All File Changes

v396_base to v397_preview (2020-03-30 to 2020-04-06) v397

• src/hg/cirm/gateway/htdocs/projects.html
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    03b614da15d6d8f07f0b974735e84d8fc42bf39c Fri Apr 3 14:25:45 2020 -0700
    Update on projects and tools page regarding NS forest and pyle
• src/hg/cirm/gateway/htdocs/tools.html
  • lines changed 7, context: html, text, full: html, text
    03b614da15d6d8f07f0b974735e84d8fc42bf39c Fri Apr 3 14:25:45 2020 -0700
    Update on projects and tools page regarding NS forest and pyle
• src/hg/hgTracks/vcfTrack.c
  • lines changed 301, context: html, text, full: html, text
    0a9372ad1d6c6498fd3818a91edb65d932d890d9 Thu Apr 2 11:37:11 2020 -0700
    VCF: new option to display haplotypes ordered by a trackDb-specified Newick tree file. Tree is drawn in left label area. refs #25278
  • lines changed 14, context: html, text, full: html, text
    04f62f226b0167adf59cc4b55980423164992934 Thu Apr 2 14:37:49 2020 -0700
    Fix bug that David H noticed in 'hapClusterMethod fileOrder' mode: depending on what tracks are viewed, sometimes sample labels were clipped instead of displayed. refs #25197
  • lines changed 15, context: html, text, full: html, text
    5839fc5f68fc919fc61fad936929af799c52f577 Fri Apr 3 12:08:21 2020 -0700
    Add RGB colors to Nextstrain trees as fake branch lengths. Make hapClusterMethod treeFile use branch lengths as RGB colors. refs #25278
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    dea7d848a3eb88f9521322b0d89650be3975d894 Sat Apr 4 13:44:50 2020 -0700
    Get rid of requirement for vcf track to have < 3000 genotypes in order to do haplotype display. Nextstrain is already up to 3365. refs #25188
• src/hg/hgc/hgc.c
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    306ef7620cf65cbd08a582f188fa49776d5ccd9d Mon Mar 30 15:36:49 2020 -0700
    Clarification suggested by Ana. refs #24695
• src/hg/htdocs/covid19.html
  • lines changed 112, context: html, text, full: html, text
    2c324299c222b07b7cde071cfbe960f43a980e09 Tue Mar 31 14:54:56 2020 -0700
    Rough first cut of COVID-19 landing page. refs #25217
  • lines changed 89, context: html, text, full: html, text
    4daf501eaae1e56b62d212476b1a991ef592763a Wed Apr 1 21:30:10 2020 -0700
    Finished first draft for review. refs #25217
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    0d3d7c88e833c16c887f0c876983646f5cc58628 Thu Apr 2 12:01:01 2020 -0700
    Response to QA and mgmt input. refs #25217
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    33b4833d627fce93888f976b19e2541656ce380a Thu Apr 2 12:13:32 2020 -0700
    Additional fine-tuning. refs #25217
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    03d77f5f3d39f406e7b77cabd31a1fa2d955a815 Thu Apr 2 19:19:55 2020 -0700
    made the R capital in BioRxiv and MedRxiv
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    f92631670e212d02082a89b8501fdfaeda9d7a55 Fri Apr 3 04:16:46 2020 -0700
    updating link to cell browser, refs #25217
• src/hg/htdocs/covid19/index.html
  • lines changed 1, context: html, text, full: html, text
    60cfecd7aaebe7f8804648537fd2fc62f2c7beb6 Thu Apr 2 16:51:55 2020 -0700
    made the R capital in BioRxiv and MedRxiv
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 225, context: html, text, full: html, text
    3081e8a9fcda2142e033075b48ddce002d742f02 Fri Apr 3 07:52:18 2020 -0700
    First data release announcement for coronavirus browser refs #25267
• src/hg/htdocs/images/canFam4.jpg
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    03c8e7e0c3f2c7a5a14508230418ef7047b2ca40 Thu Apr 2 09:05:08 2020 -0700
    German shepard stock photo from Cheryl Cox https://unsplash.com/@ccox888 refs #25279
• src/hg/htdocs/images/cellBrowserAce2EilsLung.png
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    84a8211a2ed6ab06aa661951bc847acfd5073a79 Wed Apr 1 21:32:04 2020 -0700
    Add screenshots for coronavirus landing page. refs #25217
• src/hg/htdocs/images/sarsCov2SpikeProteinsSession.png
  • lines changed 0, context: html, text, full: html, text
    84a8211a2ed6ab06aa661951bc847acfd5073a79 Wed Apr 1 21:32:04 2020 -0700
    Add screenshots for coronavirus landing page. refs #25217
• src/hg/htdocs/indexNews.html
  • lines changed 11, context: html, text, full: html, text
    3081e8a9fcda2142e033075b48ddce002d742f02 Fri Apr 3 07:52:18 2020 -0700
    First data release announcement for coronavirus browser refs #25267
• src/hg/htdocs/license/gbLicense2020.pdf
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    d2681b8f4036439c194921023e57a12f1998d0b5 Fri Apr 3 13:33:16 2020 -0700
    adding new license that includes a claim on liftover files
• src/hg/htdocs/license/index.html
  • lines changed 1, context: html, text, full: html, text
    d2681b8f4036439c194921023e57a12f1998d0b5 Fri Apr 3 13:33:16 2020 -0700
    adding new license that includes a claim on liftover files
• src/hg/inc/vcfUi.h
  • lines changed 1, context: html, text, full: html, text
    0a9372ad1d6c6498fd3818a91edb65d932d890d9 Thu Apr 2 11:37:11 2020 -0700
    VCF: new option to display haplotypes ordered by a trackDb-specified Newick tree file. Tree is drawn in left label area. refs #25278
• src/hg/lib/hdb.c
  • lines changed 3, context: html, text, full: html, text
    70108810b61b4bc14e4d0a7327b3079f1773eeda Fri Apr 3 07:00:46 2020 -0700
    don't check for existence of bigDataUrl files when loading trackDb if they're remote
• src/hg/lib/vcfUi.c
  • lines changed 1, context: html, text, full: html, text
    e18fa442e05628a15efcad248c2f1c49b1e6c008 Tue Mar 31 10:03:17 2020 -0700
    Make casing consistent in hapCluster options. Thanks Brian L! refs #25197
  • lines changed 10, context: html, text, full: html, text
    0a9372ad1d6c6498fd3818a91edb65d932d890d9 Thu Apr 2 11:37:11 2020 -0700
    VCF: new option to display haplotypes ordered by a trackDb-specified Newick tree file. Tree is drawn in left label area. refs #25278
• src/hg/makeDb/doc/asmHubs/asmHubs.mk
  • lines changed 8, context: html, text, full: html, text
    68e60a3ccfe0c3aaa48f2fa85f86ca700d681e81 Tue Mar 31 12:08:22 2020 -0700
    correct hub.txt not testHub.txt refs #23891
• src/hg/makeDb/doc/asmHubs/mkAsmStats.pl
  • lines changed 8, context: html, text, full: html, text
    68e60a3ccfe0c3aaa48f2fa85f86ca700d681e81 Tue Mar 31 12:08:22 2020 -0700
    correct hub.txt not testHub.txt refs #23891
• src/hg/makeDb/doc/asmHubs/mkHubIndex.pl
  • lines changed 42, context: html, text, full: html, text
    68e60a3ccfe0c3aaa48f2fa85f86ca700d681e81 Tue Mar 31 12:08:22 2020 -0700
    correct hub.txt not testHub.txt refs #23891
• src/hg/makeDb/doc/asmHubs/sendToHgdownload.sh
  • lines changed 35, context: html, text, full: html, text
    68e60a3ccfe0c3aaa48f2fa85f86ca700d681e81 Tue Mar 31 12:08:22 2020 -0700
    correct hub.txt not testHub.txt refs #23891
• src/hg/makeDb/doc/asmHubs/trackData.pl
  • lines changed 6, context: html, text, full: html, text
    68e60a3ccfe0c3aaa48f2fa85f86ca700d681e81 Tue Mar 31 12:08:22 2020 -0700
    correct hub.txt not testHub.txt refs #23891
• src/hg/makeDb/doc/assemblyEquivalence/README.txt
  • lines changed 138, context: html, text, full: html, text
    73cafbd4cad4da09db8158671513f36b753ae686 Mon Mar 30 10:50:51 2020 -0700
    completed all the vertebrate genbank assembly idKeys, now comparing all with all refs #24547
• src/hg/makeDb/doc/canFam4/initialBuild.txt
  • lines changed 1104, context: html, text, full: html, text
    ce1becca3b06e9fcefabd6e654a24939c95fa0ad Thu Apr 2 09:30:41 2020 -0700
    beginning build of German shepard assembly refs #25279
• src/hg/makeDb/doc/hg19.txt
  • lines changed 2, context: html, text, full: html, text
    03ee259959abfcc6dac85900579502fca9f803e5 Tue Mar 31 16:22:43 2020 -0700
    Fix up mouseovers and filter labels for gnomad structural variants, and add a filter based on variant size, refs #24179
• src/hg/makeDb/doc/wuhCor1/pdb.txt
  • lines changed 11, context: html, text, full: html, text
    9bfea7b5595737328c2df46d9413392b3b44c117 Wed Apr 1 08:22:05 2020 -0700
    adding pdb track to wuhCor1, refs #25227
• src/hg/makeDb/gnomad/gnomadSvToUcsc.awk
  • lines changed 40, context: html, text, full: html, text
    03ee259959abfcc6dac85900579502fca9f803e5 Tue Mar 31 16:22:43 2020 -0700
    Fix up mouseovers and filter labels for gnomad structural variants, and add a filter based on variant size, refs #24179
  • lines changed 28, context: html, text, full: html, text
    9592c56977d703a9f84162e8a4ed35105b93eede Wed Apr 1 10:11:28 2020 -0700
    Get a short list of genes into gnomad structural variants mouseover or a message that there are too many genes if the list is too long, also fix overflowing item boxes on details pages, refs #24179
• src/hg/makeDb/trackDb/baboon/papAnu4/trackDb.ra
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    8c4131a525393ded344af8fc3e2eb2cde04c1b6d Wed Apr 1 12:35:20 2020 -0700
    adding NCBI RefSeq composite refs #20215
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    e4a96d89b3b4a18946c6deca9ee65123fbbb70fb Wed Apr 1 12:49:36 2020 -0700
    correct space before the include refSeqComposite and no more overrides on refGene refs #20215
• src/hg/makeDb/trackDb/bats/rouAeg1/trackDb.ra
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    8c4131a525393ded344af8fc3e2eb2cde04c1b6d Wed Apr 1 12:35:20 2020 -0700
    adding NCBI RefSeq composite refs #20215
• src/hg/makeDb/trackDb/birds/ficAlb1/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    8c4131a525393ded344af8fc3e2eb2cde04c1b6d Wed Apr 1 12:35:20 2020 -0700
    adding NCBI RefSeq composite refs #20215
• src/hg/makeDb/trackDb/chinchilla/chiLan1/trackDb.ra
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    8c4131a525393ded344af8fc3e2eb2cde04c1b6d Wed Apr 1 12:35:20 2020 -0700
    adding NCBI RefSeq composite refs #20215
• src/hg/makeDb/trackDb/criGri/criGriChoV1/trackDb.ra
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    8c4131a525393ded344af8fc3e2eb2cde04c1b6d Wed Apr 1 12:35:20 2020 -0700
    adding NCBI RefSeq composite refs #20215
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    e4a96d89b3b4a18946c6deca9ee65123fbbb70fb Wed Apr 1 12:49:36 2020 -0700
    correct space before the include refSeqComposite and no more overrides on refGene refs #20215
• src/hg/makeDb/trackDb/dog/canFam4/description.html
  • lines changed 64, context: html, text, full: html, text
    99e6696a2ad0cb3e050ec09dc388514e50385394 Tue Mar 31 10:49:45 2020 -0700
    initial files from makeGenomeDb.pl refs #25279
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    ce5faabf12dba91dd80f5946edb494d5dcdd963b Thu Apr 2 09:24:19 2020 -0700
    correct photo of a German shepard refs #25279
• src/hg/makeDb/trackDb/dog/canFam4/gap.html
  • lines changed 30, context: html, text, full: html, text
    99e6696a2ad0cb3e050ec09dc388514e50385394 Tue Mar 31 10:49:45 2020 -0700
    initial files from makeGenomeDb.pl refs #25279
• src/hg/makeDb/trackDb/dog/canFam4/gold.html
  • lines changed 33, context: html, text, full: html, text
    99e6696a2ad0cb3e050ec09dc388514e50385394 Tue Mar 31 10:49:45 2020 -0700
    initial files from makeGenomeDb.pl refs #25279
• src/hg/makeDb/trackDb/dog/canFam4/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    99e6696a2ad0cb3e050ec09dc388514e50385394 Tue Mar 31 10:49:45 2020 -0700
    initial files from makeGenomeDb.pl refs #25279
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    34d85e3444934a5b77b31c6316cb5a996da0ed76 Thu Apr 2 09:45:58 2020 -0700
    adding search rule for gold/assembly track refs #52279
• src/hg/makeDb/trackDb/elephant/loxAfr3/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    8c4131a525393ded344af8fc3e2eb2cde04c1b6d Wed Apr 1 12:35:20 2020 -0700
    adding NCBI RefSeq composite refs #20215
• src/hg/makeDb/trackDb/ferret/musFur1/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    8c4131a525393ded344af8fc3e2eb2cde04c1b6d Wed Apr 1 12:35:20 2020 -0700
    adding NCBI RefSeq composite refs #20215
• src/hg/makeDb/trackDb/frog/nanPar1/trackDb.ra
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    8c4131a525393ded344af8fc3e2eb2cde04c1b6d Wed Apr 1 12:35:20 2020 -0700
    adding NCBI RefSeq composite refs #20215
• src/hg/makeDb/trackDb/human/chainSelf.html
  • lines changed 15, context: html, text, full: html, text
    a35ba8097eefaf86f7864008392237f161abf7a5 Mon Mar 30 16:51:31 2020 -0700
    Updating chainSelf desc page to be more descriptive of what the score means refs #24695
• src/hg/makeDb/trackDb/human/clinvar.html
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    395cb035f4622e5ee0d29c97c9f8b08713b2f3b3 Wed Apr 1 03:41:11 2020 -0700
    adding note about chrMT to clinvar docs, refs #24648
• src/hg/makeDb/trackDb/human/hg19/gnomadPLI.html
  • lines changed 53, context: html, text, full: html, text
    bf965889dc35e4148d19ad4284de6425ba47b3e2 Fri Apr 3 18:11:38 2020 -0700
    change pLoF track names and decription page Ref #20394
• src/hg/makeDb/trackDb/human/hg19/gnomadSv.html
  • lines changed 137, context: html, text, full: html, text
    96ac204df611e95470c96b9d9cdcab7cfbff34f4 Thu Apr 2 16:12:42 2020 -0700
    Adding description page for gnomAD structural variants track, ready for QA refs #24179
• src/hg/makeDb/trackDb/human/hg19/trackDb.gnomad.ra
  • lines changed 29, context: html, text, full: html, text
    1459eeaf122416693bf16adad92b40a8e25957a0 Mon Mar 30 16:19:05 2020 -0700
    Fixing search for gnomad PLI tracks. Adding search and mouse overs for work in progress gnomad structural variants, refs #24179
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    03ee259959abfcc6dac85900579502fca9f803e5 Tue Mar 31 16:22:43 2020 -0700
    Fix up mouseovers and filter labels for gnomad structural variants, and add a filter based on variant size, refs #24179
  • lines changed 8, context: html, text, full: html, text
    bf965889dc35e4148d19ad4284de6425ba47b3e2 Fri Apr 3 18:11:38 2020 -0700
    change pLoF track names and decription page Ref #20394
• src/hg/makeDb/trackDb/human/hg38/chainSelf.html
  • lines changed 103, context: html, text, full: html, text
    a35ba8097eefaf86f7864008392237f161abf7a5 Mon Mar 30 16:51:31 2020 -0700
    Updating chainSelf desc page to be more descriptive of what the score means refs #24695
• src/hg/makeDb/trackDb/human/hg38/encode3.ccre.ra
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    3bb2989fccbd4678d5d5d0b1448ae6fb9d647b74 Thu Apr 2 14:48:21 2020 -0700
    ENCODE cCREs from DAC megahub.
• src/hg/makeDb/trackDb/human/hg38/encode3.ra
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    3bb2989fccbd4678d5d5d0b1448ae6fb9d647b74 Thu Apr 2 14:48:21 2020 -0700
    ENCODE cCREs from DAC megahub.
• src/hg/makeDb/trackDb/human/hg38/encodeCcreCombined.html
  • lines changed 42, context: html, text, full: html, text
    3bb2989fccbd4678d5d5d0b1448ae6fb9d647b74 Thu Apr 2 14:48:21 2020 -0700
    ENCODE cCREs from DAC megahub.
• src/hg/makeDb/trackDb/kangarooRat/dipOrd2/trackDb.ra
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    8c4131a525393ded344af8fc3e2eb2cde04c1b6d Wed Apr 1 12:35:20 2020 -0700
    adding NCBI RefSeq composite refs #20215
• src/hg/makeDb/trackDb/macaca/macNem1/trackDb.ra
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    8c4131a525393ded344af8fc3e2eb2cde04c1b6d Wed Apr 1 12:35:20 2020 -0700
    adding NCBI RefSeq composite refs #20215
• src/hg/makeDb/trackDb/makefile
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    99e6696a2ad0cb3e050ec09dc388514e50385394 Tue Mar 31 10:49:45 2020 -0700
    initial files from makeGenomeDb.pl refs #25279
• src/hg/makeDb/trackDb/mammal/fukDam1/trackDb.ra
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    8c4131a525393ded344af8fc3e2eb2cde04c1b6d Wed Apr 1 12:35:20 2020 -0700
    adding NCBI RefSeq composite refs #20215
• src/hg/makeDb/trackDb/micOch/micOch1/trackDb.ra
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    8c4131a525393ded344af8fc3e2eb2cde04c1b6d Wed Apr 1 12:35:20 2020 -0700
    adding NCBI RefSeq composite refs #20215
• src/hg/makeDb/trackDb/mouseLemur/micMur3/trackDb.ra
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    8c4131a525393ded344af8fc3e2eb2cde04c1b6d Wed Apr 1 12:35:20 2020 -0700
    adding NCBI RefSeq composite refs #20215
• src/hg/makeDb/trackDb/oldWorldMonkeys/colAng1/trackDb.ra
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    8c4131a525393ded344af8fc3e2eb2cde04c1b6d Wed Apr 1 12:35:20 2020 -0700
    adding NCBI RefSeq composite refs #20215
• src/hg/makeDb/trackDb/otters/enhLutKen1/trackDb.ra
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    8c4131a525393ded344af8fc3e2eb2cde04c1b6d Wed Apr 1 12:35:20 2020 -0700
    adding NCBI RefSeq composite refs #20215
• src/hg/makeDb/trackDb/pika/ochPri3/trackDb.ra
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    8c4131a525393ded344af8fc3e2eb2cde04c1b6d Wed Apr 1 12:35:20 2020 -0700
    adding NCBI RefSeq composite refs #20215
• src/hg/makeDb/trackDb/poeRet/poeRet1/trackDb.ra
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    8c4131a525393ded344af8fc3e2eb2cde04c1b6d Wed Apr 1 12:35:20 2020 -0700
    adding NCBI RefSeq composite refs #20215
• src/hg/makeDb/trackDb/primate/aotNan1/trackDb.ra
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    8c4131a525393ded344af8fc3e2eb2cde04c1b6d Wed Apr 1 12:35:20 2020 -0700
    adding NCBI RefSeq composite refs #20215
• src/hg/makeDb/trackDb/primate/cebCap1/trackDb.ra
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    8c4131a525393ded344af8fc3e2eb2cde04c1b6d Wed Apr 1 12:35:20 2020 -0700
    adding NCBI RefSeq composite refs #20215
• src/hg/makeDb/trackDb/primate/cerAty1/trackDb.ra
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    8c4131a525393ded344af8fc3e2eb2cde04c1b6d Wed Apr 1 12:35:20 2020 -0700
    adding NCBI RefSeq composite refs #20215
• src/hg/makeDb/trackDb/primate/manLeu1/trackDb.ra
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    8c4131a525393ded344af8fc3e2eb2cde04c1b6d Wed Apr 1 12:35:20 2020 -0700
    adding NCBI RefSeq composite refs #20215
• src/hg/makeDb/trackDb/primate/proCoq1/trackDb.ra
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    8c4131a525393ded344af8fc3e2eb2cde04c1b6d Wed Apr 1 12:35:20 2020 -0700
    adding NCBI RefSeq composite refs #20215
• src/hg/makeDb/trackDb/rabbit/oryCun2/trackDb.ra
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    8c4131a525393ded344af8fc3e2eb2cde04c1b6d Wed Apr 1 12:35:20 2020 -0700
    adding NCBI RefSeq composite refs #20215
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    e4a96d89b3b4a18946c6deca9ee65123fbbb70fb Wed Apr 1 12:49:36 2020 -0700
    correct space before the include refSeqComposite and no more overrides on refGene refs #20215
• src/hg/makeDb/trackDb/rhinopithecus/rhiBie1/trackDb.ra
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    8c4131a525393ded344af8fc3e2eb2cde04c1b6d Wed Apr 1 12:35:20 2020 -0700
    adding NCBI RefSeq composite refs #20215
• src/hg/makeDb/trackDb/saiBol/saiBol1/trackDb.ra
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    8c4131a525393ded344af8fc3e2eb2cde04c1b6d Wed Apr 1 12:35:20 2020 -0700
    adding NCBI RefSeq composite refs #20215
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    e4a96d89b3b4a18946c6deca9ee65123fbbb70fb Wed Apr 1 12:49:36 2020 -0700
    correct space before the include refSeqComposite and no more overrides on refGene refs #20215
• src/hg/makeDb/trackDb/treeShrew/tupChi1/trackDb.ra
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    8c4131a525393ded344af8fc3e2eb2cde04c1b6d Wed Apr 1 12:35:20 2020 -0700
    adding NCBI RefSeq composite refs #20215
• src/hg/makeDb/trackDb/turtle/chrPic2/trackDb.ra
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    8c4131a525393ded344af8fc3e2eb2cde04c1b6d Wed Apr 1 12:35:20 2020 -0700
    adding NCBI RefSeq composite refs #20215
• src/hg/makeDb/trackDb/virus/wuhCor1/cons44way.html
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    021bf11dc6b46d9943313e1ae1badae36cc7d0c2 Mon Mar 30 12:53:23 2020 -0700
    Adding a note about the donors to the wuhCor1 multiple alignment, refs #25187
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    a1242d76743a6a904f9d58436cb985874cb1db85 Mon Mar 30 12:58:44 2020 -0700
    Adding the section 'Funding' for the funding section, refs #25187
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    a378385a83b733b67c11af082939c3cc6b738569 Mon Mar 30 13:03:41 2020 -0700
    Moving the Funding section to the end of the track description page, refs #25187
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    647e0d682cb7c1b07a6b7f553aabfc97584cb2d3 Tue Mar 31 15:28:44 2020 -0700
    Fixing some typos. Removing the ASM# id. refs #25187
• src/hg/makeDb/trackDb/virus/wuhCor1/description.html
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    b8994b5516cc6ca3f0a8b17423d881b793e7ea0e Mon Mar 30 13:23:35 2020 -0700
    correct funding statement refs #25185
• src/hg/makeDb/trackDb/virus/wuhCor1/epiValid.html
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    9639bed22747497293f93ae8b89f5c59bb31287f Thu Apr 2 10:21:05 2020 -0700
    adding docs page for the epiValid and the rosetta tracks.
• src/hg/makeDb/trackDb/virus/wuhCor1/epitopes.html
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    280bcbd7afb715d5822adbaedaaf760eeb67bf2c Mon Mar 30 13:14:55 2020 -0700
    Adding new funding section to epitopes track refs #25190
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    b66264a53d740c71d8d7641698cacf4b58278852 Thu Apr 2 08:22:12 2020 -0700
    adding ref to epitopes track
• src/hg/makeDb/trackDb/virus/wuhCor1/ncbiGeneBGP.html
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    aa2853824416870028531a30e480798ed5d99079 Mon Mar 30 14:30:33 2020 -0700
    Adding Funding section to these description pages refs #25188, 25189, 25114
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    64966988d671adcd501106884d915da5f522ccaf Tue Mar 31 09:50:40 2020 -0700
    Clarity improvements for CR refs #25258
• src/hg/makeDb/trackDb/virus/wuhCor1/nextstrainClade.html
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    aa2853824416870028531a30e480798ed5d99079 Mon Mar 30 14:30:33 2020 -0700
    Adding Funding section to these description pages refs #25188, 25189, 25114
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    b5072af78461ac930024c95a8006a3e45c78afc0 Mon Mar 30 10:47:04 2020 -0700
    Updated with situation report links from Nextstrain's March 27 report. refs #25188
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    64966988d671adcd501106884d915da5f522ccaf Tue Mar 31 09:50:40 2020 -0700
    Clarity improvements for CR refs #25258
• src/hg/makeDb/trackDb/virus/wuhCor1/nextstrainGene.html
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    aa2853824416870028531a30e480798ed5d99079 Mon Mar 30 14:30:33 2020 -0700
    Adding Funding section to these description pages refs #25188, 25189, 25114
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    64966988d671adcd501106884d915da5f522ccaf Tue Mar 31 09:50:40 2020 -0700
    Clarity improvements for CR refs #25258
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    e87d648b01ff48ce4fc33e1dd8ee891eb1d04bb6 Tue Mar 31 10:02:26 2020 -0700
    Minor change #25258
• src/hg/makeDb/trackDb/virus/wuhCor1/nextstrainSamples.html
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    aa2853824416870028531a30e480798ed5d99079 Mon Mar 30 14:30:33 2020 -0700
    Adding Funding section to these description pages refs #25188, 25189, 25114
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    64966988d671adcd501106884d915da5f522ccaf Tue Mar 31 09:50:40 2020 -0700
    Clarity improvements for CR refs #25258
• src/hg/makeDb/trackDb/virus/wuhCor1/pdb.html
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    9bfea7b5595737328c2df46d9413392b3b44c117 Wed Apr 1 08:22:05 2020 -0700
    adding pdb track to wuhCor1, refs #25227
• src/hg/makeDb/trackDb/virus/wuhCor1/primers.html
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    aa2853824416870028531a30e480798ed5d99079 Mon Mar 30 14:30:33 2020 -0700
    Adding Funding section to these description pages refs #25188, 25189, 25114
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    64966988d671adcd501106884d915da5f522ccaf Tue Mar 31 09:50:40 2020 -0700
    Clarity improvements for CR refs #25258
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    5ffc9f237c43199320994edd93d308d7e3179793 Tue Mar 31 10:11:58 2020 -0700
    Minor code review change #25258
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    5a52ab8504a4802344abb4de5f221bafcc81398e Mon Apr 6 05:55:55 2020 -0700
    updating wuhCor primers docs link to primer/kit list
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    cc453c6e9c9e8c12e317568b221040dad629fa84 Mon Apr 6 09:23:50 2020 -0700
    updating primer docs page
• src/hg/makeDb/trackDb/virus/wuhCor1/public.html
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    3af5372207d7d1782850be8dc5e0836db8cc3fde Tue Mar 31 07:18:33 2020 -0700
    adding user contributed annotations track so David can annotate this genome, no redmine yet
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    e55c6669d52e23ad1b97652f085b204e788cda20 Tue Mar 31 07:24:15 2020 -0700
    oops, wrong filename in last commit
• src/hg/makeDb/trackDb/virus/wuhCor1/publicAnnots.html
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    e55c6669d52e23ad1b97652f085b204e788cda20 Tue Mar 31 07:24:15 2020 -0700
    oops, wrong filename in last commit
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    179756430b5df7d2f6072e271a7238d5eb29b0a6 Tue Mar 31 07:25:56 2020 -0700
    typo in publicAnnots docs page
• src/hg/makeDb/trackDb/virus/wuhCor1/rosettaMhc.html
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    9639bed22747497293f93ae8b89f5c59bb31287f Thu Apr 2 10:21:05 2020 -0700
    adding docs page for the epiValid and the rosetta tracks.
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    58a33c533d1e4951557824979481c433212fd50e Fri Apr 3 07:00:21 2020 -0700
    fixing msdoc lineendings of rosetta track docs
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.nextstrain.ra
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    ac7cce26f5877b75218e08eec52eca476ddc33cc Mon Mar 30 14:52:32 2020 -0700
    Add per-clade subtracks to Nextstrain Vars for David. Also, Nextstrain changed ncov.json to use country instead of division for location. refs #25188
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    4214801d5a5c31e35507528349985b90f86fcc6b Wed Apr 1 10:19:02 2020 -0700
    Tweak heights of nextstrain VCF tracks: 1. A2 and B are much larger since they include subclades; 2. Relative heights changed with latest data. refs #25188
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    578bb3e094f40c5273d594c38879c4e22b390e1a Thu Apr 2 09:46:23 2020 -0700
    Doh -- fixing incorrect bigDataUrl for nextstrainSamplesA3. refs #25188
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    0a9372ad1d6c6498fd3818a91edb65d932d890d9 Thu Apr 2 11:37:11 2020 -0700
    VCF: new option to display haplotypes ordered by a trackDb-specified Newick tree file. Tree is drawn in left label area. refs #25278
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    2d373a6286de2fe18ccfb52308728253d97c89a7 Thu Apr 2 14:44:32 2020 -0700
    Releasing new subtracks of vars #25188
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    49fb2e815f6fec695e51400b733e2f2dbe4738a5 Thu Apr 2 15:55:36 2020 -0700
    Releasing new subtracks of vars #25188
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra
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    63f210906f26e01a9891843225b30012f5f88863 Mon Mar 30 10:32:41 2020 -0700
    Consolidating the uniprot description pages to a single one, removing the replicates refs #25192
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    005d09c090343b1e95ad6347681a75ab45c6cb2c Mon Mar 30 11:13:59 2020 -0700
    adding rosetta Mhc and validated epitopes tracks, no redmine yet
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    3af5372207d7d1782850be8dc5e0836db8cc3fde Tue Mar 31 07:18:33 2020 -0700
    adding user contributed annotations track so David can annotate this genome, no redmine yet
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    171b51f59e5f78f41de007f0bfc898b25d4de6b1 Tue Mar 31 08:58:16 2020 -0700
    updating gordon et al track
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    a062ced50a9d58439d17c11b3b90c983d13a27c1 Tue Mar 31 09:46:35 2020 -0700
    clarifying epiValid track name, no redmine
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    9bfea7b5595737328c2df46d9413392b3b44c117 Wed Apr 1 08:22:05 2020 -0700
    adding pdb track to wuhCor1, refs #25227
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.uniprot.ra
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    63f210906f26e01a9891843225b30012f5f88863 Mon Mar 30 10:32:41 2020 -0700
    Consolidating the uniprot description pages to a single one, removing the replicates refs #25192
• src/hg/makeDb/trackDb/virus/wuhCor1/unipCov2AliSwissprot.html
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    ddaa11cc3a9ae5c08162de585eb8bf6046bc1831 Mon Mar 30 13:17:39 2020 -0700
    Adding funding section to uniprot tracks refs #25192
• src/hg/makeDb/trackDb/virus/wuhCor1/unipCov2DisulfBond.html
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    63f210906f26e01a9891843225b30012f5f88863 Mon Mar 30 10:32:41 2020 -0700
    Consolidating the uniprot description pages to a single one, removing the replicates refs #25192
• src/hg/makeDb/trackDb/virus/wuhCor1/unipCov2Domain.html
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    63f210906f26e01a9891843225b30012f5f88863 Mon Mar 30 10:32:41 2020 -0700
    Consolidating the uniprot description pages to a single one, removing the replicates refs #25192
• src/hg/makeDb/trackDb/virus/wuhCor1/unipCov2Interest.html
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    ddaa11cc3a9ae5c08162de585eb8bf6046bc1831 Mon Mar 30 13:17:39 2020 -0700
    Adding funding section to uniprot tracks refs #25192
• src/hg/makeDb/trackDb/virus/wuhCor1/unipCov2LocSignal.html
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    63f210906f26e01a9891843225b30012f5f88863 Mon Mar 30 10:32:41 2020 -0700
    Consolidating the uniprot description pages to a single one, removing the replicates refs #25192
• src/hg/makeDb/trackDb/virus/wuhCor1/unipCov2LocTransMemb.html
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    63f210906f26e01a9891843225b30012f5f88863 Mon Mar 30 10:32:41 2020 -0700
    Consolidating the uniprot description pages to a single one, removing the replicates refs #25192
• src/hg/makeDb/trackDb/virus/wuhCor1/unipCov2Modif.html
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    63f210906f26e01a9891843225b30012f5f88863 Mon Mar 30 10:32:41 2020 -0700
    Consolidating the uniprot description pages to a single one, removing the replicates refs #25192
• src/hg/makeDb/trackDb/virus/wuhCor1/unipCov2Repeat.html
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    63f210906f26e01a9891843225b30012f5f88863 Mon Mar 30 10:32:41 2020 -0700
    Consolidating the uniprot description pages to a single one, removing the replicates refs #25192
• src/hg/makeDb/trackDb/virus/wuhCor1/unipCov2Struct.html
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    63f210906f26e01a9891843225b30012f5f88863 Mon Mar 30 10:32:41 2020 -0700
    Consolidating the uniprot description pages to a single one, removing the replicates refs #25192
• src/hg/makeDb/trackDb/virus/wuhCor1/uniprotCov2.html
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    ddaa11cc3a9ae5c08162de585eb8bf6046bc1831 Mon Mar 30 13:17:39 2020 -0700
    Adding funding section to uniprot tracks refs #25192
• src/hg/makeDb/trackDb/whale/orcOrc1/trackDb.ra
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    8c4131a525393ded344af8fc3e2eb2cde04c1b6d Wed Apr 1 12:35:20 2020 -0700
    adding NCBI RefSeq composite refs #20215
• src/hg/utils/automation/makeDownloads.pl
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    531a1da73a9c257444ee0ce9884d271f5f7bcd5d Thu Apr 2 14:21:28 2020 -0700
    now correctly making bigZips/genes downloads refs #24524;
• src/hg/utils/otto/lovd/checkAndLoad.sh
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    0ba0086f3d6f31f631f8496aca509c32dc19951f Mon Mar 30 13:29:15 2020 -0700
    Fix early exit from missing braces in lovd otto script, no refs
• src/hg/utils/otto/nextstrainNcov/doUpdate.sh
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    ac7cce26f5877b75218e08eec52eca476ddc33cc Mon Mar 30 14:52:32 2020 -0700
    Add per-clade subtracks to Nextstrain Vars for David. Also, Nextstrain changed ncov.json to use country instead of division for location. refs #25188
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    475424b5d722b4ff761681f1d3bd91ad666fb2d6 Wed Apr 1 10:17:03 2020 -0700
    For nested clades, add all clade samples to per-clade VCF. Also generate Newick (.nh) tree file and tweak sample name separator, in preparation for drawing the nextstrain tree in the VCF left label area. refs #25188
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    0ee9c5c6fd7e6debb4e21c88139cb2ca19056565 Thu Apr 2 09:38:30 2020 -0700
    Install per-clade .nh tree files as well. refs #25188
• src/hg/utils/otto/nextstrainNcov/makefile
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    475424b5d722b4ff761681f1d3bd91ad666fb2d6 Wed Apr 1 10:17:03 2020 -0700
    For nested clades, add all clade samples to per-clade VCF. Also generate Newick (.nh) tree file and tweak sample name separator, in preparation for drawing the nextstrain tree in the VCF left label area. refs #25188
• src/hg/utils/otto/nextstrainNcov/nextstrain.py
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    ac7cce26f5877b75218e08eec52eca476ddc33cc Mon Mar 30 14:52:32 2020 -0700
    Add per-clade subtracks to Nextstrain Vars for David. Also, Nextstrain changed ncov.json to use country instead of division for location. refs #25188
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    475424b5d722b4ff761681f1d3bd91ad666fb2d6 Wed Apr 1 10:17:03 2020 -0700
    For nested clades, add all clade samples to per-clade VCF. Also generate Newick (.nh) tree file and tweak sample name separator, in preparation for drawing the nextstrain tree in the VCF left label area. refs #25188
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    74e378797b2f1b99b00d73f49c260bf5384cf670 Thu Apr 2 09:40:56 2020 -0700
    David noticed that nextstrainClade samples & counts weren't keeping up with change to VCF subtracks, so that nested clades include all descendants. Fixed. refs #25188
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    5839fc5f68fc919fc61fad936929af799c52f577 Fri Apr 3 12:08:21 2020 -0700
    Add RGB colors to Nextstrain trees as fake branch lengths. Make hapClusterMethod treeFile use branch lengths as RGB colors. refs #25278
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    15e878a51d41f46c563209c95512fc23919ea5f3 Fri Apr 3 14:34:27 2020 -0700
    Little leap year bug (doesn't change any dates in output, but could by the end of 2020...). refs #25188
• src/hg/utils/otto/nextstrainNcov/nextstrainClade.as
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    ac7cce26f5877b75218e08eec52eca476ddc33cc Mon Mar 30 14:52:32 2020 -0700
    Add per-clade subtracks to Nextstrain Vars for David. Also, Nextstrain changed ncov.json to use country instead of division for location. refs #25188
• src/product/installer/browserSetup.sh
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    b505b8480a63f0726316c6ef29436af0f1d55dcc Tue Mar 31 04:23:10 2020 -0700
    trying to fix speed issue with GBIC, refs #25232
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    d98fc157940421537cb42251aee01a245c88c943 Wed Apr 1 08:45:49 2020 -0700
    adding encRegTfbsClusteredSources to GBIC download script, refs #25232
• src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed
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    5fda6e8bf3df270b17862b82d875f1fd2cb3e7b7 Fri Apr 3 11:41:42 2020 -0700
    Fixing ubuntu specific bug in expMatrixToBarchartBed, refs #25284
• src/utils/expMatrixToBarchartBed/makefile
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    5fda6e8bf3df270b17862b82d875f1fd2cb3e7b7 Fri Apr 3 11:41:42 2020 -0700
    Fixing ubuntu specific bug in expMatrixToBarchartBed, refs #25284
• src/utils/expMatrixToBarchartBed/tests/allOptions.output
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    5df5d33cf20e428b03a2808ec9b6ac564613a451 Fri Apr 3 10:48:40 2020 -0700
    Fixing expMatrixToBarchartBed tests
• src/utils/expMatrixToBarchartBed/tests/allOptions2.output
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    5df5d33cf20e428b03a2808ec9b6ac564613a451 Fri Apr 3 10:48:40 2020 -0700
    Fixing expMatrixToBarchartBed tests
• src/utils/expMatrixToBarchartBed/tests/extraFields.output
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    5df5d33cf20e428b03a2808ec9b6ac564613a451 Fri Apr 3 10:48:40 2020 -0700
    Fixing expMatrixToBarchartBed tests
• src/utils/expMatrixToBarchartBed/tests/test.output
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    5df5d33cf20e428b03a2808ec9b6ac564613a451 Fri Apr 3 10:48:40 2020 -0700
    Fixing expMatrixToBarchartBed tests
• src/utils/expMatrixToBarchartBed/tests/test.output2
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    5df5d33cf20e428b03a2808ec9b6ac564613a451 Fri Apr 3 10:48:40 2020 -0700
    Fixing expMatrixToBarchartBed tests
• src/utils/qa/weeklybld/buildEnv.csh
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    fce798def3a2c79c82851139bbed12afd63798f0 Mon Apr 6 10:01:49 2020 -0700
    v397 preview1

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