All File Changes

v463_preview2 to v463_base (2024-03-25 to 2024-04-01) v463

• confs/asia.hg.conf
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    0dda0e6dd1d89a61a2cc5e481173e4405d36c6c8 Sun Mar 31 01:11:21 2024 -0700
    Installing updated hg.conf files from UCSC servers
• confs/euro.hg.conf
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    0dda0e6dd1d89a61a2cc5e481173e4405d36c6c8 Sun Mar 31 01:11:21 2024 -0700
    Installing updated hg.conf files from UCSC servers
• confs/hgwdev.hg.conf
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    0dda0e6dd1d89a61a2cc5e481173e4405d36c6c8 Sun Mar 31 01:11:21 2024 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/hgTracks/hgTracks.c
  • lines changed 34, context: html, text, full: html, text
    3f5d580335f671dc10964ec9e5b549cb3cb9c367 Tue Mar 26 06:36:26 2024 -0700
    adding view chrom sizes menu entry and improving the seq view page a little, refs #25796
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    278473e4cc842cfbc4b46094dfb170572c8dbcd1 Thu Mar 28 12:16:46 2024 -0700
    taking back assembly info link for next build, email from Lou
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    997313ba169e4423867bb78b32165b8f6b858c53 Thu Mar 28 16:15:09 2024 -0700
    Revert "taking back assembly info link for next build, email from Lou" This reverts commit 278473e4cc842cfbc4b46094dfb170572c8dbcd1.
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    ae50b52c96908b7abb9af9f456d386ce141a3be3 Thu Mar 28 16:17:38 2024 -0700
    trying again to fix the build, email from Lou
• src/hg/hgTracks/menu.c
  • lines changed 3, context: html, text, full: html, text
    3f5d580335f671dc10964ec9e5b549cb3cb9c367 Tue Mar 26 06:36:26 2024 -0700
    adding view chrom sizes menu entry and improving the seq view page a little, refs #25796
• src/hg/htdocs/FAQ/FAQlink.html
  • lines changed 101, context: html, text, full: html, text
    837fb9fdc2e3db16abf0c91e3382acc7e3b84191 Thu Mar 28 12:39:08 2024 -0700
    Added optional URL parameters from customTrack.html#SHARE, updated them for hg38, and added them to FAQlink.html#trackViz, refs #30575
• src/hg/htdocs/goldenPath/help/customTrack.html
  • lines changed 24, context: html, text, full: html, text
    34a93745ddac680c98b63da5f035cb5d8f528a44 Tue Mar 26 16:29:38 2024 -0700
    Redesigning the layout of the customTrack help page. Adding a table of contents, refs #19736
• src/hg/htdocs/goldenPath/help/customTrackText.html
  • lines changed 557, context: html, text, full: html, text
    34a93745ddac680c98b63da5f035cb5d8f528a44 Tue Mar 26 16:29:38 2024 -0700
    Redesigning the layout of the customTrack help page. Adding a table of contents, refs #19736
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    d60963c11b6d1f67e678c6ff2cf9c82f2ada9e12 Tue Mar 26 17:28:58 2024 -0700
    Encouraging session use as the first option when sharing custom tracks, refs #23842
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 173, context: html, text, full: html, text
    8555ec47e45208a9e8a9466cae97238fade7699a Thu Mar 28 11:56:22 2024 -0700
    Updating the Sharing Track Hubs section for hgTrackHubHelp.html, refs #21107
• src/hg/htdocs/goldenPath/help/hgTracksHelp.html
  • lines changed 2, context: html, text, full: html, text
    34a93745ddac680c98b63da5f035cb5d8f528a44 Tue Mar 26 16:29:38 2024 -0700
    Redesigning the layout of the customTrack help page. Adding a table of contents, refs #19736
• src/hg/htdocs/goldenPath/newsarch.html
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    6598d410edef09428c6b5f1ce5bb1f5ff149cf41 Mon Mar 25 16:10:53 2024 -0700
    Fixing a typo, refs #33289
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    6a60cdb51e2832102b71d7b88c6740825720929f Tue Mar 26 12:19:53 2024 -0700
    Announcing the release of the gnomAD v4 Constraint Metrics (hg38) and gnomAD Non-cancer filter (hg19/hg38) tracks, refs #33084 #32916
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    41e0c6eca3423830e7bb7601fc1a3d45c3deb72d Tue Mar 26 12:32:58 2024 -0700
    Fixing typos, refs #33084 #32916
• src/hg/htdocs/indexNews.html
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    6a60cdb51e2832102b71d7b88c6740825720929f Tue Mar 26 12:19:53 2024 -0700
    Announcing the release of the gnomAD v4 Constraint Metrics (hg38) and gnomAD Non-cancer filter (hg19/hg38) tracks, refs #33084 #32916
• src/hg/inc/versionInfo.h
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    885271695ba17ace9cad2c1b3fff5676850cdbfe Mon Apr 1 10:59:35 2024 -0700
    New version number v463
• src/hg/js/analytics.js
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    0d65d7b55790ef74103609ba5876c776ba55dca2 Thu Mar 28 16:36:28 2024 -0700
    Using the same property for all RR machines, refs #33272
• src/hg/js/utils.js
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    3fda83d1699342b57c5512ca0b29f89be145cb4b Tue Mar 26 15:58:52 2024 -0700
    Changing the copy button to to always say the same statement, refs #33248
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    653a84792fd3352f80edde07a204524000753006 Thu Mar 28 15:06:47 2024 -0700
    Make secondary tooltop timer much longer, refs #33301
• src/hg/makeDb/doc/asmHubs/lastzRuns.txt
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    994fbb05bd562ec59ff2e8d55218fcb149543dd1 Sat Mar 30 15:21:06 2024 -0700
    oviAri3 to GCF_016772045.2 lastz/chain/net run for user, refs #33280
• src/hg/makeDb/doc/asmHubs/master.run.list
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    bc67d5db33dff1145794043430e6c6ee773ebd8a Tue Mar 26 14:04:49 2024 -0700
    adding invertebrate Corbicula_fluminea per user request, refs #29545
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    1bf83faa56e30270fe61eea966b02d3bbb3966aa Fri Mar 29 17:54:43 2024 -0700
    adding mammals Phodopus_sungorus per user liftOver request, refs #33276
• src/hg/makeDb/doc/hg38/gencode.txt
  • lines changed 1, context: html, text, full: html, text
    e5c776b067ca55054ce50c7910c195daa9637fa5 Wed Mar 27 20:16:09 2024 -0700
    reimport gencodeV46 pre-release to pick up GENCODE_Primary tag
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
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    1c8081a7e1da51c52c6221510a9afdee43081980 Tue Mar 26 14:25:47 2024 -0700
    adding Corbicula_fluminea Asian clam (DE_01 2016) refs #29545
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
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    b1868759bc1a5edcf4ac9a0dfb6843c7caa0f0c1 Fri Mar 29 18:34:55 2024 -0700
    adding Phodopus_sungorus Siberian hamster (SSSS 2022), refs #33276
• src/hg/makeDb/doc/mm10.txt
  • lines changed 83, context: html, text, full: html, text
    9f3484cc0500569ffe999e9514c79746621ef087 Sat Mar 30 15:12:29 2024 -0700
    mm10 to GCF_016772045.2 lastz/chain/net run for user, refs #33231
• src/hg/makeDb/doc/mm39/lastzRuns.txt
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    08ee8989aa3b4c6d48bd30d3e205705523cb6f9e Sat Mar 30 15:00:04 2024 -0700
    mm39 to GCA_921999005.2/GCA_921997125.2 lastz/chain/net run for user, refs #32859
• src/hg/makeDb/outside/gencode/gencodeLoad.mk
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    e5c776b067ca55054ce50c7910c195daa9637fa5 Wed Mar 27 20:16:09 2024 -0700
    reimport gencodeV46 pre-release to pick up GENCODE_Primary tag
• src/hg/makeDb/outside/gencode/lib/gencode/gencodeTags.py
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    e5c776b067ca55054ce50c7910c195daa9637fa5 Wed Mar 27 20:16:09 2024 -0700
    reimport gencodeV46 pre-release to pick up GENCODE_Primary tag
• src/hg/makeDb/schema/all.joiner
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    7974211879e0733f2ff5ee1dd8fab80e88718e5a Thu Mar 28 03:02:25 2024 -0700
    add gencode V39, I got the version numbers wrong, refs #33072
• src/hg/makeDb/trackDb/human/dosageSensitivityCollins2022.ra
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    85c13aa7f060fc28a602ad4bc49bae817317bea0 Mon Apr 1 10:29:37 2024 -0700
    Squashing old pennantIcons.
• src/hg/makeDb/trackDb/human/hg19/trackDb.gencode.ra
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    85c13aa7f060fc28a602ad4bc49bae817317bea0 Mon Apr 1 10:29:37 2024 -0700
    Squashing old pennantIcons.
• src/hg/makeDb/trackDb/human/hg19/trackDb.gnomad.ra
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    6a60cdb51e2832102b71d7b88c6740825720929f Tue Mar 26 12:19:53 2024 -0700
    Announcing the release of the gnomAD v4 Constraint Metrics (hg38) and gnomAD Non-cancer filter (hg19/hg38) tracks, refs #33084 #32916
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV45lift37.ra
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    85c13aa7f060fc28a602ad4bc49bae817317bea0 Mon Apr 1 10:29:37 2024 -0700
    Squashing old pennantIcons.
• src/hg/makeDb/trackDb/human/hg38/gnomad.constraint.public.ra
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    6a60cdb51e2832102b71d7b88c6740825720929f Tue Mar 26 12:19:53 2024 -0700
    Announcing the release of the gnomAD v4 Constraint Metrics (hg38) and gnomAD Non-cancer filter (hg19/hg38) tracks, refs #33084 #32916
• src/hg/makeDb/trackDb/human/hg38/gnomad.ra
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    6a60cdb51e2832102b71d7b88c6740825720929f Tue Mar 26 12:19:53 2024 -0700
    Announcing the release of the gnomAD v4 Constraint Metrics (hg38) and gnomAD Non-cancer filter (hg19/hg38) tracks, refs #33084 #32916
• src/hg/makeDb/trackDb/human/hg38/hprcArr.ra
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    85c13aa7f060fc28a602ad4bc49bae817317bea0 Mon Apr 1 10:29:37 2024 -0700
    Squashing old pennantIcons.
• src/hg/makeDb/trackDb/human/hg38/hprcChainNet.ra
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    85c13aa7f060fc28a602ad4bc49bae817317bea0 Mon Apr 1 10:29:37 2024 -0700
    Squashing old pennantIcons.
• src/hg/makeDb/trackDb/human/hg38/hprcVCF.ra
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    85c13aa7f060fc28a602ad4bc49bae817317bea0 Mon Apr 1 10:29:37 2024 -0700
    Squashing old pennantIcons.
• src/hg/makeDb/trackDb/human/hg38/trackDb.gencode.ra
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    85c13aa7f060fc28a602ad4bc49bae817317bea0 Mon Apr 1 10:29:37 2024 -0700
    Squashing old pennantIcons.
• src/hg/makeDb/trackDb/human/hg38/trackDb.hprc90way.ra
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    85c13aa7f060fc28a602ad4bc49bae817317bea0 Mon Apr 1 10:29:37 2024 -0700
    Squashing old pennantIcons.
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
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    85c13aa7f060fc28a602ad4bc49bae817317bea0 Mon Apr 1 10:29:37 2024 -0700
    Squashing old pennantIcons.
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV45.ra
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    85c13aa7f060fc28a602ad4bc49bae817317bea0 Mon Apr 1 10:29:37 2024 -0700
    Squashing old pennantIcons.
• src/hg/makeDb/trackDb/human/hs1/crispr.ra
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    85c13aa7f060fc28a602ad4bc49bae817317bea0 Mon Apr 1 10:29:37 2024 -0700
    Squashing old pennantIcons.
• src/hg/makeDb/trackDb/mouse/mm39/knownGene.alpha.ra
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    dc5436b691c6297a8f177be29a82a47b27e6505a Fri Mar 29 10:09:14 2024 -0700
    Initial build of knownGene VM35, refs #33083
• src/hg/makeDb/trackDb/mouse/mm39/knownGeneArchive.ra
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    dc5436b691c6297a8f177be29a82a47b27e6505a Fri Mar 29 10:09:14 2024 -0700
    Initial build of knownGene VM35, refs #33083
• src/hg/makeDb/trackDb/mouse/mm39/knownGeneVM34.html
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    dc5436b691c6297a8f177be29a82a47b27e6505a Fri Mar 29 10:09:14 2024 -0700
    Initial build of knownGene VM35, refs #33083
• src/hg/makeDb/trackDb/mouse/mm39/knownGeneVM35.html
  • lines changed 135, context: html, text, full: html, text
    dc5436b691c6297a8f177be29a82a47b27e6505a Fri Mar 29 10:09:14 2024 -0700
    Initial build of knownGene VM35, refs #33083
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    85c13aa7f060fc28a602ad4bc49bae817317bea0 Mon Apr 1 10:29:37 2024 -0700
    Squashing old pennantIcons.
• src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM34.ra
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    85c13aa7f060fc28a602ad4bc49bae817317bea0 Mon Apr 1 10:29:37 2024 -0700
    Squashing old pennantIcons.
• src/hg/makeDb/trackDb/virus/wuhCor1/variantMuts.ra
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    85c13aa7f060fc28a602ad4bc49bae817317bea0 Mon Apr 1 10:29:37 2024 -0700
    Squashing old pennantIcons.
• src/hg/utils/automation/HgAutomate.pm
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    0293401c526b33087d696a16a2d34909a36e1e11 Thu Mar 28 10:51:35 2024 -0700
    adding ram and cpu arguments .pm no redmine
• src/hg/utils/otto/clinvar/clinVarToBed
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    1942abfbe86d5b3f5ed3ad0482a31a9354587e18 Tue Mar 26 09:30:03 2024 -0700
    preparing clinvar for somatic mutations, no ticket yet
• src/hg/utils/otto/clinvar/clinvar.as
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    1942abfbe86d5b3f5ed3ad0482a31a9354587e18 Tue Mar 26 09:30:03 2024 -0700
    preparing clinvar for somatic mutations, no ticket yet
• src/hg/utils/otto/clinvar/clinvarSub.sql
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    1942abfbe86d5b3f5ed3ad0482a31a9354587e18 Tue Mar 26 09:30:03 2024 -0700
    preparing clinvar for somatic mutations, no ticket yet
• src/hg/utils/otto/decipher/processDecipher.py
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    f5a1b930828e2737ee09d3dc71b3a0c9c2068452 Wed Mar 27 08:21:03 2024 -0700
    otto job for decipher failed, otto email
• src/inc/srcVersion.h
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    885271695ba17ace9cad2c1b3fff5676850cdbfe Mon Apr 1 10:59:35 2024 -0700
    New version number v463
• src/utils/qa/checkTableStatusDump.sh
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    28aebf0195fe9254b8624931ebc0c46a8ddcf154 Sun Mar 31 15:14:41 2024 -0700
    Adding a script to replace the checkTableStatus.csh script for the TABLE STATUS dump cron, refs #32812
• src/utils/qa/makefile
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    510f283911040ce5f54ea8358e0d1ae34707ca37 Sun Mar 31 15:18:54 2024 -0700
    Adding a script to replace the checkTableStatus.csh script for the TABLE STATUS dump cron that will only email when there is an error/issue, refs #32812
• src/utils/qa/weeklybld/buildEnv.csh
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    fc7543746d67e15b9029648dba4165ae7b4d522e Mon Apr 1 10:58:49 2024 -0700
    v463 final build, refs #33267

• lines changed: 1774
• files changed: 63