All File Changes

v464_preview2 to v464_base (2024-04-15 to 2024-04-22) v464

• confs/hgwdev.hg.conf
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    33e5a8820cc4fd9a44b36f0f032ea2eb23836566 Sun Apr 21 01:11:18 2024 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/hgTracks/hgTracks.c
  • lines changed 4, context: html, text, full: html, text
    7d1ecf6c3cb9ccced03ba0f0a377be765b296811 Sat Apr 13 18:04:08 2024 -0700
    moving by at least one bp when user uses arrow the bars, second try, the first one failed miserably, refs #23343
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    4d633160cf57d928511c8e635a30cd1b4d6b17c2 Mon Apr 15 20:35:34 2024 -0700
    Revert "Revert "changing more info link such that it doesnt change the alignment anymore, refs #33065"" This reverts commit 3d4fe14b34d3a6eb335d4bb228d574300c9324e6.
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    73b17c296d69511e0e36327a873652733cdbe2ea Mon Apr 15 20:47:22 2024 -0700
    adding back link with more info to track hub in blue bar, fixing stupid bug, #33458
  • lines changed 48, context: html, text, full: html, text
    530842acf922e67838eab9fa153b7b7c0b90e9c2 Thu Apr 18 12:31:31 2024 -0700
    allow track hubs to make groups
• src/hg/hgTracks/menu.c
  • lines changed 1, context: html, text, full: html, text
    9d14e37b637c0bb899a92022673d0740efd4ec52 Mon Apr 15 21:52:12 2024 -0700
    tiny menu change, suggested by Mark
• src/hg/hgTracks/simpleTracks.c
  • lines changed 102, context: html, text, full: html, text
    80dce1b0dc80c7c4fe8f81523b3d4754a7ebc9bf Sun Apr 21 17:05:48 2024 -0700
    changing exon mouseover as per Ana and user ML, ref #33506
• src/hg/htdocs/ENCODE/contacts.html
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    db93d1ac9ffd179e8e70e2c98999c98fbb9efd5d Wed Apr 17 21:12:30 2024 -0700
    added missing or outdated ENCODE files from the rr
• src/hg/htdocs/ENCODE/dataMatrix/chipMatrix.css
  • lines changed 15, context: html, text, full: html, text
    db93d1ac9ffd179e8e70e2c98999c98fbb9efd5d Wed Apr 17 21:12:30 2024 -0700
    added missing or outdated ENCODE files from the rr
• src/hg/htdocs/ENCODE/dataMatrix/dataMatrix.css
  • lines changed 169, context: html, text, full: html, text
    db93d1ac9ffd179e8e70e2c98999c98fbb9efd5d Wed Apr 17 21:12:30 2024 -0700
    added missing or outdated ENCODE files from the rr
• src/hg/htdocs/ENCODE/dataMatrix/dataSummary.css
  • lines changed 74, context: html, text, full: html, text
    db93d1ac9ffd179e8e70e2c98999c98fbb9efd5d Wed Apr 17 21:12:30 2024 -0700
    added missing or outdated ENCODE files from the rr
• src/hg/htdocs/ENCODE/dataMatrix/encodeChipMatrixInclude.html
  • lines changed 2, context: html, text, full: html, text
    db93d1ac9ffd179e8e70e2c98999c98fbb9efd5d Wed Apr 17 21:12:30 2024 -0700
    added missing or outdated ENCODE files from the rr
• src/hg/htdocs/ENCODE/dataSummary.html
  • lines changed 2, context: html, text, full: html, text
    db93d1ac9ffd179e8e70e2c98999c98fbb9efd5d Wed Apr 17 21:12:30 2024 -0700
    added missing or outdated ENCODE files from the rr
• src/hg/htdocs/ENCODE/downloads/index.html
  • lines changed 176, context: html, text, full: html, text
    db93d1ac9ffd179e8e70e2c98999c98fbb9efd5d Wed Apr 17 21:12:30 2024 -0700
    added missing or outdated ENCODE files from the rr
• src/hg/htdocs/ENCODE/index.html
  • lines changed 1, context: html, text, full: html, text
    db93d1ac9ffd179e8e70e2c98999c98fbb9efd5d Wed Apr 17 21:12:30 2024 -0700
    added missing or outdated ENCODE files from the rr
• src/hg/htdocs/ENCODE/news_archive.html
  • lines changed 1, context: html, text, full: html, text
    db93d1ac9ffd179e8e70e2c98999c98fbb9efd5d Wed Apr 17 21:12:30 2024 -0700
    added missing or outdated ENCODE files from the rr
• src/hg/htdocs/april1.html
  • lines changed 35, context: html, text, full: html, text
    1404447d92a6d1e6e6b1b1f223db98efa80fe712 Wed Apr 17 21:36:17 2024 -0700
    save April 1 files from oblivion
• src/hg/htdocs/cauldron/breakTable.html
  • lines changed 229, context: html, text, full: html, text
    c28b00ca6c39b734b0034705ac3f3b57335b5a91 Wed Apr 17 21:42:07 2024 -0700
    added files from RR from caludron paper
• src/hg/htdocs/cauldron/syntenies.html
  • lines changed 9, context: html, text, full: html, text
    c28b00ca6c39b734b0034705ac3f3b57335b5a91 Wed Apr 17 21:42:07 2024 -0700
    added files from RR from caludron paper
• src/hg/htdocs/favicon.ico
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    aa5c3b239b54ef53ddd6276417cefdace816edc4 Thu Apr 18 13:06:56 2024 -0700
    Adding icon that was on the RR, but not in the tree. Refs #33444
• src/hg/htdocs/geneExtra/shh.gif
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    4c89e454b3249def1dc6de1d5c22c9f85e0f76cb Wed Apr 17 21:04:42 2024 -0700
    added missing geneExtra files on RR but not in git
• src/hg/htdocs/geneExtra/shh.txt
  • lines changed 6, context: html, text, full: html, text
    4c89e454b3249def1dc6de1d5c22c9f85e0f76cb Wed Apr 17 21:04:42 2024 -0700
    added missing geneExtra files on RR but not in git
• src/hg/htdocs/goldenPath/help/docker.html
  • lines changed 90, context: html, text, full: html, text
    226199234277e9c5d246ecce187873d8e8805ebc Fri Apr 19 17:45:17 2024 -0700
    Incorporating Jairo's feedback for docker.html, refs #33491
• src/hg/htdocs/goldenPath/mapPlots/RHguide.html
  • lines changed 239, context: html, text, full: html, text
    80accc5e547f9ff84da8b59ba01a0a0ec8efb33e Tue Apr 16 14:03:00 2024 -0700
    Adding older page that has been on the RR forever to git, refs #33444
• src/hg/htdocs/images/Papio_anubis.jpg
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    ca180f387523edaeba51fc6ba22590dded176e46 Tue Apr 16 13:52:45 2024 -0700
    Someone forgot to commit this image for baboon when they released the assembly. Refs #33444
• src/hg/htdocs/images/favicon.ico
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    fef449172b2d6fdc528390bb10f5aa674ed29cbe Wed Apr 17 17:05:32 2024 -0700
    Adding image present in newsArch that was never committed, refs #33444
• src/hg/htdocs/images/feature_decorators.png
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    f282feb9fd45f9cb2219a3c5286b0a318771f0e0 Wed Apr 17 17:04:44 2024 -0700
    Adding image present in newsArch that was never committed, refs #33444
• src/hg/htdocs/images/newLook.png
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    1404447d92a6d1e6e6b1b1f223db98efa80fe712 Wed Apr 17 21:36:17 2024 -0700
    save April 1 files from oblivion
• src/hg/htdocs/indexInfo.html
  • lines changed 30, context: html, text, full: html, text
    33ed38114541f79c21d4257f7b489c7e50a5906b Tue Apr 16 13:48:36 2024 -0700
    Adding two intro pages to git which has existed in the RR for a long time. I didn't want to delete it in case it was referenced elsewhere. refs #33444
• src/hg/htdocs/indexIntro.html
  • lines changed 114, context: html, text, full: html, text
    33ed38114541f79c21d4257f7b489c7e50a5906b Tue Apr 16 13:48:36 2024 -0700
    Adding two intro pages to git which has existed in the RR for a long time. I didn't want to delete it in case it was referenced elsewhere. refs #33444
• src/hg/htdocs/makefile
  • lines changed 3, context: html, text, full: html, text
    82dee17afb6a1bcbca19e301d15b1a9cc69ef829 Mon Apr 15 21:43:46 2024 -0700
    don't allow htdocs make FIND=find on hgwbeta RM 33444
  • lines changed 4, context: html, text, full: html, text
    2ac2c2372e2ab17ca7972f26bc989e8438ffd4eb Tue Apr 16 18:48:44 2024 -0700
    change check for FIND=fine to be make beta, make make on hgwbeta
  • lines changed 1, context: html, text, full: html, text
    ec42da84dda92ecdfc50b974beed6df3f453e0b1 Wed Apr 17 13:32:53 2024 -0700
    Fixing small grammar, refs #33444
• src/hg/htdocs/staff.html
  • lines changed 12, context: html, text, full: html, text
    3ce2791ee37163707b97f6582a668507d2f90d34 Mon Apr 15 21:13:40 2024 -0700
    updating with SAB, refs #33487
• src/hg/htdocs/style/HGStyle.css
  • lines changed 2, context: html, text, full: html, text
    530842acf922e67838eab9fa153b7b7c0b90e9c2 Thu Apr 18 12:31:31 2024 -0700
    allow track hubs to make groups
• src/hg/htdocs/training.html
  • lines changed 7, context: html, text, full: html, text
    b985680be2fb49fd4f2ae677c2cdbf6950a26ed4 Tue Apr 16 13:41:16 2024 -0700
    Adding a training page redirect to git which has existed in the RR for a long time, refs #33444
• src/hg/inc/trackHub.h
  • lines changed 4, context: html, text, full: html, text
    530842acf922e67838eab9fa153b7b7c0b90e9c2 Thu Apr 18 12:31:31 2024 -0700
    allow track hubs to make groups
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    66aa4f5bb547a8748b2306bc973d9e94b37ad9d2 Mon Apr 22 10:31:28 2024 -0700
    New version number v464
• src/hg/js/analytics.js
  • lines changed 2, context: html, text, full: html, text
    20d7e690abf561e49c6b5318204cc2c9958338e5 Wed Apr 17 11:27:49 2024 -0700
    Updating the analytics keys to use the correct ones for the data stream, refs #33272
• src/hg/js/utils.js
  • lines changed 9, context: html, text, full: html, text
    c9ae5ccfaa3946205580d5a663482bff5aa84afe Wed Apr 17 15:58:06 2024 -0700
    Revert "Make the tooltip messages about basic genome browser function like 'click to drag' disappear, refs Ana" This reverts commit 3336248e618a25a2b6b4ef45325ebd5ba04b542c.
• src/hg/lib/cartDb.c
  • lines changed 2, context: html, text, full: html, text
    25be2d40b2f88155cdadad7c8577642bc5a1e848 Sat Apr 20 14:12:59 2024 -0700
    sessionId's are unsigned, but we were printing them out as signed
• src/hg/lib/hui.c
  • lines changed 1, context: html, text, full: html, text
    c99f802959cf407a7c44b5a2e9cebc84bb9b6d61 Thu Apr 18 05:54:56 2024 -0700
    fixing remap filter bug, refs #24752
• src/hg/lib/trackHub.c
  • lines changed 73, context: html, text, full: html, text
    530842acf922e67838eab9fa153b7b7c0b90e9c2 Thu Apr 18 12:31:31 2024 -0700
    allow track hubs to make groups
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 1, context: html, text, full: html, text
    4680987207adaed1a830fc38f2b0cd34aa3f2fcf Tue Apr 16 10:03:43 2024 -0700
    adding GCA_023653725.1_ASM2365372v1 vertebrate Bungarus_multicinctus per user request, refs #29545
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    afc033dfd58f19bf27c8a280463473fb9679eba9 Thu Apr 18 11:50:33 2024 -0700
    adding GCF_035594765.1_rAnoCar3.1.pri vertebrate Anolis_carolinensis per user request, refs #29545
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    9bc6bee7380c7d06842b497de6bec97563a25620 Fri Apr 19 15:40:23 2024 -0700
    Documenting the build of the Lilford's wall lizard, refs #33476
• src/hg/makeDb/doc/hg19.txt
  • lines changed 203, context: html, text, full: html, text
    5eea974e049ff8f2c80085c31a50ddae484529ae Sun Apr 21 14:19:46 2024 -0700
    Making hg19 abSplice into a native track, refs #33251
• src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    69ab98f9a9e22a4ca90d5dd8d71d88df5d8d09c3 Tue Apr 16 10:15:01 2024 -0700
    adding Bungarus_multicinctus GCA_023653725.1_ASM2365372v1 many-banded krait (BM01 2022), refs #29545
  • lines changed 1, context: html, text, full: html, text
    6bad1e0c582202b4c99cc503825ce5c22deb944b Thu Apr 18 11:56:11 2024 -0700
    adding Anolis_carolinensis GCF_035594765.1_rAnoCar3.1.pri green anole (JA03-04 2024), refs #29545
  • lines changed 1, context: html, text, full: html, text
    9bc6bee7380c7d06842b497de6bec97563a25620 Fri Apr 19 15:40:23 2024 -0700
    Documenting the build of the Lilford's wall lizard, refs #33476
• src/hg/makeDb/outside/abSplice/AbSplice.hg19.makedoc
  • lines changed 184, context: html, text, full: html, text
    624a173c2cecab78c30628711418dd562fee375a Sun Apr 21 14:28:13 2024 -0700
    Adding the custom Python script for the hg19 abSplice track, refs #33251
• src/hg/makeDb/trackDb/human/hg19/abSplice.html
  • lines changed 76, context: html, text, full: html, text
    5eea974e049ff8f2c80085c31a50ddae484529ae Sun Apr 21 14:19:46 2024 -0700
    Making hg19 abSplice into a native track, refs #33251
• src/hg/makeDb/trackDb/human/hg19/abSplice.ra
  • lines changed 16, context: html, text, full: html, text
    5eea974e049ff8f2c80085c31a50ddae484529ae Sun Apr 21 14:19:46 2024 -0700
    Making hg19 abSplice into a native track, refs #33251
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    5eea974e049ff8f2c80085c31a50ddae484529ae Sun Apr 21 14:19:46 2024 -0700
    Making hg19 abSplice into a native track, refs #33251
• src/hg/makeDb/trackDb/human/hg38/mane.ra
  • lines changed 1, context: html, text, full: html, text
    6964a232878a2738bd7fccd581a8605d24e4a6dd Tue Apr 16 12:26:04 2024 -0700
    Clarifying label that MANE track includes MANE Select and MANE Plus Clinical, feedback from the SAB refs #33496
  • lines changed 1, context: html, text, full: html, text
    b025fad701388d31d9b0f1c659e3aa411d6578cc Tue Apr 16 12:37:53 2024 -0700
    Clarifying the search description label that MANE track includes MANE Select and MANE Plus Clinical, feedback from the SAB refs #33496
• src/hg/makeDb/trackDb/uniprot.html
  • lines changed 3, context: html, text, full: html, text
    5b7d2ac73787b05638a965d4305c4dd2fe944b9e Thu Apr 18 04:34:40 2024 -0700
    fixing uniprot docs, thanks to @markd
  • lines changed 6, context: html, text, full: html, text
    180a1b4affe6539979535d59eab358cae53dccd2 Thu Apr 18 04:38:13 2024 -0700
    fixing uniprot docs 2, thanks to @markd
• src/hg/utils/otto/uniprot/doUniprot
  • lines changed 4, context: html, text, full: html, text
    aa8ab619bf080d390f603cee7ab9c154dc3579c0 Fri Apr 19 06:15:49 2024 -0700
    uniprot comment
• src/inc/srcVersion.h
  • lines changed 1, context: html, text, full: html, text
    66aa4f5bb547a8748b2306bc973d9e94b37ad9d2 Mon Apr 22 10:31:28 2024 -0700
    New version number v464
• src/utils/qa/checkHubSearchCronWrapper.py
  • lines changed 57, context: html, text, full: html, text
    961be4dce41759b9b0b921e6c42b12545ba281fb Wed Apr 17 23:57:06 2024 -0700
    Adding a wrapper script for hubSearchText cron and the makeHelpDocs.sh to omit the output when there are no errors, refs #32812
• src/utils/qa/linkCheckExclude
  • lines changed 1, context: html, text, full: html, text
    c9a41bbabaadee3b802a114da96dd7ac9a7eac26 Wed Apr 17 14:13:12 2024 -0700
    Adding assemblyRequest.html to the list due to the cron output, No Redmine
• src/utils/qa/makefile
  • lines changed 1, context: html, text, full: html, text
    961be4dce41759b9b0b921e6c42b12545ba281fb Wed Apr 17 23:57:06 2024 -0700
    Adding a wrapper script for hubSearchText cron and the makeHelpDocs.sh to omit the output when there are no errors, refs #32812
• src/utils/qa/weeklybld/buildEnv.csh
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    a4260185632b76eb95e68ecc6481dfb8cc37d49f Mon Apr 22 10:30:47 2024 -0700
    v464 final build, refs #33450
• src/utils/qa/weeklybld/buildHgCentralSql.csh
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    38c3ca8c23fde6c5f3644cf17b640ec8c6c480c2 Mon Apr 22 10:28:54 2024 -0700
    Restoring hgdownload2 in build scripts, admins wanted it to receive updates
• src/utils/qa/weeklybld/doZip.csh
  • lines changed 3, context: html, text, full: html, text
    38c3ca8c23fde6c5f3644cf17b640ec8c6c480c2 Mon Apr 22 10:28:54 2024 -0700
    Restoring hgdownload2 in build scripts, admins wanted it to receive updates
• src/utils/qa/weeklybld/makeUserApps.csh
  • lines changed 4, context: html, text, full: html, text
    38c3ca8c23fde6c5f3644cf17b640ec8c6c480c2 Mon Apr 22 10:28:54 2024 -0700
    Restoring hgdownload2 in build scripts, admins wanted it to receive updates

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• files changed: 67