All File Changes

v409_preview to v409_preview2 (2021-01-04 to 2021-01-11) v409

• src/hg/hgPhyloPlace/phyloPlace.c
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    55d15bfd5b19c9755b8385df51cd002a61e2baf6 Mon Jan 4 18:04:38 2021 -0800
    When writing custom tracks, attribute public vs. GISAID sequences correctly.
• src/hg/hgPhyloPlace/phyloPlace.h
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    55d15bfd5b19c9755b8385df51cd002a61e2baf6 Mon Jan 4 18:04:38 2021 -0800
    When writing custom tracks, attribute public vs. GISAID sequences correctly.
• src/hg/hgPhyloPlace/writeCustomTracks.c
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    55d15bfd5b19c9755b8385df51cd002a61e2baf6 Mon Jan 4 18:04:38 2021 -0800
    When writing custom tracks, attribute public vs. GISAID sequences correctly.
• src/hg/hgTracks/hgTracks.c
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    e2acc858c490cbe1d1d8e51a6c704c96d30d032c Thu Jan 7 10:20:01 2021 -0800
    Fix up gnomad constraint legend to match new colors, refs #26399
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    cfb223c5751eb97c95ccb4d27b7f1f0dc5b8c4bb Thu Jan 7 13:58:23 2021 -0800
    fixes bug we do not want bed input with size 0 elements, even though other parts of our software tolerate it for SNPs. fixes#RM26772
• src/hg/hgTracks/vcfTrack.c
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    2ebfbfc9042e880ad0cdda1643d4ec57621579df Mon Jan 4 18:03:11 2021 -0800
    Warn about empty tree file and avoid seg fault.
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    6301b9d4214f464863531b4af0e0ba2c0f6106b4 Wed Jan 6 20:33:39 2021 -0800
    Increase branch width for VCF+tree display; it was really hard to follow branches with the narrow width. Russ asked to make it configurable; for now, just make it wider.
• src/hg/htdocs/covid19.html
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    af7a8303a81968ad6191744d5df9c343433336e6 Fri Jan 8 15:03:03 2021 -0800
    Updating the 'last updated' date to today. Adding the COVID Reference book to the list of 'Related publications and data resources', refs #26761
• src/hg/htdocs/goldenPath/help/bigBed.html
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    ac0316bc98d0b617a6fe83801277b8e1832902c4 Mon Jan 11 06:51:15 2021 -0800
    a few improvements for section #3 of bigBed.html, probably could use a lot more work to make the English clearer. no redmine yet, but coming today
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    e4b0792c7b643c95e039c56849f958b3b5a94f65 Mon Jan 11 07:08:43 2021 -0800
    another small bigBed.html change, no redmine yet
• src/hg/htdocs/goldenPath/help/bigLolly.html
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    e9f3044bd364e4224e05da2291fdbc126ba0895a Tue Jan 5 16:24:11 2021 -0800
    Code review edits to bigLolly.html Example 3 settings, refs #26742
• src/hg/htdocs/goldenPath/help/gbic.html
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    d8d9e8bc8fa214d169bc3011359fbe9bfd6b7c08 Tue Jan 5 17:06:01 2021 -0800
    Removing the escaped characters to clean up the markdown file (github README) refs #23297
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    66065d1a4070eda46e1f5d388e449a62f9e64c37 Fri Jan 8 14:41:41 2021 -0800
    Making the contact page an absolute link to make it work on the markdown file, refs #23297
• src/hg/htdocs/goldenPath/help/mirror.html
  • lines changed 30, context: html, text, full: html, text
    13e3653211b86d6f90e02b385f5008fc69ccd0a1 Fri Jan 8 12:44:33 2021 -0800
    changes to mirror HTML from TXT file changes
• src/hg/htdocs/goldenPath/help/mirrorManual.html
  • lines changed 132, context: html, text, full: html, text
    13e3653211b86d6f90e02b385f5008fc69ccd0a1 Fri Jan 8 12:44:33 2021 -0800
    changes to mirror HTML from TXT file changes
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
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    33311d452acc7891db5bb34ad8b7ba9c83ab7f3e Tue Jan 5 14:09:52 2021 -0800
    Adding a link to the bigLolly new help page refs #26742
• src/hg/htdocs/goldenPath/help/vcf.html
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    2965d94999b43cb6b795011e517e7610ae22e877 Wed Jan 6 17:14:56 2021 -0800
    added section briefly describing vcf format
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    24e9efad07acca531ab9640912d32034b6086145 Wed Jan 6 17:25:52 2021 -0800
    added clarification that hg18 is a human assembly
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    6cc1e1e4ce2f0553e9a45485279b6497e06a64e9 Thu Jan 7 17:09:44 2021 -0800
    added a clarifyng phrase
• src/hg/htdocs/goldenPath/history.html
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    1d8f618eb675164f82954223744046e2ea2bec3d Tue Dec 29 15:02:37 2020 -0800
    Replacing a word. refs #20314
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    2321e33442cb48591aae4c29b40424a402b182a7 Mon Jan 4 15:38:16 2021 -0800
    Adding images and captions to the history page. Still need to fix the format/style. refs #20314
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    07925c717a098e9dab3c312acad2812f9c70f3a6 Tue Jan 5 17:23:01 2021 -0800
    made some edits. added a bit of text
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    e9a4b52adf8ac5a049e2be827dcb0d906a55252a Wed Jan 6 15:44:45 2021 -0800
    Fixing the menu list on the page to match the body section, refs #20314
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    59be73feaf94cd72a1dd32ccaff5b479ccfce015 Wed Jan 6 16:25:58 2021 -0800
    Capitalizing 'genome browser' when talking about the UCSC Genome Browser. Editing a sentence from Bob's suggestions, refs #20314
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    659fdce4ba2cc6eea5b7555344d4155047125abc Wed Jan 6 17:49:14 2021 -0800
    added paragraph written by david haussler. it is more jargony than most of the page.
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    c5646cd96ffba1bf1574d26abaaa35cd021c448f Thu Jan 7 14:56:07 2021 -0800
    Centering the photos on the page. Using the new image name for the early browser group photo, refs #20314
  • lines changed 77, context: html, text, full: html, text
    8fb15b4d208ce2521a398a5dea0e547ec589f68e Thu Jan 7 17:17:36 2021 -0800
    Fixing the indentation for the div tags, refs #20314
• src/hg/htdocs/goldenPath/newsarch.html
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    b116999c2def25ea7669f7aaf99bd6b3873905aa Wed Jan 6 12:23:00 2021 -0800
    Code review edits, adding a target=_blank to GBiB link for consistency, refs #26742
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    38c888f9318cb5a7efba271865f11f1b8320573e Fri Jan 8 09:47:41 2021 -0800
    Fifth coronavirus news announcement refs #26777
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    6a2370294a64a6c3be2b2bf37e73540fde1adcf1 Fri Jan 8 15:00:24 2021 -0800
    Adding hg19 to annuncement No RM
• src/hg/htdocs/images/Jim-Kent-David-Haussler-Patrick-Gavin-Scot-Kennedy-genome-assembly-era-Group-2000.jpg
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    a69ecaf446d891e08a6fe13e938355a2b27b8dd7 Thu Jan 7 14:42:56 2021 -0800
    Fixing the order of names for one of the history.html photos, refs #20314
• src/hg/htdocs/images/Jim-Kent-David-Haussler-Scot-Kennedy-Patrick-Gavin-genome-assembly-era-Group-2000.jpg
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    a69ecaf446d891e08a6fe13e938355a2b27b8dd7 Thu Jan 7 14:42:56 2021 -0800
    Fixing the order of names for one of the history.html photos, refs #20314
• src/hg/htdocs/indexNews.html
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    38c888f9318cb5a7efba271865f11f1b8320573e Fri Jan 8 09:47:41 2021 -0800
    Fifth coronavirus news announcement refs #26777
• src/hg/lib/clinvarSubLolly.as
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    6556efb9aa9508359f3344e26ae3ad7d9d9b6cf3 Tue Jan 5 12:44:32 2021 -0800
    document what score means in clinvarSubLolly bigBed
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    a87b28fa247665d863bfcd5013e5dc929892ec81 Tue Jan 5 12:46:20 2021 -0800
    document what score means in clinvarSubLolly bigBed
• src/hg/lib/hgMaf.c
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    da6e1451531ba0147ba54f531361515e55fde9af Mon Jan 4 16:30:19 2021 -0800
    hack to hgMaf to allow for the presence of organism names with a dot in them.
• src/hg/liftOver/liftOver.c
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    0745fb7320eae8ad11e8909b96021dfdd625bb5b Thu Jan 7 13:35:55 2021 -0800
    Error found and fix suggested by user Simon Brent on github. kent issue 50, refs#RM26758
• src/hg/makeDb/doc/asmHubs/master.run.list
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    e16379ceea6b845269c76089860c5b1fff8cc1fd Tue Jan 5 14:24:44 2021 -0800
    up to date with recent plants refs #23891
• src/hg/makeDb/doc/hg19.txt
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    90f975fc8ce13316eda1bd73d05fd17d65136dea Tue Jan 5 03:07:17 2021 -0800
    adding exome probesets track made by Ana/Beagan/Pranav/Tiana, refs #24598
• src/hg/makeDb/doc/hg38/exomeProbesets.txt
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    90f975fc8ce13316eda1bd73d05fd17d65136dea Tue Jan 5 03:07:17 2021 -0800
    adding exome probesets track made by Ana/Beagan/Pranav/Tiana, refs #24598
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    dc4ce7dc067c079e4a3b1a7e51fe022b65a6cacb Thu Jan 7 05:38:23 2021 -0800
    exome probesets updates, doc page and visibility, refs #24598
• src/hg/makeDb/doc/plantsAsmHub/hub.txt
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    085d725cc166527173a5e82db9bd9a23d0c53fc9 Fri Jan 8 12:03:56 2021 -0800
    correct hub name and shortLabel refs #26765
• src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv
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    70827fe65b8f2c2af027115eba078fa2ea0d2b3a Tue Jan 5 14:14:26 2021 -0800
    up to date with 117 genomes refs #23891
• src/hg/makeDb/doc/wuhCor1/multiz7way.txt
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    bcf2b16db40f74e7d0d0e68a8cfbdffb4f900add Tue Jan 5 16:08:13 2021 -0800
    some work on improving the mafSnp display with Jim #26766
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    2de9800b29a37981842cac70727f1d49be5aaacd Wed Jan 6 16:21:40 2021 -0800
    adding phastCons and phyloP tracks refs #26728
• src/hg/makeDb/doc/wuhCor1/phylogenetics.txt
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    244a07ffab7f03e9dadc8419c14f3685246860a9 Tue Jan 5 00:47:01 2021 -0800
    Adding B.1.1.7 (US) track. refs #26753
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    4f0cb5be8dce2a3a1e070e23c8a150c375a6e979 Tue Jan 5 10:47:57 2021 -0800
    lineageB_1_1_7_US update: replace EPI_ IDs with GenBank IDs so we can share more sequences in VCF. refs #26753
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    55de0a7d0d285d4be07cd15958db764d8ed3f6ed Tue Jan 5 16:26:01 2021 -0800
    Adding New York B.1.1.7 sequence, updating GenBank links in description. refs #26753
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    04d2dd20a61dd65b51611024d31c04078276c6b3 Thu Jan 7 17:14:09 2021 -0800
    A little cleanup of some inconsistent names and a stray rev-strand sequence in preparation for rolling out incrementally updated trees of public sequences.
• src/hg/makeDb/gnomad/combine.awk
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    aeef1250267d3f03c35abbc1df8be1ffa6be13c2 Thu Jan 7 08:48:25 2021 -0800
    Update gnomad constraint build script to color by loeuf score instead of pli score, refs #26399
• src/hg/makeDb/hgLoadMaf/hgLoadMafSummary.c
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    a65c1c83911f15e20ca817725d4bd3681c8c784e Wed Jan 6 17:16:12 2021 -0800
    deal with the fact that some assemblies may have a single dot in their name
• src/hg/makeDb/outside/gencode/bin/ensToUcscMkLift
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    8ec6b110b2e1c9aad5133589c65e72ba7b478638 Fri Jan 8 08:04:17 2021 -0800
    gencode mm39 load changes
• src/hg/makeDb/outside/gencode/gencodeLoad.mk
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    8ec6b110b2e1c9aad5133589c65e72ba7b478638 Fri Jan 8 08:04:17 2021 -0800
    gencode mm39 load changes
• src/hg/makeDb/trackDb/human/clinvar.html
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    b17139af3394554630ce41a003bea745a48d2f49 Fri Jan 8 15:49:30 2021 -0800
    Jorge has done the archive move, so update the link in the clinvar docs, no redmine, emails with Chris and Jorge.
• src/hg/makeDb/trackDb/human/covidHgiGwas.ra
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    cb9e32174a5f3db831857181dd07bfbc535ce2a7 Fri Jan 8 14:57:02 2021 -0800
    Adding date to pennantIcon #25010
• src/hg/makeDb/trackDb/human/exomeProbesets.html
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    27b1ac4eb6f3c52060675eaceffb20f85f8705a9 Tue Jan 5 03:10:07 2021 -0800
    forgot to add html page for exome probesets tracks, refs #24598
• src/hg/makeDb/trackDb/human/hg19/exomeProbesets.ra
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    90f975fc8ce13316eda1bd73d05fd17d65136dea Tue Jan 5 03:07:17 2021 -0800
    adding exome probesets track made by Ana/Beagan/Pranav/Tiana, refs #24598
• src/hg/makeDb/trackDb/human/hg19/trackDb.gnomad.ra
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    9420f6640ef03c6a505ac5b67a892198bd3268be Wed Jan 6 09:45:20 2021 -0800
    Adding MAF filters to updated gnomad tracks, refs #25010,#26449
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    4db9d58832e407c701b4c4fc3cfa4e107d3be64a Wed Jan 6 10:15:45 2021 -0800
    Changing gnomAD filter label #25010
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    3942c5287c1795c87d6cb0136a46b0e40b7fdc62 Fri Jan 8 09:17:12 2021 -0800
    Add missense constraint by transcript and gene tracks and some other small changes requested by Anne O'Donnell-Luria
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
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    90f975fc8ce13316eda1bd73d05fd17d65136dea Tue Jan 5 03:07:17 2021 -0800
    adding exome probesets track made by Ana/Beagan/Pranav/Tiana, refs #24598
• src/hg/makeDb/trackDb/human/hg38/exomeProbesets.ra
  • lines changed 230, context: html, text, full: html, text
    90f975fc8ce13316eda1bd73d05fd17d65136dea Tue Jan 5 03:07:17 2021 -0800
    adding exome probesets track made by Ana/Beagan/Pranav/Tiana, refs #24598
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    dc4ce7dc067c079e4a3b1a7e51fe022b65a6cacb Thu Jan 7 05:38:23 2021 -0800
    exome probesets updates, doc page and visibility, refs #24598
• src/hg/makeDb/trackDb/human/hg38/gnomad.ra
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    9420f6640ef03c6a505ac5b67a892198bd3268be Wed Jan 6 09:45:20 2021 -0800
    Adding MAF filters to updated gnomad tracks, refs #25010,#26449
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    4db9d58832e407c701b4c4fc3cfa4e107d3be64a Wed Jan 6 10:15:45 2021 -0800
    Changing gnomAD filter label #25010
• src/hg/makeDb/trackDb/human/hg38/trackDb.gencode.ra
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    dfa33e7edb8273417ed94e429bc259e9514715c5 Thu Jan 7 14:02:15 2021 -0800
    Squashing stale pennantIcons refs #26753
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
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    90f975fc8ce13316eda1bd73d05fd17d65136dea Tue Jan 5 03:07:17 2021 -0800
    adding exome probesets track made by Ana/Beagan/Pranav/Tiana, refs #24598
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    dfa33e7edb8273417ed94e429bc259e9514715c5 Thu Jan 7 14:02:15 2021 -0800
    Squashing stale pennantIcons refs #26753
• src/hg/makeDb/trackDb/human/trackDb.clinGen.ra
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    dfa33e7edb8273417ed94e429bc259e9514715c5 Thu Jan 7 14:02:15 2021 -0800
    Squashing stale pennantIcons refs #26753
• src/hg/makeDb/trackDb/human/trackDb.dbVar.ra
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    dfa33e7edb8273417ed94e429bc259e9514715c5 Thu Jan 7 14:02:15 2021 -0800
    Squashing stale pennantIcons refs #26753
• src/hg/makeDb/trackDb/human/trackDb.ra
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    dfa33e7edb8273417ed94e429bc259e9514715c5 Thu Jan 7 14:02:15 2021 -0800
    Squashing stale pennantIcons refs #26753
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    e101dc0e743a44ea8c8813ffcc29e8cc51697f40 Fri Jan 8 13:05:26 2021 -0800
    LRG track otto updating for hg19 and hg38, refs #17877 #24672
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    03045b074b65d33e4893d9b4b2b464271f659a69 Fri Jan 8 14:43:10 2021 -0800
    Forgot the cds and fa arguments to pslToBigPsl for lrg otto build, refs #24672
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.ra
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    9fc04d8e8b4b8571e88573780d1bd07dfec5779a Fri Jan 8 13:26:28 2021 -0800
    now using ncbiRefSeq composite refs #26783
• src/hg/makeDb/trackDb/rhesus/rheMac10/trackDb.ra
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    dfa33e7edb8273417ed94e429bc259e9514715c5 Thu Jan 7 14:02:15 2021 -0800
    Squashing stale pennantIcons refs #26753
• src/hg/makeDb/trackDb/tagTypes.tab
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    cad24d48147c54fec5574b6841027b1d51a9fdf3 Thu Jan 7 17:49:28 2021 -0800
    adding chainNet plus mafNet alignments for assembly hub chainNet tracks refs #26584
• src/hg/makeDb/trackDb/trackDb.chainNet.asmHub.ra
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    cad24d48147c54fec5574b6841027b1d51a9fdf3 Thu Jan 7 17:49:28 2021 -0800
    adding chainNet plus mafNet alignments for assembly hub chainNet tracks refs #26584
• src/hg/makeDb/trackDb/trackDb.ra
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    dfa33e7edb8273417ed94e429bc259e9514715c5 Thu Jan 7 14:02:15 2021 -0800
    Squashing stale pennantIcons refs #26753
• src/hg/makeDb/trackDb/virus/wuhCor1/bloom.ra
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    dfa33e7edb8273417ed94e429bc259e9514715c5 Thu Jan 7 14:02:15 2021 -0800
    Squashing stale pennantIcons refs #26753
• src/hg/makeDb/trackDb/virus/wuhCor1/description.html
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    e2938127a66b169c0d6b23aeb4edb2e7fda98a8b Fri Jan 8 09:19:05 2021 -0800
    Adding UCSC covid resources page and hgPhyloPlace to hgGateway for wuhCor1, no RM
• src/hg/makeDb/trackDb/virus/wuhCor1/lineageB_1_1_7_US.html
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    244a07ffab7f03e9dadc8419c14f3685246860a9 Tue Jan 5 00:47:01 2021 -0800
    Adding B.1.1.7 (US) track. refs #26753
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    55de0a7d0d285d4be07cd15958db764d8ed3f6ed Tue Jan 5 16:26:01 2021 -0800
    Adding New York B.1.1.7 sequence, updating GenBank links in description. refs #26753
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    bf4c0a38e64577aa9a4ade7efc43ab705ce2c1a1 Wed Jan 6 17:12:58 2021 -0800
    Updating link for subtree with NY and San Diego sequences. refs #26753
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    09525abd6d4ced09add79f0d1e6c0475ef0fd7ab Thu Jan 7 17:13:00 2021 -0800
    No need to refer to the genome-test version of hgPhyloPlace now that the tree has been updated on the RR, thanks Lou! refs #26753, #26774
• src/hg/makeDb/trackDb/virus/wuhCor1/phylocsf.ra
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    dfa33e7edb8273417ed94e429bc259e9514715c5 Thu Jan 7 14:02:15 2021 -0800
    Squashing stale pennantIcons refs #26753
• src/hg/makeDb/trackDb/virus/wuhCor1/pond.ra
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    dfa33e7edb8273417ed94e429bc259e9514715c5 Thu Jan 7 14:02:15 2021 -0800
    Squashing stale pennantIcons refs #26753
• src/hg/makeDb/trackDb/virus/wuhCor1/sarsCov2Phylo.html
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    f52368a9198ad15b260ca56301a2a0baf653267b Mon Jan 4 18:00:09 2021 -0800
    Updating reference for Pangolin lineage nomenclature.
• src/hg/makeDb/trackDb/virus/wuhCor1/sarsCov2PhyloPub.html
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    f52368a9198ad15b260ca56301a2a0baf653267b Mon Jan 4 18:00:09 2021 -0800
    Updating reference for Pangolin lineage nomenclature.
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.7way.ra
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    a385334be766c13661bfb34a6877d43c9a015dbb Wed Jan 6 16:16:02 2021 -0800
    adding phastCons and phyloP tracks refs #26728
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    dfa33e7edb8273417ed94e429bc259e9514715c5 Thu Jan 7 14:02:15 2021 -0800
    Squashing stale pennantIcons refs #26753
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra
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    244a07ffab7f03e9dadc8419c14f3685246860a9 Tue Jan 5 00:47:01 2021 -0800
    Adding B.1.1.7 (US) track. refs #26753
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    f260f5d365a4c2eee0148ea35df12ff14995a48c Tue Jan 5 13:00:12 2021 -0800
    David suggests emphasizing in the longLabel that this track includes deletions unlike other tracks. refs #26753
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    55de0a7d0d285d4be07cd15958db764d8ed3f6ed Tue Jan 5 16:26:01 2021 -0800
    Adding New York B.1.1.7 sequence, updating GenBank links in description. refs #26753
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    dfa33e7edb8273417ed94e429bc259e9514715c5 Thu Jan 7 14:02:15 2021 -0800
    Squashing stale pennantIcons refs #26753
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    cd7f64050304b673a80b0e3eeb748bba67780b97 Thu Jan 7 17:15:34 2021 -0800
    Add correct release date for pennant icon mouseover. refs #26753
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    e3c1342cf13223f030e39a40e3a95f8c5b8e59e0 Fri Jan 8 09:26:38 2021 -0800
    Adding links to the specific release announcement to tracks refs #26777
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.uniprot.ra
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    a44e4ab558bb72979734c93141a4b64719d7f6cf Thu Jan 7 05:22:33 2021 -0800
    switching uniprot proteins to bigGenePred, refs #25192
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    4c6a8fea4efcd82fb2a46c54701c1f52971e5275 Fri Jan 8 05:19:26 2021 -0800
    tweaking the labels of the uniprot proteins track, refs #25192
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    51fc256a625a4f6ccc7c569ab33989a51e2dae19 Fri Jan 8 16:04:20 2021 -0800
    switching on codon numbering for uniprot genes on wuhCor1 and off for all other uniprot tracks, email from Angie, no redmine
• src/hg/makeDb/trackDb/virus/wuhCor1/weizmanOrfs.ra
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    dfa33e7edb8273417ed94e429bc259e9514715c5 Thu Jan 7 14:02:15 2021 -0800
    Squashing stale pennantIcons refs #26753
• src/hg/utils/automation/asmHubGatewayPage.pl
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    9bfef693a8110e2a27a49ecd834ff3f875aecb76 Fri Jan 8 14:36:20 2021 -0800
    better decision on when to be refseq asmHub refs #24396
• src/hg/utils/automation/parseLrgXml.pl
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    e101dc0e743a44ea8c8813ffcc29e8cc51697f40 Fri Jan 8 13:05:26 2021 -0800
    LRG track otto updating for hg19 and hg38, refs #17877 #24672
• src/hg/utils/mafToBigMaf/mafToBigMaf.c
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    c26a1d576fadc122a2b907b25d72935f4428ad22 Wed Jan 6 11:17:58 2021 -0800
    look for a dot in organism names if we're not finding the name without the dot
• src/hg/utils/otto/clinvar/clinvar.as
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    33bf30695c6b2c759957430de65f1e276ccee112 Thu Jan 7 10:54:35 2021 -0800
    make clinvar.as the same in the tree as it is in production
• src/hg/utils/otto/lrg/bigPsl+6.as
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    e101dc0e743a44ea8c8813ffcc29e8cc51697f40 Fri Jan 8 13:05:26 2021 -0800
    LRG track otto updating for hg19 and hg38, refs #17877 #24672
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    59a7dc6d8bac59e32e1b1841217febe0a4c7426b Mon Jan 11 09:14:12 2021 -0800
    Fix duplicate table descriptions complaint from lrgBigPsl track, refs cronjob email
• src/hg/utils/otto/lrg/buildLrg.sh
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    e101dc0e743a44ea8c8813ffcc29e8cc51697f40 Fri Jan 8 13:05:26 2021 -0800
    LRG track otto updating for hg19 and hg38, refs #17877 #24672
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    03045b074b65d33e4893d9b4b2b464271f659a69 Fri Jan 8 14:43:10 2021 -0800
    Forgot the cds and fa arguments to pslToBigPsl for lrg otto build, refs #24672
• src/hg/utils/otto/lrg/checkLrg.sh
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    e101dc0e743a44ea8c8813ffcc29e8cc51697f40 Fri Jan 8 13:05:26 2021 -0800
    LRG track otto updating for hg19 and hg38, refs #17877 #24672
• src/hg/utils/otto/lrg/lrgWrapper.sh
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    e101dc0e743a44ea8c8813ffcc29e8cc51697f40 Fri Jan 8 13:05:26 2021 -0800
    LRG track otto updating for hg19 and hg38, refs #17877 #24672
• src/hg/utils/otto/sarscov2phylo/updateIdMapping.sh
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    b9b84244ae9fbfa6d81c92028634be26e8a5898f Tue Jan 5 00:50:55 2021 -0800
    Prevent redundant seqToEpi lines from nextmeta cobbled together from old nextmeta plus manually downloaded sequences.
• src/lib/udc.c
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    fafc064148fba3ad1efdb726b3ac3fdd0784d4e1 Mon Jan 4 18:02:21 2021 -0800
    When a file has a single line of content with no newline, return the content instead of NULL.
• src/product/installer/README.md
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    d8d9e8bc8fa214d169bc3011359fbe9bfd6b7c08 Tue Jan 5 17:06:01 2021 -0800
    Removing the escaped characters to clean up the markdown file (github README) refs #23297
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    66065d1a4070eda46e1f5d388e449a62f9e64c37 Fri Jan 8 14:41:41 2021 -0800
    Making the contact page an absolute link to make it work on the markdown file, refs #23297
• src/product/mirrorDocs/staticPage.lua
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    cf9fb734d2c7025719cf204b87e9301de3044a04 Tue Jan 5 17:07:16 2021 -0800
    Adding the double quote and single quote functions, refs #23297
• src/product/mirrorManual.txt
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    e9c4b9a1ad6de5a908b24f6b04087e8d22bd87b2 Wed Jan 6 12:26:59 2021 -0800
    add instructions about using the FreeType font engine
• src/utils/qa/weeklybld/buildEnv.csh
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    4bc49c2c3d7be3392080b5ed6b815b6362293b31 Mon Jan 11 10:04:22 2021 -0800
    v409 preview2

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