All File Changes

v399_preview2 to v399_base (2020-05-25 to 2020-06-01) v399

• confs/preview.hg.conf
  • lines changed 3, context: html, text, full: html, text
    8e56b51bd4c0fba43d86a0b721dce091099f260c Sun May 31 01:11:28 2020 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/hgBlat/hgBlat.c
  • lines changed 8, context: html, text, full: html, text
    bf49fd6f88186b3800efd0a212296656a6e670e0 Wed May 27 02:01:28 2020 -0700
    improving hgBlat styling a little, OK'ed by Galt per email
  • lines changed 6, context: html, text, full: html, text
    e9fe6f3c5455766752d686cc105632684dd326f8 Fri May 29 18:51:55 2020 -0700
    Adding short paragraph explainging the new All Results checkbox. refs #25477.
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 1, context: html, text, full: html, text
    79b4be177c95cb0572f25a93f7fea9ec60809c20 Tue May 26 15:15:19 2020 -0700
    Feature for supertrack children was bleeding into composite track children. refs #24948
  • lines changed 1, context: html, text, full: html, text
    3d7e77408de77b4d07a58dd90e7f198a7d77b9f5 Thu May 28 10:04:35 2020 -0700
    Add line separating supertrack info from track config. Request of QA. refs #24948
• src/hg/hgc/hgc.c
  • lines changed 149, context: html, text, full: html, text
    f28d6cf170736d1374ccac80ea59943bb85e2cab Wed May 27 02:08:22 2020 -0700
    showing disease table on omim hgc page, refs #18419
  • lines changed 51, context: html, text, full: html, text
    cfa97200252eecb2b8dfe20d9d65cd5afd0f3ba3 Thu May 28 02:37:57 2020 -0700
    more OMIM hgc changes, refs #18419
  • lines changed 18, context: html, text, full: html, text
    8931ab6b05b124503660f86d60fe34a38266d716 Fri May 29 06:53:20 2020 -0700
    OMIM: not showing phenotype table when there are no phenotypes and add more spaces, refs #18419
• src/hg/htdocs/covid19.html
  • lines changed 4, context: html, text, full: html, text
    2174daf4543afc35f0856c16bfe81406c8bf257d Mon Jun 1 07:45:55 2020 -0700
    Update nextstrain transmission graphic to May 30. refs #25217
  • lines changed 30, context: html, text, full: html, text
    10cd6287a3c4534b8bd7fa6d9bf649b5bbfd316b Mon Jun 1 08:17:23 2020 -0700
    Add news item for GENCODE COVID-19 gene annotation public hub. refs #25217
• src/hg/htdocs/goldenPath/help/hic.html
  • lines changed 1, context: html, text, full: html, text
    77c4d21730d2f08b5b40ef01e1cab94f46c1b2ed Fri May 29 10:39:27 2020 -0700
    grammar tweak. added italics
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 54, context: html, text, full: html, text
    8ae5db39951014aa1bb2b6fc062aa8263fd1fc91 Mon May 25 14:52:06 2020 -0700
    Announcing refseq vertebrate assembly hubs refs #23891
  • lines changed 76, context: html, text, full: html, text
    260c24487a0ce4e3e145687e6a1ba65c812f67d5 Tue May 26 09:28:38 2020 -0700
    releasing new video: Browser Basics, Part Three. tweaks to training page
  • lines changed 2, context: html, text, full: html, text
    59ee91e2829e1f6d33d83b5272de6bf12ba84922 Tue May 26 10:51:40 2020 -0700
    Announcing GENCODE and GTEx #25130
  • lines changed 3, context: html, text, full: html, text
    ca12c087c64d30c9ccd2212bade60c7bb8475df5 Tue May 26 15:58:15 2020 -0700
    Minor changes CR #25624
• src/hg/htdocs/images/covid19/covid19-transmission.may30_2020.nextstrain.png
  • lines changed 0, context: html, text, full: html, text
    d5ae6e5b02cae46867681b2b1cfa0920e391601f Mon Jun 1 08:17:51 2020 -0700
    Add news item for GENCODE COVID-19 gene annotation public hub. refs #25217
• src/hg/htdocs/indexNews.html
  • lines changed 14, context: html, text, full: html, text
    8ae5db39951014aa1bb2b6fc062aa8263fd1fc91 Mon May 25 14:52:06 2020 -0700
    Announcing refseq vertebrate assembly hubs refs #23891
  • lines changed 11, context: html, text, full: html, text
    260c24487a0ce4e3e145687e6a1ba65c812f67d5 Tue May 26 09:28:38 2020 -0700
    releasing new video: Browser Basics, Part Three. tweaks to training page
  • lines changed 1, context: html, text, full: html, text
    59ee91e2829e1f6d33d83b5272de6bf12ba84922 Tue May 26 10:51:40 2020 -0700
    Announcing GENCODE and GTEx #25130
  • lines changed 12, context: html, text, full: html, text
    cdef2b15264dbbc0365542023e770d28e4855e38 Tue May 26 10:53:34 2020 -0700
    Fixing merge conflict #25130
  • lines changed 2, context: html, text, full: html, text
    933ffbd83771afc7c9a1dc03f857bce481f8cc2e Tue May 26 15:43:44 2020 -0700
    Fixing merge conflict CR #25624
• src/hg/htdocs/style/HGStyle.css
  • lines changed 26, context: html, text, full: html, text
    bf49fd6f88186b3800efd0a212296656a6e670e0 Wed May 27 02:01:28 2020 -0700
    improving hgBlat styling a little, OK'ed by Galt per email
  • lines changed 3, context: html, text, full: html, text
    cfa97200252eecb2b8dfe20d9d65cd5afd0f3ba3 Thu May 28 02:37:57 2020 -0700
    more OMIM hgc changes, refs #18419
• src/hg/htdocs/training/index.html
  • lines changed 44, context: html, text, full: html, text
    260c24487a0ce4e3e145687e6a1ba65c812f67d5 Tue May 26 09:28:38 2020 -0700
    releasing new video: Browser Basics, Part Three. tweaks to training page
  • lines changed 1, context: html, text, full: html, text
    2dc845ab52b97667dd9f750c63b29c1a973d2580 Wed May 27 09:47:37 2020 -0700
    removed quotes
• src/hg/inc/jksql.h
  • lines changed 3, context: html, text, full: html, text
    8931ab6b05b124503660f86d60fe34a38266d716 Fri May 29 06:53:20 2020 -0700
    OMIM: not showing phenotype table when there are no phenotypes and add more spaces, refs #18419
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    b07650d95d9277aced9e2027203659b0729a1060 Mon Jun 1 10:03:46 2020 -0700
    New version number v399
• src/hg/lib/annoGratorGpVar.c
  • lines changed 1, context: html, text, full: html, text
    d93f47cd567bb70aba94de233054e8b4fae00f7d Fri May 29 15:33:58 2020 -0700
    remove frameshifts from psls in hgVai
• src/hg/lib/jksql.c
  • lines changed 8, context: html, text, full: html, text
    8931ab6b05b124503660f86d60fe34a38266d716 Fri May 29 06:53:20 2020 -0700
    OMIM: not showing phenotype table when there are no phenotypes and add more spaces, refs #18419
• src/hg/lib/omimPhenotype.as
  • lines changed 2, context: html, text, full: html, text
    7beda309214a84ca208bb6b63178978f906698df Wed May 27 03:49:16 2020 -0700
    OMIM otto update for new OMIM phenotype table, refs #18419
• src/hg/lib/omimPhenotype.sql
  • lines changed 3, context: html, text, full: html, text
    7beda309214a84ca208bb6b63178978f906698df Wed May 27 03:49:16 2020 -0700
    OMIM otto update for new OMIM phenotype table, refs #18419
• src/hg/lib/variantProjector.c
  • lines changed 1, context: html, text, full: html, text
    e4b95e1845f752954f388a0c61b7d4a107baa80a Wed May 27 18:02:07 2020 -0700
    don't count frameshifts as small introns
  • lines changed 1, context: html, text, full: html, text
    a8a289ed81fa32737a91d784a3ebcc1c886770e7 Fri May 29 11:31:31 2020 -0700
    Revert "don't count frameshifts as small introns" This reverts commit e4b95e1845f752954f388a0c61b7d4a107baa80a.
• src/hg/makeDb/doc/asmHubs/asmHubs.mk
  • lines changed 44, context: html, text, full: html, text
    afee0fcf2a7b7de2eb37e1420dc126607373453e Wed May 27 17:31:45 2020 -0700
    rework scripts to allow subset hubs to be created from a list of assemblies refs #23734
• src/hg/makeDb/doc/asmHubs/commonHtml.pm
  • lines changed 97, context: html, text, full: html, text
    c8828612e3aba9e6c3072768129de10abe337878 Fri May 29 11:29:04 2020 -0700
    now allow orderList to be specifically stated and begin common set of html functions refs #23734
• src/hg/makeDb/doc/asmHubs/groups.txt
  • lines changed 5, context: html, text, full: html, text
    5da567339600782c80ebe43ef8b0a2e661b01e94 Wed May 27 11:48:06 2020 -0700
    correct full labels on the groups refs #23734
• src/hg/makeDb/doc/asmHubs/mkAsmStats.pl
  • lines changed 18, context: html, text, full: html, text
    afee0fcf2a7b7de2eb37e1420dc126607373453e Wed May 27 17:31:45 2020 -0700
    rework scripts to allow subset hubs to be created from a list of assemblies refs #23734
  • lines changed 62, context: html, text, full: html, text
    c8828612e3aba9e6c3072768129de10abe337878 Fri May 29 11:29:04 2020 -0700
    now allow orderList to be specifically stated and begin common set of html functions refs #23734
• src/hg/makeDb/doc/asmHubs/mkGenomes.pl
  • lines changed 46, context: html, text, full: html, text
    afee0fcf2a7b7de2eb37e1420dc126607373453e Wed May 27 17:31:45 2020 -0700
    rework scripts to allow subset hubs to be created from a list of assemblies refs #23734
  • lines changed 8, context: html, text, full: html, text
    c8828612e3aba9e6c3072768129de10abe337878 Fri May 29 11:29:04 2020 -0700
    now allow orderList to be specifically stated and begin common set of html functions refs #23734
• src/hg/makeDb/doc/asmHubs/mkHubIndex.pl
  • lines changed 29, context: html, text, full: html, text
    afee0fcf2a7b7de2eb37e1420dc126607373453e Wed May 27 17:31:45 2020 -0700
    rework scripts to allow subset hubs to be created from a list of assemblies refs #23734
  • lines changed 64, context: html, text, full: html, text
    c8828612e3aba9e6c3072768129de10abe337878 Fri May 29 11:29:04 2020 -0700
    now allow orderList to be specifically stated and begin common set of html functions refs #23734
• src/hg/makeDb/doc/asmHubs/mkSymLinks.pl
  • lines changed 40, context: html, text, full: html, text
    afee0fcf2a7b7de2eb37e1420dc126607373453e Wed May 27 17:31:45 2020 -0700
    rework scripts to allow subset hubs to be created from a list of assemblies refs #23734
  • lines changed 8, context: html, text, full: html, text
    c8828612e3aba9e6c3072768129de10abe337878 Fri May 29 11:29:04 2020 -0700
    now allow orderList to be specifically stated and begin common set of html functions refs #23734
• src/hg/makeDb/doc/asmHubs/trackData.pl
  • lines changed 16, context: html, text, full: html, text
    afee0fcf2a7b7de2eb37e1420dc126607373453e Wed May 27 17:31:45 2020 -0700
    rework scripts to allow subset hubs to be created from a list of assemblies refs #23734
  • lines changed 59, context: html, text, full: html, text
    c8828612e3aba9e6c3072768129de10abe337878 Fri May 29 11:29:04 2020 -0700
    now allow orderList to be specifically stated and begin common set of html functions refs #23734
• src/hg/makeDb/doc/hg38/variation.txt
  • lines changed 95, context: html, text, full: html, text
    418b11748d3ae9c1217714a92d4a7fe46b6819b9 Thu May 28 17:14:54 2020 -0700
    Added a few more trios to the 1000 Genomes trio track QA ready, refs #25582
• src/hg/makeDb/doc/mm10.txt
  • lines changed 69, context: html, text, full: html, text
    87580fb0edf5843fed1220d257c8a4edcfcf5a9b Fri May 29 11:19:56 2020 -0700
    starting chainNet per user request refs #25625
  • lines changed 26, context: html, text, full: html, text
    c3fdad60d8f01da6ff3296b216015ebae858b06c Fri May 29 17:12:51 2020 -0700
    continue lastz/chain/net run for user refs #25625
• src/hg/makeDb/doc/vgpAsmHub/altMakefile
  • lines changed 26, context: html, text, full: html, text
    ded5fbfbae9e713b69de8aeef0efad8719034b07 Wed May 27 17:34:00 2020 -0700
    rework scripts to allow subset hubs to be created from a list of assemblies refs #23734
• src/hg/makeDb/doc/vgpAsmHub/makefile
  • lines changed 26, context: html, text, full: html, text
    ded5fbfbae9e713b69de8aeef0efad8719034b07 Wed May 27 17:34:00 2020 -0700
    rework scripts to allow subset hubs to be created from a list of assemblies refs #23734
• src/hg/makeDb/doc/vgpAsmHub/trioMakefile
  • lines changed 26, context: html, text, full: html, text
    ded5fbfbae9e713b69de8aeef0efad8719034b07 Wed May 27 17:34:00 2020 -0700
    rework scripts to allow subset hubs to be created from a list of assemblies refs #23734
• src/hg/makeDb/doc/vgpAsmHub/userDataMakefile
  • lines changed 26, context: html, text, full: html, text
    ded5fbfbae9e713b69de8aeef0efad8719034b07 Wed May 27 17:34:00 2020 -0700
    rework scripts to allow subset hubs to be created from a list of assemblies refs #23734
• src/hg/makeDb/doc/vgpAsmHub/vgp.alternate.orderList.tsv
  • lines changed 68, context: html, text, full: html, text
    ded5fbfbae9e713b69de8aeef0efad8719034b07 Wed May 27 17:34:00 2020 -0700
    rework scripts to allow subset hubs to be created from a list of assemblies refs #23734
• src/hg/makeDb/doc/vgpAsmHub/vgp.legacy.orderList.tsv
  • lines changed 11, context: html, text, full: html, text
    ded5fbfbae9e713b69de8aeef0efad8719034b07 Wed May 27 17:34:00 2020 -0700
    rework scripts to allow subset hubs to be created from a list of assemblies refs #23734
• src/hg/makeDb/doc/vgpAsmHub/vgp.primary.orderList.tsv
  • lines changed 72, context: html, text, full: html, text
    ded5fbfbae9e713b69de8aeef0efad8719034b07 Wed May 27 17:34:00 2020 -0700
    rework scripts to allow subset hubs to be created from a list of assemblies refs #23734
• src/hg/makeDb/doc/vgpAsmHub/vgp.taxId,asmId.class.txt
  • lines changed 9, context: html, text, full: html, text
    f9446c7f0de844971aa819343705a0d6f1ed9eed Wed May 27 12:12:41 2020 -0700
    adding in a few that host Arang.s data tracks refs #23734
• src/hg/makeDb/doc/vgpAsmHub/vgp.taxId.asmId.class.txt
  • lines changed 168, context: html, text, full: html, text
    ded5fbfbae9e713b69de8aeef0efad8719034b07 Wed May 27 17:34:00 2020 -0700
    rework scripts to allow subset hubs to be created from a list of assemblies refs #23734
• src/hg/makeDb/doc/vgpAsmHub/vgp.trio.orderList.tsv
  • lines changed 17, context: html, text, full: html, text
    ded5fbfbae9e713b69de8aeef0efad8719034b07 Wed May 27 17:34:00 2020 -0700
    rework scripts to allow subset hubs to be created from a list of assemblies refs #23734
• src/hg/makeDb/tgpTrio/loadTables.sh
  • lines changed 24, context: html, text, full: html, text
    418b11748d3ae9c1217714a92d4a7fe46b6819b9 Thu May 28 17:14:54 2020 -0700
    Added a few more trios to the 1000 Genomes trio track QA ready, refs #25582
• src/hg/makeDb/tgpTrio/makeTrio.py
  • lines changed 311, context: html, text, full: html, text
    418b11748d3ae9c1217714a92d4a7fe46b6819b9 Thu May 28 17:14:54 2020 -0700
    Added a few more trios to the 1000 Genomes trio track QA ready, refs #25582
• src/hg/makeDb/trackDb/human/gtexGeneV8.html
  • lines changed 6, context: html, text, full: html, text
    8c31969cb13f9887a76480767e68c0b5421e2a65 Tue May 26 13:43:43 2020 -0700
    Updating html and pennantIcon #25130
• src/hg/makeDb/trackDb/human/hg38/tgpTrios.html
  • lines changed 143, context: html, text, full: html, text
    418b11748d3ae9c1217714a92d4a7fe46b6819b9 Thu May 28 17:14:54 2020 -0700
    Added a few more trios to the 1000 Genomes trio track QA ready, refs #25582
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 46, context: html, text, full: html, text
    418b11748d3ae9c1217714a92d4a7fe46b6819b9 Thu May 28 17:14:54 2020 -0700
    Added a few more trios to the 1000 Genomes trio track QA ready, refs #25582
• src/hg/makeDb/trackDb/human/omimGene2.html
  • lines changed 18, context: html, text, full: html, text
    4a646e64a0e5a56c6dfd9cd097538f1e44edf2e5 Fri May 29 19:40:03 2020 -0700
    added explanation brackets, braces, question mark to display conventions refs #18419
• src/hg/makeDb/trackDb/human/trackDb.gtex.ra
  • lines changed 1, context: html, text, full: html, text
    8c31969cb13f9887a76480767e68c0b5421e2a65 Tue May 26 13:43:43 2020 -0700
    Updating html and pennantIcon #25130
• src/hg/makeDb/trackDb/virus/wuhCor1/PhyloCSF_Raw.html
  • lines changed 175, context: html, text, full: html, text
    3d375f7832e1dce0140ba088b24dc32c11650fae Wed May 27 09:31:27 2020 -0700
    adding phyloCsf tracks, no redmine yet.
• src/hg/makeDb/trackDb/virus/wuhCor1/PhyloCSF_power.html
  • lines changed 175, context: html, text, full: html, text
    3d375f7832e1dce0140ba088b24dc32c11650fae Wed May 27 09:31:27 2020 -0700
    adding phyloCsf tracks, no redmine yet.
• src/hg/makeDb/trackDb/virus/wuhCor1/PhyloCSF_power.html.1
  • lines changed 175, context: html, text, full: html, text
    b9b283bb296c06bb56f478543c354de68e7c19d5 Fri May 29 07:43:23 2020 -0700
    forgot PhyloCSF docs pages, refs #25644
• src/hg/makeDb/trackDb/virus/wuhCor1/PhyloCSF_smooth.html
  • lines changed 175, context: html, text, full: html, text
    b9b283bb296c06bb56f478543c354de68e7c19d5 Fri May 29 07:43:23 2020 -0700
    forgot PhyloCSF docs pages, refs #25644
• src/hg/makeDb/trackDb/virus/wuhCor1/description.html
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    5d698f432bac3970d42df0170d11e119ac7abe25 Tue May 26 11:51:45 2020 -0700
    Making a code review edit in real-time and stashing some comments on pubs.html for future publications refs #25619
• src/hg/makeDb/trackDb/virus/wuhCor1/phylocsf.ra
  • lines changed 153, context: html, text, full: html, text
    3d375f7832e1dce0140ba088b24dc32c11650fae Wed May 27 09:31:27 2020 -0700
    adding phyloCsf tracks, no redmine yet.
  • lines changed 119, context: html, text, full: html, text
    69f9fe583924590fc46fb4b40e5efc54a5f03eb9 Fri May 29 07:40:09 2020 -0700
    adding a phyloCSF track from the public hub, refs #25644
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra
  • lines changed 15, context: html, text, full: html, text
    3d375f7832e1dce0140ba088b24dc32c11650fae Wed May 27 09:31:27 2020 -0700
    adding phyloCsf tracks, no redmine yet.
• src/hg/ratStuff/mafRc/expected/test1-rc.maf
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    d41531259de6cb8aafd3b0d336518f2e8d6cfb61 Tue May 26 17:13:04 2020 -0700
    Hiram is right, this is useless; what is really needed is for mafOrder to have an option to orient the reference sequence to the positive strand
• src/hg/ratStuff/mafRc/expected/testHg16-rc.maf
  • lines changed 501, context: html, text, full: html, text
    d41531259de6cb8aafd3b0d336518f2e8d6cfb61 Tue May 26 17:13:04 2020 -0700
    Hiram is right, this is useless; what is really needed is for mafOrder to have an option to orient the reference sequence to the positive strand
• src/hg/ratStuff/mafRc/mafRc.c
  • lines changed 85, context: html, text, full: html, text
    d41531259de6cb8aafd3b0d336518f2e8d6cfb61 Tue May 26 17:13:04 2020 -0700
    Hiram is right, this is useless; what is really needed is for mafOrder to have an option to orient the reference sequence to the positive strand
• src/hg/ratStuff/mafRc/makefile
  • lines changed 20, context: html, text, full: html, text
    d41531259de6cb8aafd3b0d336518f2e8d6cfb61 Tue May 26 17:13:04 2020 -0700
    Hiram is right, this is useless; what is really needed is for mafOrder to have an option to orient the reference sequence to the positive strand
• src/hg/ratStuff/makefile
  • lines changed 1, context: html, text, full: html, text
    d41531259de6cb8aafd3b0d336518f2e8d6cfb61 Tue May 26 17:13:04 2020 -0700
    Hiram is right, this is useless; what is really needed is for mafOrder to have an option to orient the reference sequence to the positive strand
• src/hg/utils/automation/asmHubNcbiRefSeq.pl
  • lines changed 9, context: html, text, full: html, text
    428bacd2dcbaca9304763d3f2dca7ccffd088caa Tue May 26 11:18:06 2020 -0700
    correct br tags refs #23734
• src/hg/utils/automation/asmHubRmsk.pl
  • lines changed 1, context: html, text, full: html, text
    09f1e0f6809ff44752b332ea72c7faacdf085e99 Tue May 26 11:16:06 2020 -0700
    correct usage message refs #23734
• src/hg/utils/automation/asmHubTrackDb.sh
  • lines changed 141, context: html, text, full: html, text
    69809a6ecef72bb253a4191e80c40e426af5d14a Tue May 26 11:15:20 2020 -0700
    fixup rmsk correct composite track definitions and fixup ncbiGene organization refs #23734
• src/hg/utils/automation/asmHubXenoRefGene.pl
  • lines changed 3, context: html, text, full: html, text
    428bacd2dcbaca9304763d3f2dca7ccffd088caa Tue May 26 11:18:06 2020 -0700
    correct br tags refs #23734
• src/hg/utils/automation/doBlastzChainNet.pl
  • lines changed 8, context: html, text, full: html, text
    3eaf4d4b81181d543facc006791bbfc433f26528 Mon Jun 1 09:26:37 2020 -0700
    no need to fail on certificate from genome-source.soe.ucsc.edu refs #25625
• src/hg/utils/automation/doRecipBest.pl
  • lines changed 4, context: html, text, full: html, text
    3eaf4d4b81181d543facc006791bbfc433f26528 Mon Jun 1 09:26:37 2020 -0700
    no need to fail on certificate from genome-source.soe.ucsc.edu refs #25625
• src/hg/utils/automation/doRepeatMasker.pl
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    3d89934724dbec3c67aa29cd5a1c089e69d611eb Tue May 26 11:19:04 2020 -0700
    remove debug statement refs #23734
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    bca05e23f34ba02d4048494770e9ccaa2f178cd5 Thu May 28 12:02:00 2020 -0700
    due to removed duplicates from NCBI assemblies, warn and drop contigs not in the UCSC assembly refs #23734
• src/hg/utils/blatServersCheck/blatServersCheck.c
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    51d1bcdbeac4b2ee7ce4d749c2a975e8bd8a72b1 Wed May 27 18:34:11 2020 -0700
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    ec245098815310f5064a4f43174a458508a7571f Sat May 30 02:05:07 2020 -0700
    tweak input order of blatServers table
• src/hg/utils/otto/nextstrainNcov/doUpdate.sh
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    b38a548970c6920b3c9d7b6d2685e88cc1797365 Wed May 27 16:38:35 2020 -0700
    Remove pre-existing results before installing updates because it's possible for a clade to suddenly not exist in a new release (e.g. clade A2 disappeared in second update today). refs #25188
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    66cc826badeb152795b09b2081232bbfa4fd98ac Wed May 27 23:34:03 2020 -0700
    Argh, forgot -r for directory. refs #25188
• src/hg/utils/otto/omim/buildOmimTracks.sh
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    7beda309214a84ca208bb6b63178978f906698df Wed May 27 03:49:16 2020 -0700
    OMIM otto update for new OMIM phenotype table, refs #18419
• src/hg/utils/otto/omim/doOmimPhenotype.pl
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    7beda309214a84ca208bb6b63178978f906698df Wed May 27 03:49:16 2020 -0700
    OMIM otto update for new OMIM phenotype table, refs #18419
• src/hg/utils/otto/omim/doOmimPhenotypeNew
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    7beda309214a84ca208bb6b63178978f906698df Wed May 27 03:49:16 2020 -0700
    OMIM otto update for new OMIM phenotype table, refs #18419
• src/hg/utils/otto/omim/makefile
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    7beda309214a84ca208bb6b63178978f906698df Wed May 27 03:49:16 2020 -0700
    OMIM otto update for new OMIM phenotype table, refs #18419
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    69aca8aee8f6cf99943256bc817f3fcf838ed507 Wed May 27 09:44:07 2020 -0700
    removing the PREFIX from omim otto makefile, refs #18419
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• src/inc/psl.h
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    d93f47cd567bb70aba94de233054e8b4fae00f7d Fri May 29 15:33:58 2020 -0700
    remove frameshifts from psls in hgVai
• src/inc/srcVersion.h
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    b07650d95d9277aced9e2027203659b0729a1060 Mon Jun 1 10:03:46 2020 -0700
    New version number v399
• src/lib/net.c
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    51d1bcdbeac4b2ee7ce4d749c2a975e8bd8a72b1 Wed May 27 18:34:11 2020 -0700
    added -timeout=1 and -host=blat1a options
• src/lib/psl.c
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    d93f47cd567bb70aba94de233054e8b4fae00f7d Fri May 29 15:33:58 2020 -0700
    remove frameshifts from psls in hgVai
• src/utils/makefile
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    7455616a47bc45dbaf93df347345abe1747390c1 Sat May 30 09:10:32 2020 -0700
    add tests for pslRemoveFrameShifts
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    7455616a47bc45dbaf93df347345abe1747390c1 Sat May 30 09:10:32 2020 -0700
    add tests for pslRemoveFrameShifts
• src/utils/pslRemoveFrameShifts/pslRemoveFrameShifts.c
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    7455616a47bc45dbaf93df347345abe1747390c1 Sat May 30 09:10:32 2020 -0700
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    7455616a47bc45dbaf93df347345abe1747390c1 Sat May 30 09:10:32 2020 -0700
    add tests for pslRemoveFrameShifts
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    7455616a47bc45dbaf93df347345abe1747390c1 Sat May 30 09:10:32 2020 -0700
    add tests for pslRemoveFrameShifts
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    7455616a47bc45dbaf93df347345abe1747390c1 Sat May 30 09:10:32 2020 -0700
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    7455616a47bc45dbaf93df347345abe1747390c1 Sat May 30 09:10:32 2020 -0700
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    7455616a47bc45dbaf93df347345abe1747390c1 Sat May 30 09:10:32 2020 -0700
    add tests for pslRemoveFrameShifts
• src/utils/qa/weeklybld/buildEnv.csh
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    3c575ff9551ac6cb939a4ee7f9516d41e0a9c4d0 Mon Jun 1 10:02:00 2020 -0700
    v399 final build
• src/utils/qa/whoMadeIt.csh
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    7ef296f999c35a96bf0150092a30784b1821d50e Wed May 27 09:45:13 2020 -0700
    added no whitespace flag to git blame statement to get past massive change that obscures true owner of lines in newsarch.html
• src/utils/trackDbIndexBb/tests/in/trackDb.smallExample.ra
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    98b25e3170373c357d24b1cbf66d04bf74396112 Wed May 27 16:44:41 2020 -0700
    Fixing up trackDbIndexBb based on CR feedback, refs #25590
• src/utils/trackDbIndexBb/tests/in/trackDb.smallExample.txt
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    98b25e3170373c357d24b1cbf66d04bf74396112 Wed May 27 16:44:41 2020 -0700
    Fixing up trackDbIndexBb based on CR feedback, refs #25590
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    92dbf17afa86167de018d4887e746322ee117b5e Mon May 25 15:29:13 2020 -0700
    Accidentally committed test parameters when dealing with merge conflict, no RM
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    98b25e3170373c357d24b1cbf66d04bf74396112 Wed May 27 16:44:41 2020 -0700
    Fixing up trackDbIndexBb based on CR feedback, refs #25590
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    98b25e3170373c357d24b1cbf66d04bf74396112 Wed May 27 16:44:41 2020 -0700
    Fixing up trackDbIndexBb based on CR feedback, refs #25590
• src/utils/trackDbIndexBb/trackDbIndexBb
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    98b25e3170373c357d24b1cbf66d04bf74396112 Wed May 27 16:44:41 2020 -0700
    Fixing up trackDbIndexBb based on CR feedback, refs #25590

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