All File Changes

v394_preview to v394_preview2 (2020-02-03 to 2020-02-10) v394

• src/hg/bedItemOverlapCount/bedItemOverlapCount.c
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    110329b274d3e77d46cedfea05ac44a20682719e Wed Feb 5 13:12:28 2020 -0800
    use mitochondrial code on chrMT
• src/hg/cirm/cdw/cdwRenameDataset/cdwRenameDataset.c
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    a5aa2d25502abd6260c4dc5629797e40b8c5ec35 Wed Feb 5 12:28:05 2020 -0800
    extend help on cdwRenameDataset
• src/hg/cirm/gateway/htdocs/inc/header.html
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    69c6327f5270936f105f3556a8ba2c69e02c7428 Fri Feb 7 19:37:42 2020 -0800
    oops script should appear inside head or body, but not BETWEEN them.
• src/hg/getRnaPred/getRnaPred.c
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    110329b274d3e77d46cedfea05ac44a20682719e Wed Feb 5 13:12:28 2020 -0800
    use mitochondrial code on chrMT
• src/hg/hgTables/bigBed.c
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    68cc14ec70003fd37e8d3d0e28e54c349fe00ff0 Wed Feb 5 12:28:50 2020 -0800
    check identifier list when outputing sequence for bigBeds (refs #24916)
• src/hg/hgTables/mainPage.c
  • lines changed 19, context: html, text, full: html, text
    e14906744b1316f4d4c2abc81b69168ac070d5ad Wed Feb 5 03:10:21 2020 -0800
    adding note about precooked gtf files to table browser, refs #24810
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    48490b259deed7ec0de7a554bc853ee78dd3d024 Thu Feb 6 15:03:52 2020 -0800
    Revert "Revert "Removing link to openhelix from table browser text, refs #21947" -OpenHelix works again and adding back the link to OpenHelix on the Table Browser" This reverts commit cb59efe858749d4bdf974cb58e9a9da3c92236ac.
• src/hg/hgTrackUi/hgTrackUi.c
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    0321e1b641fe03c00dac6f6fe56488de3f95eba2 Mon Feb 3 14:38:19 2020 -0800
    Minor styling changes to supertrack child explanatory message. refs #24664
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    e2512af39b614b00d3f78f3336ed30c2c666003c Tue Feb 4 03:18:24 2020 -0800
    trackUi composite changes suggested by Kate, refs #24664
• src/hg/hgTracks/cds.c
  • lines changed 1, context: html, text, full: html, text
    110329b274d3e77d46cedfea05ac44a20682719e Wed Feb 5 13:12:28 2020 -0800
    use mitochondrial code on chrMT
• src/hg/htdocs/FAQ/FAQdownloads.html
  • lines changed 7, context: html, text, full: html, text
    5213780827a2014f3c84e64b803424686068b7ff Tue Feb 4 09:22:42 2020 -0800
    Adding mention of new generated GTF files to FAQ refs #20867
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    586a03e6ff6d676406d62106ae7e2e8539f52a4d Tue Feb 4 11:22:26 2020 -0800
    Documenting GTF downloads directory #20867
• src/hg/htdocs/FAQ/FAQformat.html
  • lines changed 1, context: html, text, full: html, text
    586a03e6ff6d676406d62106ae7e2e8539f52a4d Tue Feb 4 11:22:26 2020 -0800
    Documenting GTF downloads directory #20867
• src/hg/htdocs/FAQ/FAQgenes.html
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    f67479340a8ea3cec099d85b085d6be8cbaa2715 Wed Feb 5 10:13:36 2020 -0800
    Added entry about new GTF files to genes FAQ refs #20867
• src/hg/htdocs/FAQ/FAQlink.html
  • lines changed 25, context: html, text, full: html, text
    586a03e6ff6d676406d62106ae7e2e8539f52a4d Tue Feb 4 11:22:26 2020 -0800
    Documenting GTF downloads directory #20867
• src/hg/htdocs/goldenPath/help/GTF.html
  • lines changed 6, context: html, text, full: html, text
    586a03e6ff6d676406d62106ae7e2e8539f52a4d Tue Feb 4 11:22:26 2020 -0800
    Documenting GTF downloads directory #20867
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
  • lines changed 1, context: html, text, full: html, text
    628ff9b7267bf4b9e72f21c8888f9a014788bca8 Wed Feb 5 13:00:09 2020 -0800
    Change values of hideEmptySubtracks to on/off for better clarity (by popular demand). refs #23365
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v2.html
  • lines changed 1, context: html, text, full: html, text
    3490a15de1f287ff63afb1ceb8aa39168c92e68d Mon Feb 3 12:04:11 2020 -0800
    Fixing a small mistake in docs no RM
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    628ff9b7267bf4b9e72f21c8888f9a014788bca8 Wed Feb 5 13:00:09 2020 -0800
    Change values of hideEmptySubtracks to on/off for better clarity (by popular demand). refs #23365
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 9, context: html, text, full: html, text
    a74453f8ad8a689660fae9fb38f538f6b614235e Tue Feb 4 14:50:27 2020 -0800
    Clarifying filter docs, dots are required for non-+ type bb tracks to enable filters no RM
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    628ff9b7267bf4b9e72f21c8888f9a014788bca8 Wed Feb 5 13:00:09 2020 -0800
    Change values of hideEmptySubtracks to on/off for better clarity (by popular demand). refs #23365
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 43, context: html, text, full: html, text
    835218d8879807acc8e062091c59685388b5ab71 Thu Feb 6 15:15:20 2020 -0800
    News announcement for avada + mastermind refs #24156 #24157
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    2e0215c987a36fd3291baee2cd9a30598aa21ef5 Fri Feb 7 16:22:47 2020 -0800
    Adding announcement entry for #24604
• src/hg/htdocs/images/variantsInPapersNewsArch2020.png
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    89bf229ae425720c3d691d12f7873f4d3f459f94 Thu Feb 6 12:17:07 2020 -0800
    Uploading image for avada/mastermind newsArch refs #24156
• src/hg/htdocs/indexNews.html
  • lines changed 11, context: html, text, full: html, text
    a3307a8d705e9259f03ec285fb8f04d11a37613b Thu Feb 6 15:29:37 2020 -0800
    Updating indexNews for avada + mastermind refs #24156 #24157
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    bd5e46c5ca5ebde77cd05a0a6cc2fdca9d27c175 Fri Feb 7 08:41:24 2020 -0800
    Updating indexNews for avada + mastermind refs #24156 #24157
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    2e0215c987a36fd3291baee2cd9a30598aa21ef5 Fri Feb 7 16:22:47 2020 -0800
    Adding announcement entry for #24604
• src/hg/htdocs/training/index.html
  • lines changed 37, context: html, text, full: html, text
    c45eb977e95507ea5e4691a1f725d2afce986037 Thu Feb 6 19:43:18 2020 -0800
    dropping completed ucla workshop. added links for nijmegen, asilomar. moved acmg into next-four list. added iasu. made brno visible
• src/hg/htdocs/util.html
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    7f2b62a70d0544af28cca22d3a7028dc164ec2c1 Wed Feb 5 07:56:35 2020 -0800
    documenting third part tools that use UCSC file formats or servers, refs #24666
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    7ef475c3faf058d5248baa20520901a9b3f84da7 Wed Feb 5 08:48:17 2020 -0800
    Adding MakeHub to Max's new addition of utilities refs #24666
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    cece76ea1e41b78fe22af022ad0ec3dbcbd25fb6 Wed Feb 5 08:52:26 2020 -0800
    Small changes to Max's new addition of utilities refs #24666
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    6c0944e7d8e0bb76773b6c3013b0a5fbd0e95ecf Thu Feb 6 10:45:07 2020 -0800
    Adding message to utils about non-tested external tools and adding more links refs #24920
  • lines changed 7, context: html, text, full: html, text
    fa2882adc770708866434b167cd7ab7f3eb992f1 Fri Feb 7 13:20:09 2020 -0800
    Adding more secondary tools and rewording phrase refs #24920
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    3ab70ceed5c8f3cf96c9f18b35c20db477e5e1aa Fri Feb 7 13:29:37 2020 -0800
    Alphabetizing growing list of secondary tools refs #24920
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    e512638bd4659cdb12d9898c209bcb1d64d387aa Fri Feb 7 16:19:50 2020 -0800
    Making the HTML text less than 100 characters per line. Fixing a typo (missing 'to' in the second sentence), no Redmine.
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    18938391767504e0ef3e867023eaa23943fdf7b8 Fri Feb 7 16:25:49 2020 -0800
    Removing my added 'to' and changing 'provide' to past tense, no Redmine.
• src/hg/inc/hdb.h
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    110329b274d3e77d46cedfea05ac44a20682719e Wed Feb 5 13:12:28 2020 -0800
    use mitochondrial code on chrMT
• src/hg/js/dbDbTaxonomy.js
  • lines changed 13, context: html, text, full: html, text
    73d5d95546fe4a76f4d6496afadfc7539394fde6 Wed Feb 5 14:16:15 2020 -0800
    Adding Wuhan virus and the Southern sea otters
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    a45fb4cc1f361361c355f561cd357cbdfff019b6 Thu Feb 6 09:54:50 2020 -0800
    shorten the Wuhan virus name refs #24851
• src/hg/lib/genePred.c
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    110329b274d3e77d46cedfea05ac44a20682719e Wed Feb 5 13:12:28 2020 -0800
    use mitochondrial code on chrMT
• src/hg/lib/hdb.c
  • lines changed 6, context: html, text, full: html, text
    110329b274d3e77d46cedfea05ac44a20682719e Wed Feb 5 13:12:28 2020 -0800
    use mitochondrial code on chrMT
• src/hg/lib/hui.c
  • lines changed 6, context: html, text, full: html, text
    628ff9b7267bf4b9e72f21c8888f9a014788bca8 Wed Feb 5 13:00:09 2020 -0800
    Change values of hideEmptySubtracks to on/off for better clarity (by popular demand). refs #23365
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    5c9b5b1f419655737a44e3bdef3d9f42bbb9f281 Wed Feb 5 15:08:32 2020 -0800
    Fixing missing filterValues dropdown for subtracks, refs #24795
• src/hg/lib/tablesTables.c
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    84769302d77939430b003999bd6397ecc64207b5 Fri Feb 7 15:33:28 2020 -0800
    CIRM cdwWebBrowse: Placing the Clear-All-Facets button in a more logical location. Now only visble if some facets have been chosen.
• src/hg/lib/trackDbCustom.c
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    2438b4e0f4dc26dfbef722eb65b3625173a26e41 Wed Feb 5 13:13:07 2020 -0800
    Revert "allow trackDb variables to have an empty value, useful for filters" This reverts commit 8e3f3a01dbb1b2ac9d3c7fed4fb2840dcb6014f6.
• src/hg/makeDb/doc/encode3/tfbs.txt
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    1363e072831a0b48576d349379f32d1b9e5d5076 Wed Feb 5 12:32:52 2020 -0800
    Add user-friendly downloads file for TF Clusters. refs #24848
• src/hg/makeDb/doc/hg19.txt
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    4517be681f866a76adedd0aee1203b1028ff7511 Thu Feb 6 15:12:46 2020 -0800
    begin documentation for doseSensitivity track refs #24818
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    bbeaefa58e83db818c7e57f778510e1802aa32ea Thu Feb 6 15:17:34 2020 -0800
    add toUcsc.pl script refs #24818
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    9d63cc04f4da43dc2f454a55c1144b1604c29ab1 Thu Feb 6 15:23:56 2020 -0800
    add .as file and ftp location script refs #24818
• src/hg/makeDb/doc/wuhCor1/initialBuild.txt
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    196c636d851bf2cda5a0b8a5279fbb911e0fffa1 Tue Feb 4 15:39:59 2020 -0800
    cleaned up completed documentation refs #24851
• src/hg/makeDb/genbank/etc/hgwbeta.dbs
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    9d5c58b86d6c1fbf089e8c2294b762974d2f9a9a Wed Feb 5 15:59:24 2020 -0800
    Adding the wuhCor1 assembly to the hgwbeta.dbs file now that the assembly is on the beta, refs #24851
• src/hg/makeDb/genbank/etc/hgwdev.dbs
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    e8b50532cccbe1551681f7c378b475b3983a93cf Wed Feb 5 15:57:09 2020 -0800
    Adding the wuhCor1 assembly to hgwdev.dbs for the assembly release, refs #24851
• src/hg/makeDb/genbank/etc/rr.dbs
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    4c42a5d8cb28f0a4a6c2b4287f9454f03d105c7e Fri Feb 7 16:01:33 2020 -0800
    Adding wuhCor1 to the rr.dbs file now that it is released, refs #24851
• src/hg/makeDb/trackDb/human/avada.html
  • lines changed 4, context: html, text, full: html, text
    0cb3ed51ec356e4ace67ffd13690994fa022719e Mon Feb 10 09:34:27 2020 -0800
    Tweaking AVADA desc page in response to PI email no RM
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
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    6c4b557c5f49b0eb3a0ae813ce303ab5b3c70f90 Wed Feb 5 15:07:31 2020 -0800
    Fixing broken Problematic (heh) track in hg19 after settings options changed, refs #23365
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    ab5ee73ba548db44a6e6eb7a204c45c4144eb322 Thu Feb 6 15:47:09 2020 -0800
    trying the doseSensitivity as part of the ClinGen CNVs composite refs #24818
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    605b30da8394e16952523b94d16ebd44bcb32fbb Mon Feb 10 08:06:25 2020 -0800
    adding rmsk Hmmer track no redmine
• src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.html
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    baa003293f4696349ad054ea84feee19a374dc0d Fri Feb 7 17:31:31 2020 -0800
    Adding data access section to Encode refs #24847
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg.html
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    baa003293f4696349ad054ea84feee19a374dc0d Fri Feb 7 17:31:31 2020 -0800
    Adding data access section to Encode refs #24847
• src/hg/makeDb/trackDb/human/trackDb.geneHancer.ra
  • lines changed 2, context: html, text, full: html, text
    d07efced464a4cca97c51924f0c0814fc72fa6ec Wed Feb 5 13:21:29 2020 -0800
    Change mouseover on GeneHancer elements to show element type. refs #23903
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 32, context: html, text, full: html, text
    ab5ee73ba548db44a6e6eb7a204c45c4144eb322 Thu Feb 6 15:47:09 2020 -0800
    trying the doseSensitivity as part of the ClinGen CNVs composite refs #24818
• src/hg/makeDb/trackDb/refSeqComposite.html
  • lines changed 28, context: html, text, full: html, text
    88698eb950684dcb444901797b366a52cacb3f96 Thu Feb 6 15:44:35 2020 -0800
    Shortening longlabels to <80 char and removing views info, adding GTF, API info refs #24604
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    088d56b1cb6093896823dbd1bd1f7e93f46e1675 Fri Feb 7 16:24:11 2020 -0800
    Adding pennantIcon, removing antique documentation #24604
• src/hg/makeDb/trackDb/refSeqComposite.ra
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    88698eb950684dcb444901797b366a52cacb3f96 Thu Feb 6 15:44:35 2020 -0800
    Shortening longlabels to <80 char and removing views info, adding GTF, API info refs #24604
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    088d56b1cb6093896823dbd1bd1f7e93f46e1675 Fri Feb 7 16:24:11 2020 -0800
    Adding pennantIcon, removing antique documentation #24604
• src/hg/makeDb/trackDb/virus/wuhCor1/description.html
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    e95f882f90f7dcca6e8c9f36a1aec62b97cda977 Wed Feb 5 11:01:37 2020 -0800
    Removing the link to the NCBI BioSample ID since it does not exist, refs #24851
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    8f47c2e1f9c13682c59a0b4e9ed8fbd8feb3987a Thu Feb 6 13:15:29 2020 -0800
    Adding more external links for the wuhCor1 assemlby's gateway page, refs #24851
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    823e8e7d9b32c7917424adfaf0f0db2a2ab5f794 Fri Feb 7 16:14:09 2020 -0800
    Updating the links on the gateway page for wuhCor1, refs #24851
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra
  • lines changed 7, context: html, text, full: html, text
    674d93aa435c3f73f6e626dcbab70eec0ed2b3a6 Wed Feb 5 10:49:08 2020 -0800
    outlink to NCBI for ncbiGene and add search method refs #24851
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    b9bceb4f866d0d5058835fb4fde2270356e30e71 Wed Feb 5 17:06:57 2020 -0800
    Turning on the crisprAllTargets track by default for wuhCor1, refs #24851
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    f399ac0a36a8fbc7e6bd3c7e8892b895017a55d8 Fri Feb 7 08:56:40 2020 -0800
    Turning off the CRISPR track by default, refs #24851
• src/hg/makeDb/trackDb/zebrafish/danRer4/multiz7way.html
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    bb952990b39c750c3d3059bd2b859a834cd7d6ec Thu Feb 6 10:08:17 2020 -0800
    Updating redirected links found by the uiLinks cronjob, no Redmine
• src/hg/makeDb/trackDb/zebrafish/danRer4/rhMap.html
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    bb952990b39c750c3d3059bd2b859a834cd7d6ec Thu Feb 6 10:08:17 2020 -0800
    Updating redirected links found by the uiLinks cronjob, no Redmine
• src/hg/ratStuff/mafRc/expected/test1-rc.maf
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    a32f737bf8921c365afc2234e612e3b7b1507578 Sat Feb 8 12:24:01 2020 -0800
    create mafRc to reverse-completment MAF files
• src/hg/ratStuff/mafRc/expected/testHg16-rc.maf
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    a32f737bf8921c365afc2234e612e3b7b1507578 Sat Feb 8 12:24:01 2020 -0800
    create mafRc to reverse-completment MAF files
• src/hg/ratStuff/mafRc/mafRc.c
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    a32f737bf8921c365afc2234e612e3b7b1507578 Sat Feb 8 12:24:01 2020 -0800
    create mafRc to reverse-completment MAF files
• src/hg/ratStuff/mafRc/makefile
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    a32f737bf8921c365afc2234e612e3b7b1507578 Sat Feb 8 12:24:01 2020 -0800
    create mafRc to reverse-completment MAF files
• src/hg/ratStuff/makefile
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    a32f737bf8921c365afc2234e612e3b7b1507578 Sat Feb 8 12:24:01 2020 -0800
    create mafRc to reverse-completment MAF files
• src/hg/utils/archiveTracks.sh
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    ae5edd37c55752e0694c17530a5412701605f782 Mon Feb 3 13:51:03 2020 -0800
    Add a -c check option for archiveTracks.sh so you can check what would be backed up, feedback from BrianL
• src/hg/utils/automation/asmHubTrackDb.sh
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    dd27449e2ac4790137f84c232f6f3ff3f79e1556 Tue Feb 4 14:07:15 2020 -0800
    now using the new GCF FTP hierarchy layout refs #23891
• src/hg/utils/automation/doAssemblyHub.pl
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    dd27449e2ac4790137f84c232f6f3ff3f79e1556 Tue Feb 4 14:07:15 2020 -0800
    now using the new GCF FTP hierarchy layout refs #23891
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    ab2031dab96a23d652266a19f0fe12992304bd84 Thu Feb 6 16:53:56 2020 -0800
    warn only for liftUp not error out duplicates cause missing refs #23891
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    b9032792e3f2d0e704ecaf56b1fac45457acaa37 Fri Feb 7 14:54:23 2020 -0800
    eliminate : in chr names and correctly reading dup list where needed refs #23891
• src/hg/utils/automation/doNcbiRefSeq.pl
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    dd27449e2ac4790137f84c232f6f3ff3f79e1556 Tue Feb 4 14:07:15 2020 -0800
    now using the new GCF FTP hierarchy layout refs #23891
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    4513440c373f2ba57b4d28910e832b4dc85108f5 Thu Feb 6 16:53:25 2020 -0800
    warn only for liftUp not error out duplicates cause missing refs #23891
• src/utils/qa/weeklybld/buildEnv.csh
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    5d0c599ded777f232aa8bd0d29d5e8161c2e6661 Mon Feb 10 10:04:37 2020 -0800
    v394 preview2, refs #24908

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• files changed: 86