All File Changes

v415_preview to v415_preview2 (2021-05-10 to 2021-05-17) v415

• confs/asia.hg.conf
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    77402a1026f86d66caf4d13a1ed85113a69266d5 Sun May 16 01:11:51 2021 -0700
    Installing updated hg.conf files from UCSC servers
• confs/euro.hg.conf
  • lines changed 3, context: html, text, full: html, text
    77402a1026f86d66caf4d13a1ed85113a69266d5 Sun May 16 01:11:51 2021 -0700
    Installing updated hg.conf files from UCSC servers
• confs/hgwbeta.hg.conf
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    77402a1026f86d66caf4d13a1ed85113a69266d5 Sun May 16 01:11:51 2021 -0700
    Installing updated hg.conf files from UCSC servers
• confs/rr.hg.conf
  • lines changed 3, context: html, text, full: html, text
    77402a1026f86d66caf4d13a1ed85113a69266d5 Sun May 16 01:11:51 2021 -0700
    Installing updated hg.conf files from UCSC servers
• src/hca/toHca/hcaAffixTsvToTemplate/hcaAffixTsvToTemplate.c
  • lines changed 172, context: html, text, full: html, text
    a6f3ed94b533d5ffa08d7ff8f7c87a2956848e11 Mon May 10 13:37:24 2021 -0700
    A program that takes tab separated files with column labels in the 1st row that we generate to templates with column labels in the 4th row like HCA likes.
• src/hca/toHca/hcaAffixTsvToTemplate/makefile
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    a6f3ed94b533d5ffa08d7ff8f7c87a2956848e11 Mon May 10 13:37:24 2021 -0700
    A program that takes tab separated files with column labels in the 1st row that we generate to templates with column labels in the 4th row like HCA likes.
• src/hg/hgGeneGraph/hgGeneGraph
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    48bd0207312b284f34c601ad59618e3e70cc72e7 Fri May 14 13:17:13 2021 -0700
    Suppressing graphviz dot function errors to clear up apache error logs, refs #27557
• src/hg/hgTracks/renderMain.c
  • lines changed 6, context: html, text, full: html, text
    07c8057829439a6a024e60d9a1070af9b480b43f Wed May 12 09:56:38 2021 -0700
    Added ifdef disables code for hgRenderTracks to generate PDFs rather than PNGs. Not sure how to integrate this yet
• src/hg/htdocs/FAQ/FAQformat.html
  • lines changed 16, context: html, text, full: html, text
    33adf27afa5f8d959d92d6c6fc5ab52b06e2b62f Mon May 10 14:56:06 2021 -0700
    Adding a longTabix entry on data formats after Max email, refs #20885
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    0c36df1d737872a5482eee2b1842ec0b5c89efa9 Tue May 11 09:34:24 2021 -0700
    Fixing a typo refs #20885
• src/hg/htdocs/FAQ/FAQgenes.html
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    81c2c4b94d02441ac67de2fe14d47c03b4ff1f31 Thu May 13 16:24:02 2021 -0700
    grammar nit
• src/hg/htdocs/covid19.html
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    35bbdbb24ededa5368e4f3570af0b92d4c5ef6fb Tue May 11 10:07:35 2021 -0700
    Adding the release of the Vaccines track to the COVID landing page, refs #27312
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html
  • lines changed 39, context: html, text, full: html, text
    cb88ec00dcbcad71f0b108fb09b1c0200cf3371e Fri May 14 19:30:54 2021 -0700
    With v3 trackDb versioning, set all new settings that were in v2 to full in v3. All settings now added will be status new ref #26598
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 32, context: html, text, full: html, text
    7f9e0d7817167dfd2da6b9fe0ce3f4a6e366ff3d Tue May 11 11:27:31 2021 -0700
    Announcing the Vaccines track for wuhCor1, refs #27312
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 3, context: html, text, full: html, text
    1c703fa89040e459da7d719da05927a2e14d5179 Tue May 11 17:01:26 2021 -0700
    Adding a PMCID to a publication now available
  • lines changed 22, context: html, text, full: html, text
    5e27d82ebfe5ff7e366a47767f72965fcef09b5d Wed May 12 15:13:42 2021 -0700
    Adding now available PMCIDs and new publication
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    6f21db733dabba0c3f77cb5957f6bc7f3f79e521 Fri May 14 08:03:00 2021 -0700
    added PMIDs for two old important papers
• src/hg/htdocs/images/singleCell/intestineWang-figS1e.jpg
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    6acd84f29f1ffa6a57ac95960cf7d6801084c31b Wed May 12 12:31:54 2021 -0700
    Adding image for figure S1e from paper for colonWang rectumWang ileumWang track. refs #26969
• src/hg/htdocs/images/singleCell/pancreasBaron-fig1a.jpg
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    a89b54ae468f1b6bf7746dd1f49b7b3a932bd5cc Wed May 12 12:04:51 2021 -0700
    Adding image for figure 1a from paper for pancreasBaron track. refs #26966
• src/hg/htdocs/images/singleCell/pancreasBaron-fig1d.jpg
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    832dc4141fe6ccefe7bcc82bb56a6a4a2a11fcfe Wed May 12 11:57:28 2021 -0700
    Adding images for figures 1d and 1f from paper for pancreasBaron track. refs #26966
• src/hg/htdocs/images/singleCell/pancreasBaron-fig1f.jpg
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    832dc4141fe6ccefe7bcc82bb56a6a4a2a11fcfe Wed May 12 11:57:28 2021 -0700
    Adding images for figures 1d and 1f from paper for pancreasBaron track. refs #26966
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    7f9e0d7817167dfd2da6b9fe0ce3f4a6e366ff3d Tue May 11 11:27:31 2021 -0700
    Announcing the Vaccines track for wuhCor1, refs #27312
• src/hg/inc/cartRewrite.h
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    aab035611a8db56bc79be824f83e87e31fd3387e Thu May 13 15:29:02 2021 -0700
    oops, forgot about this include file
• src/hg/inc/hubConnect.h
  • lines changed 6, context: html, text, full: html, text
    d58aec2ee04b5a1d5004b30a04696df4741c5023 Tue May 11 17:04:04 2021 -0700
    check to make sure genark table exists before using it.
• src/hg/lib/cart.c
  • lines changed 1, context: html, text, full: html, text
    b6388f2c60d4bee4e859eecd59ca7f1ea9894953 Thu May 13 13:40:41 2021 -0700
    Change CGI Cache-control HTTP header to no-cache, which allows web browsers to cache responses if they are unchanged, but serve a fresh response otherwise, refs Hiram email
• src/hg/lib/cartRewrite.c
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    98aa95938f3af948c60e20044318595f10fee780 Thu May 13 15:22:00 2021 -0700
    ongoing work on cart rewrite system
• src/hg/lib/hubConnect.c
  • lines changed 18, context: html, text, full: html, text
    d58aec2ee04b5a1d5004b30a04696df4741c5023 Tue May 11 17:04:04 2021 -0700
    check to make sure genark table exists before using it.
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    98aa95938f3af948c60e20044318595f10fee780 Thu May 13 15:22:00 2021 -0700
    ongoing work on cart rewrite system
• src/hg/makeDb/doc/asmHubs/mkGenomes.pl
  • lines changed 2, context: html, text, full: html, text
    b9f7ddc7bbae881dd79b74932bc6c94d26b94bdf Mon May 10 11:47:23 2021 -0700
    turning on dynamic blat for both hgwdev and the hgdownload files refs #26658
• src/hg/makeDb/doc/asmHubs/mkSymLinks.pl
  • lines changed 2, context: html, text, full: html, text
    b9f7ddc7bbae881dd79b74932bc6c94d26b94bdf Mon May 10 11:47:23 2021 -0700
    turning on dynamic blat for both hgwdev and the hgdownload files refs #26658
• src/hg/makeDb/doc/canFam6/initialBuild.txt
  • lines changed 1263, context: html, text, full: html, text
    c516c8baafafb02e61279dcb6f55a3ee11caf902 Wed May 12 14:54:54 2021 -0700
    beginning canFam6 build running RepeatMasker refs #27546
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    e42a6c8b3f120d7ce0234e1277977b6de2b198f7 Thu May 13 11:50:34 2021 -0700
    ready for the chainNet lastz runs refs #27546
• src/hg/makeDb/doc/hg38/cactus241way.txt
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    d822406ab76774a681c2509b4232dd3a31f459ea Fri May 14 12:49:29 2021 -0700
    completed documentation for cactus 241 way track refs #27519
• src/hg/makeDb/doc/hg38/ncbiRefSeq.txt
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    b7a13e758fbac753f9abd086f0aa01ca357d54da Thu May 13 14:20:03 2021 -0700
    run up update refs #27552
• src/hg/makeDb/genbank/etc/align.dbs
  • lines changed 1, context: html, text, full: html, text
    19fa382f6aae23ca45153161c026c20aa92102c1 Thu May 13 10:58:11 2021 -0700
    Added canFam6 - dog refs #27546
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 18, context: html, text, full: html, text
    bf4b7a0faf40fc5c2c30fb25e31440e9d5b1d142 Thu May 13 10:57:12 2021 -0700
    Added canFam6 dog; refs #27546
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • lines changed 2, context: html, text, full: html, text
    19fa382f6aae23ca45153161c026c20aa92102c1 Thu May 13 10:58:11 2021 -0700
    Added canFam6 - dog refs #27546
• src/hg/makeDb/schema/all.joiner
  • lines changed 8, context: html, text, full: html, text
    9bcc66741dba603dc21ffdf16e66bd237611e58d Thu May 13 11:41:11 2021 -0700
    adding rules for canFam6 refs #27546
• src/hg/makeDb/trackDb/augustusGene.html
  • lines changed 1, context: html, text, full: html, text
    70952dc60bde84f731bfae4d9a7af4ba50b29bdb Wed May 12 07:02:54 2021 -0700
    Updating redirected links found the the uiLinks cronjob for danRer3, no Redmine
• src/hg/makeDb/trackDb/dog/canFam6/description.html
  • lines changed 64, context: html, text, full: html, text
    ee5fb71ffc745a779ad96a5026035d807379b5ce Wed May 12 14:05:51 2021 -0700
    adding canFam6 dog to the browser refs #27546
• src/hg/makeDb/trackDb/dog/canFam6/gap.html
  • lines changed 30, context: html, text, full: html, text
    ee5fb71ffc745a779ad96a5026035d807379b5ce Wed May 12 14:05:51 2021 -0700
    adding canFam6 dog to the browser refs #27546
• src/hg/makeDb/trackDb/dog/canFam6/gold.html
  • lines changed 33, context: html, text, full: html, text
    ee5fb71ffc745a779ad96a5026035d807379b5ce Wed May 12 14:05:51 2021 -0700
    adding canFam6 dog to the browser refs #27546
• src/hg/makeDb/trackDb/dog/canFam6/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    ee5fb71ffc745a779ad96a5026035d807379b5ce Wed May 12 14:05:51 2021 -0700
    adding canFam6 dog to the browser refs #27546
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    941fb54cd21a4fbc5bd4f3fe4b03b71524eb4440 Thu May 13 11:29:06 2021 -0700
    adding refSeqComposite and search rule for gold/assembly track refs #27546
• src/hg/makeDb/trackDb/human/caddSuper.html
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    10f32665170eccacad0809cde549542165f39d12 Thu May 13 16:43:34 2021 -0700
    fixed weird chars to tilde
• src/hg/makeDb/trackDb/human/hg19/exomeProbesets.ra
  • lines changed 30, context: html, text, full: html, text
    c1243e8c3647b9e17d2dc64006adf2e91e8712d1 Tue May 11 16:23:12 2021 -0700
    Revert "Fixing plus signs that caused errors refs #27515" This reverts commit c6f55ceb4ba3de1d914c08a167a19f7f40e76a7f.
  • lines changed 8, context: html, text, full: html, text
    d5efc514b444f39743344e1ca71e77e06a73cf5e Tue May 11 16:30:26 2021 -0700
    Adding the + back to short and longLabels, while removing only from track names. Also fixed 2 cases of mislabeled V4/V5 data. Refs #27515
• src/hg/makeDb/trackDb/human/hg38/cons241way.html
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    14a9a1f2db57dd3e729c55265099691017295c05 Fri May 14 12:22:29 2021 -0700
    clarify single directory for downloads refs #27519
• src/hg/makeDb/trackDb/human/hg38/exomeProbesets.ra
  • lines changed 26, context: html, text, full: html, text
    c1243e8c3647b9e17d2dc64006adf2e91e8712d1 Tue May 11 16:23:12 2021 -0700
    Revert "Fixing plus signs that caused errors refs #27515" This reverts commit c6f55ceb4ba3de1d914c08a167a19f7f40e76a7f.
  • lines changed 8, context: html, text, full: html, text
    d5efc514b444f39743344e1ca71e77e06a73cf5e Tue May 11 16:30:26 2021 -0700
    Adding the + back to short and longLabels, while removing only from track names. Also fixed 2 cases of mislabeled V4/V5 data. Refs #27515
• src/hg/makeDb/trackDb/human/hg38/trackDb.241way.ra
  • lines changed 5, context: html, text, full: html, text
    e4d67578fecb028413b3fc205816eecc26321601 Thu May 13 07:57:41 2021 -0700
    renamed Cactus Zoonomia tracks per Jim's suggestion
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    c452b251239a5b6079fab90b2993fe8c73496555 Thu May 13 08:17:11 2021 -0700
    no need to have 7-way and 20-way tracks on for the RR set them to alpha only refs #27519
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
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    c452b251239a5b6079fab90b2993fe8c73496555 Thu May 13 08:17:11 2021 -0700
    no need to have 7-way and 20-way tracks on for the RR set them to alpha only refs #27519
• src/hg/makeDb/trackDb/makefile
  • lines changed 1, context: html, text, full: html, text
    ee5fb71ffc745a779ad96a5026035d807379b5ce Wed May 12 14:05:51 2021 -0700
    adding canFam6 dog to the browser refs #27546
• src/hg/makeDb/trackDb/microsat.html
  • lines changed 2, context: html, text, full: html, text
    662f174fa35c933852dabfc4b66654180be3058a Thu May 13 08:42:32 2021 -0700
    Updating HTTP to HTTPS for redirected links, uiLinks cronjob.
• src/hg/makeDb/trackDb/relatedTracks.ra
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    4bbef1e0af5cf6ac493a0e8ee2b00a3ca518517f Fri May 14 16:40:30 2021 -0700
    Starting off the related tracks file with a few relationships to get everyone started, refs #27550
• src/hg/makeDb/trackDb/simpleRepeat.html
  • lines changed 2, context: html, text, full: html, text
    662f174fa35c933852dabfc4b66654180be3058a Thu May 13 08:42:32 2021 -0700
    Updating HTTP to HTTPS for redirected links, uiLinks cronjob.
• src/hg/makeDb/trackDb/spMut.html
  • lines changed 1, context: html, text, full: html, text
    662f174fa35c933852dabfc4b66654180be3058a Thu May 13 08:42:32 2021 -0700
    Updating HTTP to HTTPS for redirected links, uiLinks cronjob.
• src/hg/makeDb/trackDb/uniprot.html
  • lines changed 1, context: html, text, full: html, text
    662f174fa35c933852dabfc4b66654180be3058a Thu May 13 08:42:32 2021 -0700
    Updating HTTP to HTTPS for redirected links, uiLinks cronjob.
• src/hg/makeDb/trackDb/virus/wuhCor1/vaccines.ra
  • lines changed 2, context: html, text, full: html, text
    1e3ef3396153d19e39361e65774df4e908952d96 Tue May 11 15:02:25 2021 -0700
    Adding the new pennantIcon for the vaccines track, refs #27312
• src/hg/makeDb/trackDb/xenTro/xenTro10/trackDb.ra
  • lines changed 13, context: html, text, full: html, text
    0d654881a9a34e35f1817f365566e1536f91e40a Fri May 14 14:54:55 2021 -0700
    Changing xenTro10 tracks priority and changing shortLabel name to display mm10, refs #24693
• src/hg/makeDb/trackDb/zebrafish/danRer3/bacEndPairs.html
  • lines changed 1, context: html, text, full: html, text
    70952dc60bde84f731bfae4d9a7af4ba50b29bdb Wed May 12 07:02:54 2021 -0700
    Updating redirected links found the the uiLinks cronjob for danRer3, no Redmine
• src/hg/makeDb/trackDb/zebrafish/danRer3/bacEndSingles.html
  • lines changed 1, context: html, text, full: html, text
    70952dc60bde84f731bfae4d9a7af4ba50b29bdb Wed May 12 07:02:54 2021 -0700
    Updating redirected links found the the uiLinks cronjob for danRer3, no Redmine
• src/hg/makeDb/trackDb/zebrafish/danRer3/rhMap.html
  • lines changed 1, context: html, text, full: html, text
    70952dc60bde84f731bfae4d9a7af4ba50b29bdb Wed May 12 07:02:54 2021 -0700
    Updating redirected links found the the uiLinks cronjob for danRer3, no Redmine
• src/hg/testRewrite/makefile
  • lines changed 4, context: html, text, full: html, text
    07d51d0d49c4c9f7c8a3933ec92b4f6af03d994b Tue May 11 15:29:20 2021 -0700
    first cut at cart re-write library
• src/hg/testRewrite/testRewrite.c
  • lines changed 224, context: html, text, full: html, text
    07d51d0d49c4c9f7c8a3933ec92b4f6af03d994b Tue May 11 15:29:20 2021 -0700
    first cut at cart re-write library
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    98aa95938f3af948c60e20044318595f10fee780 Thu May 13 15:22:00 2021 -0700
    ongoing work on cart rewrite system
• src/hg/utils/automation/altScaffoldPlacementToBed.pl
  • lines changed 4, context: html, text, full: html, text
    5c41c93386c2b2b36bd68423799d197e9c49675a Wed May 12 00:07:13 2021 -0700
    oops. mm10 does not need lower-case IDs.
• src/hg/utils/automation/doNcbiRefSeq.pl
  • lines changed 12, context: html, text, full: html, text
    9a2f1da0c665b5b5afb248b89e2a18418f993aac Thu May 13 13:15:15 2021 -0700
    better naming for archived versions refs #24735
• src/inc/regexHelper.h
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    98aa95938f3af948c60e20044318595f10fee780 Thu May 13 15:22:00 2021 -0700
    ongoing work on cart rewrite system
• src/lib/regexHelper.c
  • lines changed 159, context: html, text, full: html, text
    98aa95938f3af948c60e20044318595f10fee780 Thu May 13 15:22:00 2021 -0700
    ongoing work on cart rewrite system
• src/oneShot/adiposeRelabelImmune/adiposeRelabelImmune.c
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    4b4e6832927f7648993eb55e5062aac73a55f3d2 Wed Apr 28 16:01:50 2021 -0700
    Writing something to massage data for an adipose single cell data set to get a good meta.tsv file.
• src/oneShot/adiposeRelabelImmune/makefile
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    4b4e6832927f7648993eb55e5062aac73a55f3d2 Wed Apr 28 16:01:50 2021 -0700
    Writing something to massage data for an adipose single cell data set to get a good meta.tsv file.
• src/utils/qa/weeklybld/buildEnv.csh
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    a0cd718f5bcb97bfa1b00e3554e4b47d57ec11ba Mon May 17 10:03:45 2021 -0700
    v415 preview2, refs #27542

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• files changed: 74