All File Changes

v460_preview to v460_preview2 (2024-01-16 to 2024-01-22) v460

• src/hg/hgGene/hgGeneData/Human/hg16/links.ra
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    318d20c5e363bf0d29d9511234f175a1cf600a55 Mon Jan 22 06:32:52 2024 -0800
    adding back to genome browser and short exact DNA match links to menu, refs #32893
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    563135c16d2a4cd28013260439afebcb5e4bc6aa Mon Jan 22 06:32:52 2024 -0800
    adding back to genome browser and short exact DNA match links to menu, refs #32893
• src/hg/hgGene/hgGeneData/Human/hg17/links.ra
  • lines changed 1, context: html, text, full: html, text
    318d20c5e363bf0d29d9511234f175a1cf600a55 Mon Jan 22 06:32:52 2024 -0800
    adding back to genome browser and short exact DNA match links to menu, refs #32893
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    563135c16d2a4cd28013260439afebcb5e4bc6aa Mon Jan 22 06:32:52 2024 -0800
    adding back to genome browser and short exact DNA match links to menu, refs #32893
• src/hg/hgGene/hgGeneData/Human/hg18/links.ra
  • lines changed 2, context: html, text, full: html, text
    318d20c5e363bf0d29d9511234f175a1cf600a55 Mon Jan 22 06:32:52 2024 -0800
    adding back to genome browser and short exact DNA match links to menu, refs #32893
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    563135c16d2a4cd28013260439afebcb5e4bc6aa Mon Jan 22 06:32:52 2024 -0800
    adding back to genome browser and short exact DNA match links to menu, refs #32893
• src/hg/hgGene/hgGeneData/Human/hg19/links.ra
  • lines changed 1, context: html, text, full: html, text
    318d20c5e363bf0d29d9511234f175a1cf600a55 Mon Jan 22 06:32:52 2024 -0800
    adding back to genome browser and short exact DNA match links to menu, refs #32893
  • lines changed 1, context: html, text, full: html, text
    563135c16d2a4cd28013260439afebcb5e4bc6aa Mon Jan 22 06:32:52 2024 -0800
    adding back to genome browser and short exact DNA match links to menu, refs #32893
• src/hg/hgGene/hgGeneData/Human/hg38/links.ra
  • lines changed 1, context: html, text, full: html, text
    318d20c5e363bf0d29d9511234f175a1cf600a55 Mon Jan 22 06:32:52 2024 -0800
    adding back to genome browser and short exact DNA match links to menu, refs #32893
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    563135c16d2a4cd28013260439afebcb5e4bc6aa Mon Jan 22 06:32:52 2024 -0800
    adding back to genome browser and short exact DNA match links to menu, refs #32893
• src/hg/hgGene/hgGeneData/Mouse/mm10/links.ra
  • lines changed 1, context: html, text, full: html, text
    318d20c5e363bf0d29d9511234f175a1cf600a55 Mon Jan 22 06:32:52 2024 -0800
    adding back to genome browser and short exact DNA match links to menu, refs #32893
  • lines changed 1, context: html, text, full: html, text
    563135c16d2a4cd28013260439afebcb5e4bc6aa Mon Jan 22 06:32:52 2024 -0800
    adding back to genome browser and short exact DNA match links to menu, refs #32893
• src/hg/hgGene/hgGeneData/Mouse/mm39/links.ra
  • lines changed 1, context: html, text, full: html, text
    318d20c5e363bf0d29d9511234f175a1cf600a55 Mon Jan 22 06:32:52 2024 -0800
    adding back to genome browser and short exact DNA match links to menu, refs #32893
  • lines changed 1, context: html, text, full: html, text
    563135c16d2a4cd28013260439afebcb5e4bc6aa Mon Jan 22 06:32:52 2024 -0800
    adding back to genome browser and short exact DNA match links to menu, refs #32893
• src/hg/hgGene/hgGeneData/Mouse/mm6/links.ra
  • lines changed 1, context: html, text, full: html, text
    318d20c5e363bf0d29d9511234f175a1cf600a55 Mon Jan 22 06:32:52 2024 -0800
    adding back to genome browser and short exact DNA match links to menu, refs #32893
  • lines changed 1, context: html, text, full: html, text
    563135c16d2a4cd28013260439afebcb5e4bc6aa Mon Jan 22 06:32:52 2024 -0800
    adding back to genome browser and short exact DNA match links to menu, refs #32893
• src/hg/hgGene/hgGeneData/Mouse/mm9/links.ra
  • lines changed 1, context: html, text, full: html, text
    318d20c5e363bf0d29d9511234f175a1cf600a55 Mon Jan 22 06:32:52 2024 -0800
    adding back to genome browser and short exact DNA match links to menu, refs #32893
  • lines changed 1, context: html, text, full: html, text
    563135c16d2a4cd28013260439afebcb5e4bc6aa Mon Jan 22 06:32:52 2024 -0800
    adding back to genome browser and short exact DNA match links to menu, refs #32893
• src/hg/hgGeneGraph/hgGeneGraph
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    a7a5686cb5b960d9dab9536fa40fcfcdf1a72393 Wed Jan 17 08:03:49 2024 -0800
    harden hgGeneGraph, ongoing build patch, no redmine ID yet
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    b2b604a79d0823e6e52524365371c0307961bfef Wed Jan 17 08:30:16 2024 -0800
    small tweak to RR hotfix, the previous limits very extremely strict, refs #32876
• src/hg/hgSearch/hgSearch.c
  • lines changed 3, context: html, text, full: html, text
    8cc029f3383ea3d872b3d87910ee869e3232c8bd Fri Jan 19 09:18:42 2024 -0800
    Forgot to check if we actually got a trackDb for fixing up mrna single pos searches, refs Max email
• src/hg/hgTables/hgTables.c
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    0041b20e68b02a86962e10a3ba591c8d205b3178 Wed Jan 17 10:11:57 2024 -0800
    Fix Table Browser csv output of header when there is an itemRgb field in the field list, which went through a special print function for some reason, refs #32865
• src/hg/hgTracks/bigBedTrack.c
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    c59e64a740c3fc788be41013586bc78bbbf42651 Thu Jan 18 11:14:35 2024 -0800
    use 10,000 for the number of items to load from a bigBed
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    5a73e86ce8424ee217b2b8de96d3a6b1ff6fe470 Thu Jan 18 12:02:46 2024 -0800
    limit VCF track loads to 10,000 items
• src/hg/hgTracks/hgTracks.c
  • lines changed 6, context: html, text, full: html, text
    0b69879792272a9ebc910a90be65a9c31dab2329 Mon Jan 22 05:59:38 2024 -0800
    adding menu entry and button for highlight here feature, refs #32892
• src/hg/hgTracks/menu.c
  • lines changed 3, context: html, text, full: html, text
    0b69879792272a9ebc910a90be65a9c31dab2329 Mon Jan 22 05:59:38 2024 -0800
    adding menu entry and button for highlight here feature, refs #32892
• src/hg/hgTracks/vcfTrack.c
  • lines changed 18, context: html, text, full: html, text
    5a73e86ce8424ee217b2b8de96d3a6b1ff6fe470 Thu Jan 18 12:02:46 2024 -0800
    limit VCF track loads to 10,000 items
• src/hg/htdocs/goldenPath/hgTracks.html
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    d75c6f151b94b5431684147d3c2ec365cc4568ae Tue Jan 16 14:47:02 2024 -0800
    Fixing root path for include files in a random static doc, refs Jairo email
• src/hg/htdocs/goldenPath/newsarch.html
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    c2a8601791cea0c84ffd87e717783a1b7b36a390 Fri Jan 19 17:04:02 2024 -0800
    Staging the HPRC track group and tracks release announcement, refs#32287
• src/hg/htdocs/images/HPRCsession.png
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    c2a8601791cea0c84ffd87e717783a1b7b36a390 Fri Jan 19 17:04:02 2024 -0800
    Staging the HPRC track group and tracks release announcement, refs#32287
• src/hg/htdocs/images/HPRCtrackGroup.png
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    c2a8601791cea0c84ffd87e717783a1b7b36a390 Fri Jan 19 17:04:02 2024 -0800
    Staging the HPRC track group and tracks release announcement, refs#32287
• src/hg/htdocs/inc/globalNavBar.inc
  • lines changed 4, context: html, text, full: html, text
    318d20c5e363bf0d29d9511234f175a1cf600a55 Mon Jan 22 06:32:52 2024 -0800
    adding back to genome browser and short exact DNA match links to menu, refs #32893
  • lines changed 4, context: html, text, full: html, text
    563135c16d2a4cd28013260439afebcb5e4bc6aa Mon Jan 22 06:32:52 2024 -0800
    adding back to genome browser and short exact DNA match links to menu, refs #32893
• src/hg/htdocs/indexMeetings.html
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    2002eb7fad70c06b004bb399a381c01bfce9f6d1 Wed Jan 17 16:23:20 2024 -0800
    Updating conferences, refs b0b
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    50517d44c9f952f2272c43c2b90ba78aa8147cb8 Wed Jan 17 16:55:36 2024 -0800
    Ordering meetings.
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    c2a8601791cea0c84ffd87e717783a1b7b36a390 Fri Jan 19 17:04:02 2024 -0800
    Staging the HPRC track group and tracks release announcement, refs#32287
• src/hg/makeDb/doc/bosTau9/lastzRuns.txt
  • lines changed 140, context: html, text, full: html, text
    c139f35504866c1dcf0eec5e3e07a83da8866fe5 Tue Jan 16 19:49:03 2024 -0800
    adding makedocs for various lastz runs for liftOver files in MLQ request, refs #32804
• src/hg/makeDb/doc/hg19.txt
  • lines changed 162, context: html, text, full: html, text
    c139f35504866c1dcf0eec5e3e07a83da8866fe5 Tue Jan 16 19:49:03 2024 -0800
    adding makedocs for various lastz runs for liftOver files in MLQ request, refs #32804
• src/hg/makeDb/doc/hg38/avada.txt
  • lines changed 6, context: html, text, full: html, text
    04c20121fff7f778085032a7ee82ef3f77c482dc Mon Jan 22 05:04:54 2024 -0800
    adding avada makedoc, refs #32746
• src/hg/makeDb/doc/hg38/lastzRuns.txt
  • lines changed 383, context: html, text, full: html, text
    c139f35504866c1dcf0eec5e3e07a83da8866fe5 Tue Jan 16 19:49:03 2024 -0800
    adding makedocs for various lastz runs for liftOver files in MLQ request, refs #32804
• src/hg/makeDb/doc/hg38/patchUpdate.11.txt
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    282d648d8896a7bb45af20bbc306873f6a5ffb87 Wed Jan 17 11:03:32 2024 -0800
    Added chrUn_KI270752v1 to hg38.{p11,p12,p13}.chromAlias.txt files after user pointed out in MLQ #32874 that it was missing. It is present in hg38.p14.chromAlias.txt and all *chromAlias.bb files.
• src/hg/makeDb/doc/hg38/patchUpdate.12.txt
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    282d648d8896a7bb45af20bbc306873f6a5ffb87 Wed Jan 17 11:03:32 2024 -0800
    Added chrUn_KI270752v1 to hg38.{p11,p12,p13}.chromAlias.txt files after user pointed out in MLQ #32874 that it was missing. It is present in hg38.p14.chromAlias.txt and all *chromAlias.bb files.
• src/hg/makeDb/doc/hg38/patchUpdate.13.txt
  • lines changed 21, context: html, text, full: html, text
    282d648d8896a7bb45af20bbc306873f6a5ffb87 Wed Jan 17 11:03:32 2024 -0800
    Added chrUn_KI270752v1 to hg38.{p11,p12,p13}.chromAlias.txt files after user pointed out in MLQ #32874 that it was missing. It is present in hg38.p14.chromAlias.txt and all *chromAlias.bb files.
• src/hg/makeDb/doc/mm10.txt
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    c139f35504866c1dcf0eec5e3e07a83da8866fe5 Tue Jan 16 19:49:03 2024 -0800
    adding makedocs for various lastz runs for liftOver files in MLQ request, refs #32804
• src/hg/makeDb/trackDb/human/hg38/hprcArr.ra
  • lines changed 1, context: html, text, full: html, text
    c2a8601791cea0c84ffd87e717783a1b7b36a390 Fri Jan 19 17:04:02 2024 -0800
    Staging the HPRC track group and tracks release announcement, refs#32287
• src/hg/makeDb/trackDb/human/hg38/hprcChainNet.ra
  • lines changed 1, context: html, text, full: html, text
    c2a8601791cea0c84ffd87e717783a1b7b36a390 Fri Jan 19 17:04:02 2024 -0800
    Staging the HPRC track group and tracks release announcement, refs#32287
• src/hg/makeDb/trackDb/human/hg38/hprcVCF.ra
  • lines changed 2, context: html, text, full: html, text
    c2a8601791cea0c84ffd87e717783a1b7b36a390 Fri Jan 19 17:04:02 2024 -0800
    Staging the HPRC track group and tracks release announcement, refs#32287
• src/hg/makeDb/trackDb/human/hg38/trackDb.hprc90way.ra
  • lines changed 1, context: html, text, full: html, text
    c2a8601791cea0c84ffd87e717783a1b7b36a390 Fri Jan 19 17:04:02 2024 -0800
    Staging the HPRC track group and tracks release announcement, refs#32287
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    8952fb88f8c87e5440d1ed298dde430d7d01782d Thu Jan 18 16:24:35 2024 -0800
    Updating shortLabel and moving the covidMuts track to phenDis bluebar group, email from Bob, refs #32844
• src/hg/pyLib/hgLib3.py
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    a7a5686cb5b960d9dab9536fa40fcfcdf1a72393 Wed Jan 17 08:03:49 2024 -0800
    harden hgGeneGraph, ongoing build patch, no redmine ID yet
  • lines changed 4, context: html, text, full: html, text
    b2b604a79d0823e6e52524365371c0307961bfef Wed Jan 17 08:30:16 2024 -0800
    small tweak to RR hotfix, the previous limits very extremely strict, refs #32876
• src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv
  • lines changed 47, context: html, text, full: html, text
    d3871113f7407a94dfb3eb8b137df9facd39776e Wed Jan 17 11:06:45 2024 -0800
    New lineages as well as some path tweaks for older lineages found to be missing a lot of designated sequences.
• src/inc/vcf.h
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    9f6fab9eaa43645fe4a0e2816d7623301df2b13b Thu Jan 18 12:08:09 2024 -0800
    forgot to check in vcf.h
• src/lib/vcf.c
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    5a73e86ce8424ee217b2b8de96d3a6b1ff6fe470 Thu Jan 18 12:02:46 2024 -0800
    limit VCF track loads to 10,000 items
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    e247aa7c4fbf61b34f5bdffcba8ea466bd6dc694 Sat Jan 20 10:35:38 2024 -0800
    oops ... left in a printf
• src/utils/qa/weeklybld/buildEnv.csh
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    271a53686f9359a8988b996f3fb939503c3af238 Mon Jan 22 11:51:02 2024 -0800
    v460 preview2, refs #32867

• lines changed: 1347
• files changed: 56