86c1248833257efe Mon Nov 17 18:50:32 2025 -0800
    changing rest of genome-source references to github, refs #34485
• src/userApps/fetchKentSource.sh
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    62b1428915cc2c8b9acbf46a86c1248833257efe Mon Nov 17 18:50:32 2025 -0800
    changing rest of genome-source references to github, refs #34485
• src/utils/qa/generateTipOfDay.py
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    61241bfbbff01f7888533518b5394984ee64536e Tue Nov 18 12:16:57 2025 -0800
    Adding new tip of the day feature. Only for .ucsc domains, it will display a new tip every weekday on the home page. The script generateTipOfDay.py runs weekdays and overwrites the tipOfDay page using the raw page, saving the used tips in a hash file on the running user (e.g. hive qateam), then recycling the list picking a random tip again once the full list has been run through. This is page and allTips page are autoPushed daily. Refs #19784
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    5cb46a8ecf2d401cf580f74780ca329f1dbc7a62 Tue Nov 18 15:56:45 2025 -0800
    Tweaking the directory for the save file since otto doesn't have a hive dir.
• src/utils/qa/makefile
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    fc9a0597b86ca7e934a3b4b3b495b310bc17321d Tue Nov 18 12:19:13 2025 -0800
    Forgot to add the script to the makefile, refs #19784

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