All File Changes

v419_preview to v419_preview2 (2021-08-02 to 2021-08-09) v419

• confs/asia.hg.conf
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    e1c46418e51d543846e6f4ef428c9d7c6680c666 Sun Aug 8 01:11:46 2021 -0700
    Installing updated hg.conf files from UCSC servers
• confs/euro.hg.conf
  • lines changed 3, context: html, text, full: html, text
    e1c46418e51d543846e6f4ef428c9d7c6680c666 Sun Aug 8 01:11:46 2021 -0700
    Installing updated hg.conf files from UCSC servers
• confs/hgwdev.hg.conf
  • lines changed 4, context: html, text, full: html, text
    e1c46418e51d543846e6f4ef428c9d7c6680c666 Sun Aug 8 01:11:46 2021 -0700
    Installing updated hg.conf files from UCSC servers
• confs/rr.hg.conf
  • lines changed 3, context: html, text, full: html, text
    e1c46418e51d543846e6f4ef428c9d7c6680c666 Sun Aug 8 01:11:46 2021 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/cirm/cdw/cdwMakeEnrichments/cdwMakeEnrichments.c
  • lines changed 1, context: html, text, full: html, text
    f14c003e98375586810203f2b6250aae02c064ff Wed Aug 4 15:22:47 2021 -0700
    Adding png to the cdwEnrichments ignore list as requested.
• src/hg/hgBlat/hgBlat.c
  • lines changed 1, context: html, text, full: html, text
    8d173a831311398255e4b096eb922d291118d950 Thu Aug 5 09:06:55 2021 -0700
    adding JSON to hgBlat as an output format, refs #27950
• src/hg/hgTracks/hgTracks.c
  • lines changed 6, context: html, text, full: html, text
    8d83056073da90aad4a8fa216c8e92112c8ea0ea Tue Aug 3 11:34:28 2021 -0700
    Fixing overzealous decrement in highlight parsing, refs #27891
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    e7af8dfcae1e729064d3f6c584ce536e9b443554 Thu Aug 5 09:02:09 2021 -0700
    fixing invalid text within an html tag for a button on hgTracks, no redmine, permission request to Braney has been sent
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    272ce7d17ccd6584fe03f8e226cd32c77ff900c1 Thu Aug 5 10:28:28 2021 -0700
    do not try to open the json mouseOver file when it is not possible refs #27954
• src/hg/htdocs/FAQ/FAQreleases.html
  • lines changed 2, context: html, text, full: html, text
    79dd40dabe4ec7e66369d62747967bf323c1a3df Mon Aug 2 13:21:17 2021 -0700
    Adding xenTro10 to the list of releases, refs #24693
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    f070d4f6c29949f7e5291282f6dc6090e99811d1 Wed Aug 4 11:19:49 2021 -0700
    Mentioning GenArk in our FAQ about looking for a genome assembly refs #27880
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 13, context: html, text, full: html, text
    eedcd119a8dda673907ecb1e2a1f5224ea3c2613 Mon Aug 2 17:14:55 2021 -0700
    Adding new assembly xenTro10 to credits.html, refs #24693
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 18, context: html, text, full: html, text
    a4bd219e77d824f808e182c7f1cc1881459dd381 Wed Aug 4 13:08:16 2021 -0700
    Adding references to the new filters quick start guide refs #24327
• src/hg/htdocs/goldenPath/help/hubQuickStartFilter.html
  • lines changed 526, context: html, text, full: html, text
    c61185431f821e1c3ca71b08130d03de507b35d8 Wed Aug 4 13:07:25 2021 -0700
    Committing the Filters Quick Start guide, refs #24327
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 9, context: html, text, full: html, text
    a4bd219e77d824f808e182c7f1cc1881459dd381 Wed Aug 4 13:08:16 2021 -0700
    Adding references to the new filters quick start guide refs #24327
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 44, context: html, text, full: html, text
    ff44777ccc8784341c946036e870b540dfefedd8 Mon Aug 2 17:27:01 2021 -0700
    Adding new assembly xenTro10 to newsarch page, refs #24693
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    36b3c149c3ed0e7016544e2c01f368b48838fcba Mon Aug 2 17:28:53 2021 -0700
    Adding new assembly xenTro10 to indexNews page, refs #24693
• src/hg/htdocs/robots.rr.txt
  • lines changed 14, context: html, text, full: html, text
    8ecaa12a2e01c4438e7e9290e6cfb657c5da9795 Thu Aug 5 09:36:49 2021 -0700
    changing robots.txt, refs #27953
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    424489e691ecb3e1b7f5acb7b3fc441f45b424cc Fri Aug 6 07:50:38 2021 -0700
    adding back crawl delay to robots.txt , refs #27953
• src/hg/htdocs/training/index.html
  • lines changed 14, context: html, text, full: html, text
    72bbd0c6b4ba9a950881e85468daa6dd49f2f714 Wed Aug 4 14:33:34 2021 -0700
    removing completed jax workshop. adding comment abt opening up for F2F
• src/hg/js/utils.js
  • lines changed 5, context: html, text, full: html, text
    6175c83c03b0d6b249b4eef4ed71ecc723f3f54c Thu Aug 5 08:54:44 2021 -0700
    make button click tracking fall back to the id or other button attributes if name is not set, refs #21916
• src/hg/lib/hgFind.c
  • lines changed 1, context: html, text, full: html, text
    01b4a7f506b3b44d7dcf1a8250e4829511a7cb64 Wed Aug 4 10:06:31 2021 -0700
    Fixing cruft found during code review, refs #27942
  • lines changed 57, context: html, text, full: html, text
    1eb02994652b9a06a33024bc629520aeeeb0a2f1 Fri Aug 6 11:18:49 2021 -0700
    When a user has searched for a psuedo hgvs term, if the term does not map to any transcripts, warn the user but head to the general location around where they meant to go, refs #15554, #27942
  • lines changed 5, context: html, text, full: html, text
    071f5846776ec79a7bd4589f826adfcc20e3a444 Fri Aug 6 12:46:53 2021 -0700
    Fixing unitialized variable, refs #15554, #27942
• src/hg/lib/hgHgvs.c
  • lines changed 2, context: html, text, full: html, text
    01b4a7f506b3b44d7dcf1a8250e4829511a7cb64 Wed Aug 4 10:06:31 2021 -0700
    Fixing cruft found during code review, refs #27942
• src/hg/makeDb/genbank/etc/hgwbeta.dbs
  • lines changed 2, context: html, text, full: html, text
    f8501a86bf35a3ce42d5f2532648ec8d11b84294 Mon Aug 2 13:18:56 2021 -0700
    Get list of genbank databases up to date with what has been built, refs #27924
• src/hg/makeDb/genbank/etc/rr.dbs
  • lines changed 9, context: html, text, full: html, text
    f8501a86bf35a3ce42d5f2532648ec8d11b84294 Mon Aug 2 13:18:56 2021 -0700
    Get list of genbank databases up to date with what has been built, refs #27924
  • lines changed 22, context: html, text, full: html, text
    99e1611b9ef9337bb482a746b2d0fd50967304f6 Thu Aug 5 15:21:31 2021 -0700
    Adding genbank dbs missing from the rr list from the last few years. Ask Chris Lee or Lou Nassar for details if needed. No RM.
• src/hg/makeDb/trackDb/baboon/papAnu2/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    a18a205d07a1cdae9cf89d88faf40085e9be179f Fri Aug 6 13:51:44 2021 -0700
    Releasing refSeq tracks for 16 forgotten assemblies, refs #23851
• src/hg/makeDb/trackDb/baboon/papAnu2/trackDb.refGene.ra
  • lines changed 2, context: html, text, full: html, text
    a18a205d07a1cdae9cf89d88faf40085e9be179f Fri Aug 6 13:51:44 2021 -0700
    Releasing refSeq tracks for 16 forgotten assemblies, refs #23851
• src/hg/makeDb/trackDb/bonobo/panPan1/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    a18a205d07a1cdae9cf89d88faf40085e9be179f Fri Aug 6 13:51:44 2021 -0700
    Releasing refSeq tracks for 16 forgotten assemblies, refs #23851
• src/hg/makeDb/trackDb/bonobo/panPan1/trackDb.refGene.ra
  • lines changed 2, context: html, text, full: html, text
    a18a205d07a1cdae9cf89d88faf40085e9be179f Fri Aug 6 13:51:44 2021 -0700
    Releasing refSeq tracks for 16 forgotten assemblies, refs #23851
• src/hg/makeDb/trackDb/cat/felCat8/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    a18a205d07a1cdae9cf89d88faf40085e9be179f Fri Aug 6 13:51:44 2021 -0700
    Releasing refSeq tracks for 16 forgotten assemblies, refs #23851
• src/hg/makeDb/trackDb/chicken/galGal5/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    a18a205d07a1cdae9cf89d88faf40085e9be179f Fri Aug 6 13:51:44 2021 -0700
    Releasing refSeq tracks for 16 forgotten assemblies, refs #23851
• src/hg/makeDb/trackDb/chimp/panTro4/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    a18a205d07a1cdae9cf89d88faf40085e9be179f Fri Aug 6 13:51:44 2021 -0700
    Releasing refSeq tracks for 16 forgotten assemblies, refs #23851
• src/hg/makeDb/trackDb/chimp/panTro4/trackDb.refGene.ra
  • lines changed 2, context: html, text, full: html, text
    a18a205d07a1cdae9cf89d88faf40085e9be179f Fri Aug 6 13:51:44 2021 -0700
    Releasing refSeq tracks for 16 forgotten assemblies, refs #23851
• src/hg/makeDb/trackDb/dog/canFam4/altAllele.ra
  • lines changed 1, context: html, text, full: html, text
    5c0821c1f1ffe84356bb0b0a6fe03f38705aefa1 Mon Aug 2 13:04:24 2021 -0700
    Squashing stale pennantIcons, no RM.
• src/hg/makeDb/trackDb/dog/canFam4/miRNA.ra
  • lines changed 1, context: html, text, full: html, text
    5c0821c1f1ffe84356bb0b0a6fe03f38705aefa1 Mon Aug 2 13:04:24 2021 -0700
    Squashing stale pennantIcons, no RM.
• src/hg/makeDb/trackDb/dog/canFam4/structVar.ra
  • lines changed 1, context: html, text, full: html, text
    5c0821c1f1ffe84356bb0b0a6fe03f38705aefa1 Mon Aug 2 13:04:24 2021 -0700
    Squashing stale pennantIcons, no RM.
• src/hg/makeDb/trackDb/dog/canFam4/uuGene.ra
  • lines changed 1, context: html, text, full: html, text
    5c0821c1f1ffe84356bb0b0a6fe03f38705aefa1 Mon Aug 2 13:04:24 2021 -0700
    Squashing stale pennantIcons, no RM.
• src/hg/makeDb/trackDb/drosophila/droPer1/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    a18a205d07a1cdae9cf89d88faf40085e9be179f Fri Aug 6 13:51:44 2021 -0700
    Releasing refSeq tracks for 16 forgotten assemblies, refs #23851
• src/hg/makeDb/trackDb/fugu/fr3/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    a18a205d07a1cdae9cf89d88faf40085e9be179f Fri Aug 6 13:51:44 2021 -0700
    Releasing refSeq tracks for 16 forgotten assemblies, refs #23851
• src/hg/makeDb/trackDb/gator/allMis1/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    a18a205d07a1cdae9cf89d88faf40085e9be179f Fri Aug 6 13:51:44 2021 -0700
    Releasing refSeq tracks for 16 forgotten assemblies, refs #23851
• src/hg/makeDb/trackDb/human/gtexCov.ra
  • lines changed 333, context: html, text, full: html, text
    357825329da34addd845542d78cf3686b0839c1a Mon Aug 9 03:47:05 2021 -0700
    adding gtex coverage trackdb, documentation still missing waiting for feedback from Gtex portal, refs #27964
• src/hg/makeDb/trackDb/human/hg38/cons241way.html
  • lines changed 5, context: html, text, full: html, text
    b7b54eb4d88a180d078025e480422f6e979d0055 Fri Aug 6 15:57:37 2021 -0700
    correct list of assemblies and their gene annotations refs #27519
• src/hg/makeDb/trackDb/human/hg38/ileumWang.html
  • lines changed 1, context: html, text, full: html, text
    e8ad15eff5cf25a332d35ece5cecf01b397a7d7d Tue Aug 3 10:18:07 2021 -0700
    Fixed typos.
• src/hg/makeDb/trackDb/human/hg38/placentaVentoTormo.html
  • lines changed 2, context: html, text, full: html, text
    e8ad15eff5cf25a332d35ece5cecf01b397a7d7d Tue Aug 3 10:18:07 2021 -0700
    Fixed typos.
  • lines changed 1, context: html, text, full: html, text
    1c050930f70b6ce26d99fbff71355b384abd8a38 Tue Aug 3 12:49:00 2021 -0700
    Small typo fix.
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    1d8b693fc4607684564e76eb19b4f20e346b8669 Tue Aug 3 12:52:58 2021 -0700
    Small edit fix.
• src/hg/makeDb/trackDb/human/hg38/placentaVentoTormo.ra
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    501a878adf4e2b5411ce9cf1972dceab60974bdd Wed Aug 4 16:12:52 2021 -0700
    Fixing some barChartBar tags that were missing or cut and pasted from wrong source in the smart-seq2 parts of the placentaVentoTormo single cell RNA-seq tracks.
• src/hg/makeDb/trackDb/human/hg38/trackDb.241way.ra
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    58606171ab68447b4b32d8626e08791427e604a6 Fri Aug 6 16:14:09 2021 -0700
    reset 241way to a table version and the bigMaf as the primary and with default set off and on refs #27519
  • lines changed 3, context: html, text, full: html, text
    9a1b622c14ff6e50279f450f1577a28b61411a13 Fri Aug 6 16:21:08 2021 -0700
    eliminate the bigWig bigMaf labels refs #27519
• src/hg/makeDb/trackDb/human/hg38/trackDb.241wayBM.ra
  • lines changed 34, context: html, text, full: html, text
    f96d181caeb6337ba7f4bc9d18351012abbba37d Tue Aug 3 16:15:15 2021 -0700
    trying out the remote file bigDataUrl version refs #11636
• src/hg/makeDb/trackDb/human/hg38/trackDb.241wayT.ra
  • lines changed 116, context: html, text, full: html, text
    58606171ab68447b4b32d8626e08791427e604a6 Fri Aug 6 16:14:09 2021 -0700
    reset 241way to a table version and the bigMaf as the primary and with default set off and on refs #27519
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    58606171ab68447b4b32d8626e08791427e604a6 Fri Aug 6 16:14:09 2021 -0700
    reset 241way to a table version and the bigMaf as the primary and with default set off and on refs #27519
• src/hg/makeDb/trackDb/human/trackDb.gtex.ra
  • lines changed 1, context: html, text, full: html, text
    357825329da34addd845542d78cf3686b0839c1a Mon Aug 9 03:47:05 2021 -0700
    adding gtex coverage trackdb, documentation still missing waiting for feedback from Gtex portal, refs #27964
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    5c0821c1f1ffe84356bb0b0a6fe03f38705aefa1 Mon Aug 2 13:04:24 2021 -0700
    Squashing stale pennantIcons, no RM.
• src/hg/makeDb/trackDb/mouseLemur/micMur2/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    a18a205d07a1cdae9cf89d88faf40085e9be179f Fri Aug 6 13:51:44 2021 -0700
    Releasing refSeq tracks for 16 forgotten assemblies, refs #23851
• src/hg/makeDb/trackDb/oreNil/oreNil2/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    a18a205d07a1cdae9cf89d88faf40085e9be179f Fri Aug 6 13:51:44 2021 -0700
    Releasing refSeq tracks for 16 forgotten assemblies, refs #23851
• src/hg/makeDb/trackDb/pig/susScr3/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    a18a205d07a1cdae9cf89d88faf40085e9be179f Fri Aug 6 13:51:44 2021 -0700
    Releasing refSeq tracks for 16 forgotten assemblies, refs #23851
• src/hg/makeDb/trackDb/pig/susScr3/trackDb.refGene.ra
  • lines changed 2, context: html, text, full: html, text
    a18a205d07a1cdae9cf89d88faf40085e9be179f Fri Aug 6 13:51:44 2021 -0700
    Releasing refSeq tracks for 16 forgotten assemblies, refs #23851
• src/hg/makeDb/trackDb/rhesus/rheMac8/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    a18a205d07a1cdae9cf89d88faf40085e9be179f Fri Aug 6 13:51:44 2021 -0700
    Releasing refSeq tracks for 16 forgotten assemblies, refs #23851
• src/hg/makeDb/trackDb/rhinopithecus/rhiRox1/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    a18a205d07a1cdae9cf89d88faf40085e9be179f Fri Aug 6 13:51:44 2021 -0700
    Releasing refSeq tracks for 16 forgotten assemblies, refs #23851
• src/hg/makeDb/trackDb/sheep/oviAri3/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    a18a205d07a1cdae9cf89d88faf40085e9be179f Fri Aug 6 13:51:44 2021 -0700
    Releasing refSeq tracks for 16 forgotten assemblies, refs #23851
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 9, context: html, text, full: html, text
    dde4e74de87d026755d57d54a23beceba4a6ab9d Tue Aug 3 16:17:07 2021 -0700
    a few additional bigMaf types added refs #11636
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    58606171ab68447b4b32d8626e08791427e604a6 Fri Aug 6 16:14:09 2021 -0700
    reset 241way to a table version and the bigMaf as the primary and with default set off and on refs #27519
• src/hg/makeDb/trackDb/tenrec/echTel2/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    a18a205d07a1cdae9cf89d88faf40085e9be179f Fri Aug 6 13:51:44 2021 -0700
    Releasing refSeq tracks for 16 forgotten assemblies, refs #23851
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    0831c6df812bb7ed7883c79681e4873a12aeddca Mon Aug 2 12:59:14 2021 -0700
    Fixing trackDB and turning on uniprot all otto cron refs #27756
• src/hg/makeDb/trackDb/trackDb.uniprot.ra
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    0831c6df812bb7ed7883c79681e4873a12aeddca Mon Aug 2 12:59:14 2021 -0700
    Fixing trackDB and turning on uniprot all otto cron refs #27756
• src/hg/makeDb/trackDb/uniprot.alpha.ra
  • lines changed 226, context: html, text, full: html, text
    0831c6df812bb7ed7883c79681e4873a12aeddca Mon Aug 2 12:59:14 2021 -0700
    Fixing trackDB and turning on uniprot all otto cron refs #27756
• src/hg/makeDb/trackDb/virus/wuhCor1/strains.ra
  • lines changed 3, context: html, text, full: html, text
    5c0821c1f1ffe84356bb0b0a6fe03f38705aefa1 Mon Aug 2 13:04:24 2021 -0700
    Squashing stale pennantIcons, no RM.
• src/hg/makeDb/trackDb/virus/wuhCor1/vaccines.ra
  • lines changed 1, context: html, text, full: html, text
    5c0821c1f1ffe84356bb0b0a6fe03f38705aefa1 Mon Aug 2 13:04:24 2021 -0700
    Squashing stale pennantIcons, no RM.
• src/hg/makeDb/trackDb/zebraFinch/taeGut2/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    a18a205d07a1cdae9cf89d88faf40085e9be179f Fri Aug 6 13:51:44 2021 -0700
    Releasing refSeq tracks for 16 forgotten assemblies, refs #23851
• src/inc/common.mk
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    cf8ff2ea2319888ff5b5befeecfb014cb14a11be Wed Aug 4 14:38:09 2021 -0700
    use static freetype lib on Mac OSX refs #27906
• src/utils/browserRace
  • lines changed 1, context: html, text, full: html, text
    a396c1d6eeb298a1a17b4b20ebc0cafe07dab49a Mon Aug 9 03:57:39 2021 -0700
    small addition to browserrace tool, no redmine
• src/utils/chromToUcsc/chromToUcsc
  • lines changed 7, context: html, text, full: html, text
    89a6d1a02972c7da55afb55e81a871870a03f260 Thu Aug 5 03:54:34 2021 -0700
    improving docs for chromToUcsc, refs #27919
  • lines changed 3, context: html, text, full: html, text
    4f36ff46dc1f285afd7478ddcf87f4777f7c4672 Thu Aug 5 04:00:42 2021 -0700
    improving chromToUcsc docs, refs #27919
  • lines changed 1, context: html, text, full: html, text
    c7ea1782a59a1cf6cfac9eff94f4774ffb525c83 Mon Aug 9 03:58:20 2021 -0700
    tiny docs change for chromToUcsc, no redmine
• src/utils/chromToUcsc/tests/makefile
  • lines changed 1, context: html, text, full: html, text
    821235f817c0dc329532c6ec43333581b2bb723c Thu Aug 5 03:56:42 2021 -0700
    fixing stray filename in makefile, refs #27919
• src/utils/makefile
  • lines changed 1, context: html, text, full: html, text
    e68fd2843bbc4de152931f807101a9258567bc76 Thu Aug 5 15:37:19 2021 -0700
    Include the scripts when building utils during beta week, refs #27919
• src/utils/qa/checkSyncAndMetaDataAll.py
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    9569314078469a67c56e832c06406f5d4984200e Wed Aug 4 13:40:27 2021 -0700
    Updating the cron to expect 3 table discrepancy due to the relatedTrack table in hg38, no RM
• src/utils/qa/weeklybld/buildEnv.csh
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    151e11cd4913ac8457d3f40db9a7abf9c6e25794 Mon Aug 9 10:04:02 2021 -0700
    v419 preview2, refs #27946

• lines changed: 1673
• files changed: 82