All File Changes

v408_preview2 to v408_base (2020-11-30 to 2020-12-07) v408

• confs/hgwdev.hg.conf
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    bd2a8017d2c58ef19d75f4bdbdeebbeb89df49e2 Sun Dec 6 01:11:31 2020 -0800
    Installing updated hg.conf files from UCSC servers
• src/hg/hgPhyloPlace/hgPhyloPlace.c
  • lines changed 21, context: html, text, full: html, text
    fe68a3b72e3c63ac173d41a68122cb99a2a4f578 Mon Nov 30 16:41:55 2020 -0800
    David requests: point out that Nextstrain has drag-and-drop local private metadata display & link back to covid19.html landing page.
  • lines changed 4, context: html, text, full: html, text
    ce76a7bd0cd856b6cc1aa35360849af7fe224c45 Tue Dec 1 10:14:32 2020 -0800
    Another link & wording tweak suggested by David. Also update Nextstrain drag-and-drop link to new location.
• src/hg/hgPhyloPlace/phyloPlace.c
  • lines changed 4, context: html, text, full: html, text
    ce76a7bd0cd856b6cc1aa35360849af7fe224c45 Tue Dec 1 10:14:32 2020 -0800
    Another link & wording tweak suggested by David. Also update Nextstrain drag-and-drop link to new location.
  • lines changed 157, context: html, text, full: html, text
    7c0d73b5b9eb8303ee04ba236d31a6703552581c Wed Dec 2 16:32:15 2020 -0800
    hgPhyloPlace metadata: add Nextstrain_clade and genbank_accession columns, refactor in prep for public data. * Move the metadatafile-reading code into phyloPlace.c so metadata file can be used for looking up lineage (no need for separate idToLineage file). * Support looking up metadata by GenBank ID in addition to EPI_ISL ID, in preparation for using protobuf and metadata from public sequences instead of GISAID.
• src/hg/hgPhyloPlace/phyloPlace.h
  • lines changed 2, context: html, text, full: html, text
    ce76a7bd0cd856b6cc1aa35360849af7fe224c45 Tue Dec 1 10:14:32 2020 -0800
    Another link & wording tweak suggested by David. Also update Nextstrain drag-and-drop link to new location.
  • lines changed 27, context: html, text, full: html, text
    7c0d73b5b9eb8303ee04ba236d31a6703552581c Wed Dec 2 16:32:15 2020 -0800
    hgPhyloPlace metadata: add Nextstrain_clade and genbank_accession columns, refactor in prep for public data. * Move the metadatafile-reading code into phyloPlace.c so metadata file can be used for looking up lineage (no need for separate idToLineage file). * Support looking up metadata by GenBank ID in addition to EPI_ISL ID, in preparation for using protobuf and metadata from public sequences instead of GISAID.
• src/hg/hgPhyloPlace/treeToAuspiceJson.c
  • lines changed 2, context: html, text, full: html, text
    ce76a7bd0cd856b6cc1aa35360849af7fe224c45 Tue Dec 1 10:14:32 2020 -0800
    Another link & wording tweak suggested by David. Also update Nextstrain drag-and-drop link to new location.
  • lines changed 136, context: html, text, full: html, text
    7c0d73b5b9eb8303ee04ba236d31a6703552581c Wed Dec 2 16:32:15 2020 -0800
    hgPhyloPlace metadata: add Nextstrain_clade and genbank_accession columns, refactor in prep for public data. * Move the metadatafile-reading code into phyloPlace.c so metadata file can be used for looking up lineage (no need for separate idToLineage file). * Support looking up metadata by GenBank ID in addition to EPI_ISL ID, in preparation for using protobuf and metadata from public sequences instead of GISAID.
• src/hg/hgTracks/wigTrack.c
  • lines changed 2, context: html, text, full: html, text
    c1a9283f4164879abb6d6eb36a7ae39537706c73 Fri Dec 4 15:19:37 2020 -0800
    restore two lines which were thought to be dead code. Resurrected from the dead. refs #26637
• src/hg/hgc/hgc.c
  • lines changed 12, context: html, text, full: html, text
    9e45ac752c5cf71c74e6e874fee99e21b272f768 Wed Dec 2 09:41:24 2020 -0800
    Fixing spurious cartDump empty hgsid messages generated by expanding/collapsing tables on hgc, refs #26619
• src/hg/htdocs/FAQ/FAQgenes.html
  • lines changed 4, context: html, text, full: html, text
    4fabe6e7b2e485192b45e9ea0efbb86e7f96e872 Thu Dec 3 00:40:11 2020 -0800
    fixing the FAQ section about single transcript display, now pointing to the next section, refs #26617
• src/hg/htdocs/covid19.html
  • lines changed 2, context: html, text, full: html, text
    2c76ae5d23c2333c06b7854909d11d00a27f06ca Wed Dec 2 17:17:38 2020 -0800
    added mention of the initial browser release on 2/7/2020
  • lines changed 2, context: html, text, full: html, text
    fa9d92f5c135862902a73d9f8616b699df121672 Thu Dec 3 08:07:12 2020 -0800
    broke line apart
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 2, context: html, text, full: html, text
    61ecef777c66121b1e0967660d9c0121a455b794 Thu Dec 3 17:50:32 2020 -0800
    changed a link found while working w gerardo
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 258, context: html, text, full: html, text
    9fa743ca51710376f192e7689e768a77f94d9dda Mon Nov 30 14:26:57 2020 -0800
    News announcement for new uniprot tracks refs #25784
  • lines changed 2, context: html, text, full: html, text
    838b934e56937186c1016dd7e493b338c00f54e3 Wed Dec 2 09:51:22 2020 -0800
    Adding a line to news announcement about uniprot being on otto refs #25784
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    9fa743ca51710376f192e7689e768a77f94d9dda Mon Nov 30 14:26:57 2020 -0800
    News announcement for new uniprot tracks refs #25784
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    bd784c0cd021f8e050ff1f78e9bae128a71682f6 Mon Dec 7 09:56:52 2020 -0800
    New version number v408
• src/hg/makeDb/doc/asmHubs/asmHubs.mk
  • lines changed 3, context: html, text, full: html, text
    86b6f856f6131c16ac920d1604a1c1fe3ef9845f Fri Dec 4 16:40:35 2020 -0800
    adding legacy hub and correct links in trackData refs #23891
• src/hg/makeDb/doc/asmHubs/commonHtml.pm
  • lines changed 4, context: html, text, full: html, text
    86b6f856f6131c16ac920d1604a1c1fe3ef9845f Fri Dec 4 16:40:35 2020 -0800
    adding legacy hub and correct links in trackData refs #23891
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 449, context: html, text, full: html, text
    04e6795d4c5c364da07a3d2c1e73585310e5ad41 Mon Nov 30 16:22:52 2020 -0800
    keeping track of the assembly hub production, this is a list of hubs completed refs #23891
  • lines changed 44, context: html, text, full: html, text
    16b6442ca6e05286dae290d65ca4508734143a33 Tue Dec 1 12:35:04 2020 -0800
    catching up with updated build list refs #23891
  • lines changed 17, context: html, text, full: html, text
    a7c4f2e7ca8a5d7f1bc28c43f6e243206b58ac51 Sun Dec 6 12:01:29 2020 -0800
    catching up more vertebrates refs #23891
• src/hg/makeDb/doc/asmHubs/mkSymLinks.pl
  • lines changed 1, context: html, text, full: html, text
    7b56acab5e13b635fa964e8ef6707cccaf0e640c Fri Dec 4 16:34:28 2020 -0800
    better information on what is missing refs #23891
• src/hg/makeDb/doc/asmHubs/runBuild
  • lines changed 153, context: html, text, full: html, text
    76cb5f9fd7108a71a14b834d8e5a9def0fdd2150 Sat Dec 5 22:53:37 2020 -0800
    capture current build script refs #23891
• src/hg/makeDb/doc/bacteriaAsmHub/bacteria.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    00dd865686fa361f20b8750606d3607a977ca3ef Fri Dec 4 16:33:29 2020 -0800
    catching up with new assembly hubs refs #23891
• src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv
  • lines changed 11, context: html, text, full: html, text
    00dd865686fa361f20b8750606d3607a977ca3ef Fri Dec 4 16:33:29 2020 -0800
    catching up with new assembly hubs refs #23891
• src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv
  • lines changed 6, context: html, text, full: html, text
    00dd865686fa361f20b8750606d3607a977ca3ef Fri Dec 4 16:33:29 2020 -0800
    catching up with new assembly hubs refs #23891
• src/hg/makeDb/doc/hg19.txt
  • lines changed 49, context: html, text, full: html, text
    b5ea08a66e208b8bc4852fb84bd9929fcdaae241 Wed Dec 2 10:59:31 2020 -0800
    Add makedoc for hg19 gnomAD v2.1.1 update, refs #25010
• src/hg/makeDb/doc/hg38/gencode.txt
  • lines changed 30, context: html, text, full: html, text
    ca4a86fe7fc738163a6d9cb209f0e9f80cf6bf14 Mon Nov 30 16:35:39 2020 -0800
    import of GENCODE V36
• src/hg/makeDb/doc/legacyAsmHub/hub.txt
  • lines changed 6, context: html, text, full: html, text
    47f51f1afeb71f16b2a29cabfc5e81b4615d2966 Mon Nov 30 13:03:36 2020 -0800
    beginning to move out of date hubs to this legacy group refs #23891
• src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv
  • lines changed 7, context: html, text, full: html, text
    47f51f1afeb71f16b2a29cabfc5e81b4615d2966 Mon Nov 30 13:03:36 2020 -0800
    beginning to move out of date hubs to this legacy group refs #23891
  • lines changed 4, context: html, text, full: html, text
    00dd865686fa361f20b8750606d3607a977ca3ef Fri Dec 4 16:33:29 2020 -0800
    catching up with new assembly hubs refs #23891
• src/hg/makeDb/doc/legacyAsmHub/makefile
  • lines changed 26, context: html, text, full: html, text
    47f51f1afeb71f16b2a29cabfc5e81b4615d2966 Mon Nov 30 13:03:36 2020 -0800
    beginning to move out of date hubs to this legacy group refs #23891
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 11, context: html, text, full: html, text
    00dd865686fa361f20b8750606d3607a977ca3ef Fri Dec 4 16:33:29 2020 -0800
    catching up with new assembly hubs refs #23891
• src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv
  • lines changed 4, context: html, text, full: html, text
    00dd865686fa361f20b8750606d3607a977ca3ef Fri Dec 4 16:33:29 2020 -0800
    catching up with new assembly hubs refs #23891
• src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    00dd865686fa361f20b8750606d3607a977ca3ef Fri Dec 4 16:33:29 2020 -0800
    catching up with new assembly hubs refs #23891
• src/hg/makeDb/doc/vgpAsmHub/vgp.legacy.orderList.tsv
  • lines changed 4, context: html, text, full: html, text
    f93e98fc9967bd790a6155e82cc7d2409139b2f9 Mon Nov 30 17:01:26 2020 -0800
    catching up with new assemblies refs #23734
  • lines changed 1, context: html, text, full: html, text
    00dd865686fa361f20b8750606d3607a977ca3ef Fri Dec 4 16:33:29 2020 -0800
    catching up with new assembly hubs refs #23891
• src/hg/makeDb/doc/vgpAsmHub/vgp.primary.orderList.tsv
  • lines changed 16, context: html, text, full: html, text
    f93e98fc9967bd790a6155e82cc7d2409139b2f9 Mon Nov 30 17:01:26 2020 -0800
    catching up with new assemblies refs #23734
  • lines changed 1, context: html, text, full: html, text
    00dd865686fa361f20b8750606d3607a977ca3ef Fri Dec 4 16:33:29 2020 -0800
    catching up with new assembly hubs refs #23891
• src/hg/makeDb/doc/vgpAsmHub/vgp.taxId,asmId.class.txt
  • lines changed 166, context: html, text, full: html, text
    bc8e1eda6f35a3b241241b30ca5b5028f802e86f Mon Nov 30 17:04:05 2020 -0800
    incorrect file name refs #23734
• src/hg/makeDb/doc/vgpAsmHub/vgp.taxId.asmId.class.txt
  • lines changed 8, context: html, text, full: html, text
    f93e98fc9967bd790a6155e82cc7d2409139b2f9 Mon Nov 30 17:01:26 2020 -0800
    catching up with new assemblies refs #23734
  • lines changed 2, context: html, text, full: html, text
    eb6ffba6a690073514ca8977c6e0410f8657e20d Fri Dec 4 16:49:49 2020 -0800
    catching up with new assembly hubs refs #23891
• src/hg/makeDb/doc/vgpAsmHub/vgp.trio.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    00dd865686fa361f20b8750606d3607a977ca3ef Fri Dec 4 16:33:29 2020 -0800
    catching up with new assembly hubs refs #23891
• src/hg/makeDb/outside/gencode/bin/gencodeGenerateTrackDbs
  • lines changed 24, context: html, text, full: html, text
    ca4a86fe7fc738163a6d9cb209f0e9f80cf6bf14 Mon Nov 30 16:35:39 2020 -0800
    import of GENCODE V36
• src/hg/makeDb/outside/gencode/gencodeHgGene2Load.mk
  • lines changed 420, context: html, text, full: html, text
    ca4a86fe7fc738163a6d9cb209f0e9f80cf6bf14 Mon Nov 30 16:35:39 2020 -0800
    import of GENCODE V36
• src/hg/makeDb/outside/gencode/gencodeHgGeneLoad.mk
  • lines changed 421, context: html, text, full: html, text
    ca4a86fe7fc738163a6d9cb209f0e9f80cf6bf14 Mon Nov 30 16:35:39 2020 -0800
    import of GENCODE V36
• src/hg/makeDb/schema/all.joiner
  • lines changed 79, context: html, text, full: html, text
    ca4a86fe7fc738163a6d9cb209f0e9f80cf6bf14 Mon Nov 30 16:35:39 2020 -0800
    import of GENCODE V36
• src/hg/makeDb/trackDb/ensGene.html
  • lines changed 4, context: html, text, full: html, text
    015637918009663e66e4ac49162523770167becb Thu Dec 3 10:21:43 2020 -0800
    Adding note about track archive for the current archived tracks, ensGene, geneReviews, gwasCatalog, mastermind, refSeqComposite, refs #21825
• src/hg/makeDb/trackDb/https/api.wenglab.org/screen_v13/hubs/dna20/genomes.txt/bitmap
  • lines changed 0, context: html, text, full: html, text
    95b322edfc47c03fe3d515a703b1f49c4a7ce52f Tue Dec 1 12:08:51 2020 -0800
    Fixing gnomAD typos refs #25010
  • lines changed 0, context: html, text, full: html, text
    4f992a6b554492f5f7ea526ff79dc73de7d8cace Tue Dec 1 12:12:11 2020 -0800
    removing accidental commits, never pushed No RM
• src/hg/makeDb/trackDb/https/api.wenglab.org/screen_v13/hubs/dna20/genomes.txt/sparseData
  • lines changed 10, context: html, text, full: html, text
    95b322edfc47c03fe3d515a703b1f49c4a7ce52f Tue Dec 1 12:08:51 2020 -0800
    Fixing gnomAD typos refs #25010
  • lines changed 10, context: html, text, full: html, text
    4f992a6b554492f5f7ea526ff79dc73de7d8cace Tue Dec 1 12:12:11 2020 -0800
    removing accidental commits, never pushed No RM
• src/hg/makeDb/trackDb/https/api.wenglab.org/screen_v13/hubs/dna20/hub.txt/bitmap
  • lines changed 0, context: html, text, full: html, text
    95b322edfc47c03fe3d515a703b1f49c4a7ce52f Tue Dec 1 12:08:51 2020 -0800
    Fixing gnomAD typos refs #25010
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    4f992a6b554492f5f7ea526ff79dc73de7d8cace Tue Dec 1 12:12:11 2020 -0800
    removing accidental commits, never pushed No RM
• src/hg/makeDb/trackDb/https/api.wenglab.org/screen_v13/hubs/dna20/hub.txt/sparseData
  • lines changed 7, context: html, text, full: html, text
    95b322edfc47c03fe3d515a703b1f49c4a7ce52f Tue Dec 1 12:08:51 2020 -0800
    Fixing gnomAD typos refs #25010
  • lines changed 7, context: html, text, full: html, text
    4f992a6b554492f5f7ea526ff79dc73de7d8cace Tue Dec 1 12:12:11 2020 -0800
    removing accidental commits, never pushed No RM
• src/hg/makeDb/trackDb/https/api.wenglab.org/screen_v13/hubs/integrative52/genomes.txt/bitmap
  • lines changed 0, context: html, text, full: html, text
    95b322edfc47c03fe3d515a703b1f49c4a7ce52f Tue Dec 1 12:08:51 2020 -0800
    Fixing gnomAD typos refs #25010
  • lines changed 0, context: html, text, full: html, text
    4f992a6b554492f5f7ea526ff79dc73de7d8cace Tue Dec 1 12:12:11 2020 -0800
    removing accidental commits, never pushed No RM
• src/hg/makeDb/trackDb/https/api.wenglab.org/screen_v13/hubs/integrative52/genomes.txt/sparseData
  • lines changed 5, context: html, text, full: html, text
    95b322edfc47c03fe3d515a703b1f49c4a7ce52f Tue Dec 1 12:08:51 2020 -0800
    Fixing gnomAD typos refs #25010
  • lines changed 5, context: html, text, full: html, text
    4f992a6b554492f5f7ea526ff79dc73de7d8cace Tue Dec 1 12:12:11 2020 -0800
    removing accidental commits, never pushed No RM
• src/hg/makeDb/trackDb/https/api.wenglab.org/screen_v13/hubs/integrative52/hub.txt/bitmap
  • lines changed 0, context: html, text, full: html, text
    95b322edfc47c03fe3d515a703b1f49c4a7ce52f Tue Dec 1 12:08:51 2020 -0800
    Fixing gnomAD typos refs #25010
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    4f992a6b554492f5f7ea526ff79dc73de7d8cace Tue Dec 1 12:12:11 2020 -0800
    removing accidental commits, never pushed No RM
• src/hg/makeDb/trackDb/https/api.wenglab.org/screen_v13/hubs/integrative52/hub.txt/sparseData
  • lines changed 7, context: html, text, full: html, text
    95b322edfc47c03fe3d515a703b1f49c4a7ce52f Tue Dec 1 12:08:51 2020 -0800
    Fixing gnomAD typos refs #25010
  • lines changed 7, context: html, text, full: html, text
    4f992a6b554492f5f7ea526ff79dc73de7d8cace Tue Dec 1 12:12:11 2020 -0800
    removing accidental commits, never pushed No RM
• src/hg/makeDb/trackDb/https/api.wenglab.org/screen_v13/hubs/rna22/genomes.txt/bitmap
  • lines changed 0, context: html, text, full: html, text
    95b322edfc47c03fe3d515a703b1f49c4a7ce52f Tue Dec 1 12:08:51 2020 -0800
    Fixing gnomAD typos refs #25010
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    4f992a6b554492f5f7ea526ff79dc73de7d8cace Tue Dec 1 12:12:11 2020 -0800
    removing accidental commits, never pushed No RM
• src/hg/makeDb/trackDb/https/api.wenglab.org/screen_v13/hubs/rna22/genomes.txt/sparseData
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    95b322edfc47c03fe3d515a703b1f49c4a7ce52f Tue Dec 1 12:08:51 2020 -0800
    Fixing gnomAD typos refs #25010
  • lines changed 12, context: html, text, full: html, text
    4f992a6b554492f5f7ea526ff79dc73de7d8cace Tue Dec 1 12:12:11 2020 -0800
    removing accidental commits, never pushed No RM
• src/hg/makeDb/trackDb/https/api.wenglab.org/screen_v13/hubs/rna22/hub.txt/bitmap
  • lines changed 0, context: html, text, full: html, text
    95b322edfc47c03fe3d515a703b1f49c4a7ce52f Tue Dec 1 12:08:51 2020 -0800
    Fixing gnomAD typos refs #25010
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    4f992a6b554492f5f7ea526ff79dc73de7d8cace Tue Dec 1 12:12:11 2020 -0800
    removing accidental commits, never pushed No RM
• src/hg/makeDb/trackDb/https/api.wenglab.org/screen_v13/hubs/rna22/hub.txt/sparseData
  • lines changed 7, context: html, text, full: html, text
    95b322edfc47c03fe3d515a703b1f49c4a7ce52f Tue Dec 1 12:08:51 2020 -0800
    Fixing gnomAD typos refs #25010
  • lines changed 7, context: html, text, full: html, text
    4f992a6b554492f5f7ea526ff79dc73de7d8cace Tue Dec 1 12:12:11 2020 -0800
    removing accidental commits, never pushed No RM
• src/hg/makeDb/trackDb/human/geneReviews.html
  • lines changed 4, context: html, text, full: html, text
    015637918009663e66e4ac49162523770167becb Thu Dec 3 10:21:43 2020 -0800
    Adding note about track archive for the current archived tracks, ensGene, geneReviews, gwasCatalog, mastermind, refSeqComposite, refs #21825
• src/hg/makeDb/trackDb/human/gwasCatalog.html
  • lines changed 12, context: html, text, full: html, text
    015637918009663e66e4ac49162523770167becb Thu Dec 3 10:21:43 2020 -0800
    Adding note about track archive for the current archived tracks, ensGene, geneReviews, gwasCatalog, mastermind, refSeqComposite, refs #21825
• src/hg/makeDb/trackDb/human/hg19/gnomad.html
  • lines changed 1, context: html, text, full: html, text
    95b322edfc47c03fe3d515a703b1f49c4a7ce52f Tue Dec 1 12:08:51 2020 -0800
    Fixing gnomAD typos refs #25010
• src/hg/makeDb/trackDb/human/hg19/gnomadVariants.html
  • lines changed 1, context: html, text, full: html, text
    95b322edfc47c03fe3d515a703b1f49c4a7ce52f Tue Dec 1 12:08:51 2020 -0800
    Fixing gnomAD typos refs #25010
• src/hg/makeDb/trackDb/human/hg38/gencodeV36.html
  • lines changed 47, context: html, text, full: html, text
    ca4a86fe7fc738163a6d9cb209f0e9f80cf6bf14 Mon Nov 30 16:35:39 2020 -0800
    import of GENCODE V36
• src/hg/makeDb/trackDb/human/hg38/gencodeV36.ra
  • lines changed 287, context: html, text, full: html, text
    ca4a86fe7fc738163a6d9cb209f0e9f80cf6bf14 Mon Nov 30 16:35:39 2020 -0800
    import of GENCODE V36
• src/hg/makeDb/trackDb/human/hg38/knownGene.ra
  • lines changed 1, context: html, text, full: html, text
    70f371ba140fb626fe9aa748588b2a2bab1e5a8a Wed Dec 2 01:52:18 2020 -0800
    adding exonNumbers back to hg38 knownGene, temporary fix for a bug in 407 that will be fixed in 408, refs #25325
• src/hg/makeDb/trackDb/human/hg38/trackDb.gencode.ra
  • lines changed 2, context: html, text, full: html, text
    ca4a86fe7fc738163a6d9cb209f0e9f80cf6bf14 Mon Nov 30 16:35:39 2020 -0800
    import of GENCODE V36
• src/hg/makeDb/trackDb/human/mastermind.html
  • lines changed 4, context: html, text, full: html, text
    015637918009663e66e4ac49162523770167becb Thu Dec 3 10:21:43 2020 -0800
    Adding note about track archive for the current archived tracks, ensGene, geneReviews, gwasCatalog, mastermind, refSeqComposite, refs #21825
• src/hg/makeDb/trackDb/opossum/monDom4/multiz7way.html
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    87dcf1d1cdf69eb66659ba9bbf09c19e338844b9 Wed Dec 2 09:41:19 2020 -0800
    Updating http to https for monDom4, uiLinks cronjob.
• src/hg/makeDb/trackDb/refSeqComposite.html
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    015637918009663e66e4ac49162523770167becb Thu Dec 3 10:21:43 2020 -0800
    Adding note about track archive for the current archived tracks, ensGene, geneReviews, gwasCatalog, mastermind, refSeqComposite, refs #21825
• src/hg/makeDb/trackDb/refSeqComposite.ra
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    38c87e0a9eae2c8edd257c97dd2369ce1b0812f9 Mon Nov 30 14:48:30 2020 -0800
    Squashing old pennantIcon no RM
• src/hg/makeDb/trackDb/trackDb.chainNet.asmHub.ra
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    1596652e312cb81a414ccbd0f393bfb0921d5f90 Wed Dec 2 12:56:30 2020 -0800
    trying a chainNet with dot names refs #26584
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    8583c65794346572e48e118f4854f7980256a458 Wed Dec 2 13:03:47 2020 -0800
    type bigChain needs a database name refs #26584
• src/hg/makeDb/trackDb/trackDb.ra
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    63da8d75a92aa0dbde9397c20534628fae6ba488 Mon Dec 7 09:00:22 2020 -0800
    adding exon numbers to Ensembl genes again, temporary fix, refs #25325
• src/hg/makeDb/trackDb/trackDb.uniprot.ra
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    882e725e37132c0fec2d7d4041b649e3065ef4ef Mon Nov 30 14:49:26 2020 -0800
    Adding new and updated uniprot tracks pennantIcon refs #25784
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra
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    d52c93797e86b6fc5766ac9ceb69b05d4d824e06 Wed Dec 2 09:42:37 2020 -0800
    Staging the Phylo tracks for wuhCor1 on hgwbeta, refs #26530
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    189052a3d5c1b173ec527b347d622c1c15c295c4 Fri Dec 4 14:40:44 2020 -0800
    Staging the phylogenetic tracks for wuhCor1 on the RR, refs #26530
• src/hg/utils/automation/doAssemblyHub.pl
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    9a693302d1b139fb9e045ac1032345ccbef293a3 Mon Nov 30 15:48:45 2020 -0800
    correct order of names file for fakeAgp refs #24396
• src/hg/utils/automation/doIdKeys.pl
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    71839b5c94882709f10f982ff4d91b8da3e23ec4 Fri Dec 4 23:34:55 2020 -0800
    twoBitDup has been improved can now run up very large contig counts in one go refs #23891
• src/hg/utils/automation/doNcbiRefSeq.pl
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    06be530f59c8628ccc70d7087528b2d78eaca226 Mon Nov 30 15:49:52 2020 -0800
    correctly removing duplicate names refs #24396
• src/hg/utils/otto/sarscov2phylo/addUnmappedPublic.sh
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    f78b8c4c7e8c23acd998ce19c7ef5af7c404adc4 Wed Dec 2 16:54:28 2020 -0800
    Use Yatish's find_parsimonious_assignments program to make parsimony score bigWigs. Also save full output of find_parsimonious_assignments for collaborators (Russ request).
• src/hg/utils/otto/sarscov2phylo/mapPublic.sh
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    f78b8c4c7e8c23acd998ce19c7ef5af7c404adc4 Wed Dec 2 16:54:28 2020 -0800
    Use Yatish's find_parsimonious_assignments program to make parsimony score bigWigs. Also save full output of find_parsimonious_assignments for collaborators (Russ request).
• src/hg/utils/otto/sarscov2phylo/processRelease.sh
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    f78b8c4c7e8c23acd998ce19c7ef5af7c404adc4 Wed Dec 2 16:54:28 2020 -0800
    Use Yatish's find_parsimonious_assignments program to make parsimony score bigWigs. Also save full output of find_parsimonious_assignments for collaborators (Russ request).
• src/hg/utils/otto/uniprot/doUniprot
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    5358ee1515addae44abe0138f520fe2a170da534 Fri Dec 4 06:13:46 2020 -0800
    a lot of updates for the uniprot otto script, refs #26630
• src/inc/srcVersion.h
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    bd784c0cd021f8e050ff1f78e9bae128a71682f6 Mon Dec 7 09:56:52 2020 -0800
    New version number v408
• src/lib/bamFile.c
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    ff5530a2dba0cbf6730cb36524ad2ce2fbc45adc Mon Nov 30 09:49:58 2020 -0800
    Add support for SARS-CoV-2 RefSeq or GenBank accesion in bam.
• src/lib/freeType.c
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    a74948671544248fedd95414623a86dd4c8b6c39 Fri Dec 4 08:18:31 2020 -0800
    added some comments and a default case in response to code review
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    195ec8849a5062e6eee7d907ea4bc333a6ff28d7 Fri Dec 4 09:57:16 2020 -0800
    a little more commenting
• src/utils/qa/weeklybld/buildEnv.csh
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    f9ea2e61a8be765cb09d5b16539bf06b0477b7c5 Mon Nov 30 09:42:43 2020 -0800
    v408 preview2
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    83373a04d8b849c39bd00238a7d5dfeafc2dffed Mon Dec 7 09:55:12 2020 -0800
    v408 final build
• src/utils/twoBitDup/twoBitDup.c
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    469949aeb805fd5ad78395c248fe62bc583ccbf9 Fri Dec 4 23:28:46 2020 -0800
    use MD5() from openssl instead of md5HexForString() hundreds of times faster refs #23891
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    8a2514bdfd594490e0a459fa72364af995a56ddb Sat Dec 5 23:07:19 2020 -0800
    no longer need the warning about excessive time with the keyList option refs #23891

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