All File Changes

v425_preview2 to v425_base (2021-12-20 to 2022-01-10) v425

• confs/hgwdev.hg.conf
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    76ce670ad4e6ea4a359a5c354cfe72cfbd8bcf03 Sun Jan 2 01:11:33 2022 -0800
    Installing updated hg.conf files from UCSC servers
• src/hg/cgilib/tests/expected/annoGrator/gpFx.txt
  • lines changed 41, context: html, text, full: html, text
    2bae96e80097649d2db3657dc818656a3a9fd633 Fri Jan 7 09:29:30 2022 -0800
    rewind annogrator expected test results to use the ancient version of ucsc genes
• src/hg/cgilib/tests/expected/annoGrator/pgSnpKgDbToGpFx.txt
  • lines changed 87, context: html, text, full: html, text
    2bae96e80097649d2db3657dc818656a3a9fd633 Fri Jan 7 09:29:30 2022 -0800
    rewind annogrator expected test results to use the ancient version of ucsc genes
• src/hg/cgilib/tests/expected/annoGrator/pgSnpKgDbToTabOutShort.txt
  • lines changed 10, context: html, text, full: html, text
    2bae96e80097649d2db3657dc818656a3a9fd633 Fri Jan 7 09:29:30 2022 -0800
    rewind annogrator expected test results to use the ancient version of ucsc genes
• src/hg/hgPhyloPlace/treeToAuspiceJson.c
  • lines changed 35, context: html, text, full: html, text
    1ab96609fb58d6c6053425989043e9e7c5dd9f99 Mon Jan 10 08:56:42 2022 -0800
    Update Nextstrain clade names and color spectrum in Auspice JSON output.
• src/hg/hgc/facetedBar.c
  • lines changed 1, context: html, text, full: html, text
    c9cbc02d602f92f2a1175a2e2666d9626f2d991c Tue Jan 4 13:20:24 2022 -0800
    Making it show 7 items per facet before unfolding rather than 6, so as to be consistent with hgTrackUi.
• src/hg/htdocs/FAQ/FAQformat.html
  • lines changed 4, context: html, text, full: html, text
    9566841ff621a05a0c72f23625bf109d8405514d Mon Dec 27 16:03:24 2021 -0800
    Moving down the widget include so htmlCheck is happy, refs #28034
• src/hg/htdocs/FAQ/FAQmaillist.html
  • lines changed 14, context: html, text, full: html, text
    c0d4c0101b2624c34e39d4eab46da587f36dd1f8 Tue Dec 28 09:52:32 2021 -0800
    Adding a FAQ about the Track Hub Mailing List refs #27878
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    f15af1bc1d0e1230dc5f681bf3104c0caef6702d Tue Dec 28 09:58:58 2021 -0800
    Adding a link to the genome-mirror mailing list archives on FAQmaillist.html
• src/hg/htdocs/FAQ/FAQreleases.html
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    52366a76db92bb37d90bd4a941686685185558ee Mon Dec 27 10:39:34 2021 -0800
    Adding a link to GenArk Blog posts from FAQ about finding assemblies
• src/hg/htdocs/FAQ/index.html
  • lines changed 4, context: html, text, full: html, text
    9566841ff621a05a0c72f23625bf109d8405514d Mon Dec 27 16:03:24 2021 -0800
    Moving down the widget include so htmlCheck is happy, refs #28034
• src/hg/htdocs/contacts.html
  • lines changed 23, context: html, text, full: html, text
    82dfe7f55138b1deb289f23b0ef470d9d1a8367e Mon Dec 27 14:15:30 2021 -0800
    Adding a Track Hub mailing list entry on the Contact Us page refs #27878
  • lines changed 4, context: html, text, full: html, text
    9566841ff621a05a0c72f23625bf109d8405514d Mon Dec 27 16:03:24 2021 -0800
    Moving down the widget include so htmlCheck is happy, refs #28034
• src/hg/htdocs/goldenPath/help/hgTracksHelp.html
  • lines changed 4, context: html, text, full: html, text
    9566841ff621a05a0c72f23625bf109d8405514d Mon Dec 27 16:03:24 2021 -0800
    Moving down the widget include so htmlCheck is happy, refs #28034
• src/hg/htdocs/goldenPath/help/query.html
  • lines changed 24, context: html, text, full: html, text
    21f0ab2df4174e7897add1f68b87226954fd0945 Wed Dec 29 09:30:16 2021 -0800
    Added some identifiers to the Sample queries list, refs #28588
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    f747cb35b9ea0e5a78aa07fbc87c81a79cb3bfaf Mon Jan 3 05:29:27 2022 -0800
    updating hgvs query example desc, refs #28588
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    41a33c5c70f4d253723b6dd09404329bb80030a7 Mon Jan 3 14:36:30 2022 -0800
    Adding a fixed column width for query refs #28588
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    e1ba1311138c92cc9c93e2bb5f08c303e79e1eeb Tue Jan 4 09:12:50 2022 -0800
    Updated the wording of my previous query entries, refs #28588
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 11, context: html, text, full: html, text
    3ed7433ed047d87cf875bfb8e0391dbe8e4b06f3 Mon Dec 20 15:03:03 2021 -0800
    Adding news announcement about 3rd GenArk blog post refs #27990
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    6555c07c46923b7bc97b960093312de9130c3369 Wed Dec 22 12:36:38 2021 -0800
    added link to top of 2021. combined 2001 and 2002 links to keep columns balanced. Refs #28570
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    e781406b15b673238b9464eb0cc4ab68fe5958ba Wed Dec 22 12:39:35 2021 -0800
    removed anchor for year-end that got left bejhind in october. Refs #28580
• src/hg/htdocs/inc/gbPageStartHardcoded.html
  • lines changed 1, context: html, text, full: html, text
    626b7dbf428411bf7e5c04b666ea8ffc7a9c76b4 Mon Dec 27 13:08:56 2021 -0800
    Putting link Contact Us back under menu About Us, removed by 12c7c561
• src/hg/htdocs/inc/globalNavBar.inc
  • lines changed 1, context: html, text, full: html, text
    626b7dbf428411bf7e5c04b666ea8ffc7a9c76b4 Mon Dec 27 13:08:56 2021 -0800
    Putting link Contact Us back under menu About Us, removed by 12c7c561
• src/hg/htdocs/inc/recTrackSets.hg19.tab
  • lines changed 1, context: html, text, full: html, text
    511fbd283db6b034fdfa80458b15d577ca77d8b5 Tue Jan 4 17:16:58 2022 -0800
    Adding new RTS for problematic regions, refs #28707
• src/hg/htdocs/indexNews.html
  • lines changed 11, context: html, text, full: html, text
    3ed7433ed047d87cf875bfb8e0391dbe8e4b06f3 Mon Dec 20 15:03:03 2021 -0800
    Adding news announcement about 3rd GenArk blog post refs #27990
• src/hg/htdocs/training/index.html
  • lines changed 1, context: html, text, full: html, text
    7e865a52c3b943cea1156b14adaa293f7a5dfe35 Tue Dec 21 09:56:31 2021 -0800
    rephrased a section header
• src/hg/inc/versionInfo.h
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    1d27cd7fb6e35a4328ee06a73f1a5b0821956b81 Mon Jan 10 10:35:20 2022 -0800
    New version number v425
• src/hg/lib/cart.c
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    b5b728962504fdcb8db437f2b3d209557cbbc318 Wed Jan 5 06:17:50 2022 -0800
    Removing incognito mode entirely, as feature turned out too complicated for little value, refs #28520
• src/hg/lib/tablesTables.c
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    4cfe50ad2c533ab2b51e09dd1c50dc422c59223d Tue Jan 4 13:21:24 2022 -0800
    Only show the number by the merge if not all are being merged
• src/hg/lib/tests/expected/hgvs/clinVarHgvs.txt
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    cc4e71ba07ac0df9f1f108834ae80ab8f2fceb73 Wed Dec 22 13:05:05 2021 -0800
    Repairing test - PHB on hg38 now has the symbol PHB1, no ticket
• src/hg/lib/tests/input/hgvs/clinVarHgvs.txt
  • lines changed 1, context: html, text, full: html, text
    cc4e71ba07ac0df9f1f108834ae80ab8f2fceb73 Wed Dec 22 13:05:05 2021 -0800
    Repairing test - PHB on hg38 now has the symbol PHB1, no ticket
• src/hg/logCrawl/dbTrackAndSearchUsage/generateSearchUse.py
  • lines changed 3, context: html, text, full: html, text
    20f3ae78bc51d736e9785a99a8509077cf409eb5 Mon Dec 20 13:44:24 2021 -0800
    Get search term log miner to correctly handle non-ascii user input
• src/hg/makeDb/doc/asmHubs/hgdownload.index.html
  • lines changed 30, context: html, text, full: html, text
    571d56486794183897e7eb88719fe1025d1ea442 Mon Dec 20 21:32:19 2021 -0800
    up to date with zoonomia added no redmine
• src/hg/makeDb/doc/asmHubs/lastzRuns.txt
  • lines changed 321, context: html, text, full: html, text
    0f63b81106ac90c3e8b459a7b56cfea702ca6bce Tue Dec 21 13:02:11 2021 -0800
    sheep GCF_016772045.1 vs. oviAri3(/4)(sheep GCF_002742125.1) lastz/chain/net run for user, refs #28648
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    8e4313e37e6c53753fcc42e5d068b05250db629b Wed Dec 22 11:53:51 2021 -0800
    sheep GCF_002742125.1 vs. mm39 lastz/chain/net run for user, refs #28668
• src/hg/makeDb/doc/asmHubs/master.run.list
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    ce6a8cb8e1eeaa44acef44a163feb17db12bea17 Fri Dec 31 11:09:54 2021 -0800
    updating a couple new primate assemblies no redmine
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    9f169d8c921625fb5f806420dbda13524b8c4f85 Fri Dec 31 21:34:31 2021 -0800
    adding new mammals and fish no redmine
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    538e939377d7a736914c2a1cdce300a0a0b8b06a Sat Jan 1 15:47:22 2022 -0800
    adding 11 new fungi no redmine
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    2f1373c09ad0c6ba9067e58717dd31aeee05c576 Tue Jan 4 21:03:39 2022 -0800
    adding 21 new invertebrates no redmine
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    9719e1a0ead12c9fa95a82d0f1e1a119f3fdbcc1 Tue Jan 4 21:04:33 2022 -0800
    adding 6 new plants no redmine
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    97e0b5f2881c91ae5dbc87f6eea3e19993545d09 Thu Jan 6 14:07:36 2022 -0800
    adding a second very large wheat genome no redmine
• src/hg/makeDb/doc/asmHubs/mkAsmStats.pl
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    1aa2bfd8c15486f23f6efeec5f4358f366cfad53 Wed Dec 29 12:45:41 2021 -0800
    updated scripts to tolerate database assemblies in the listings no redmine
• src/hg/makeDb/doc/asmHubs/mkGenomes.pl
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    d79d3e1568e732852f341062f1604b7484572d8f Mon Dec 20 21:27:53 2021 -0800
    now using fully qualified domain name to dynablat-01 refs #28654
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    1aa2bfd8c15486f23f6efeec5f4358f366cfad53 Wed Dec 29 12:45:41 2021 -0800
    updated scripts to tolerate database assemblies in the listings no redmine
• src/hg/makeDb/doc/asmHubs/mkHubIndex.pl
  • lines changed 68, context: html, text, full: html, text
    1aa2bfd8c15486f23f6efeec5f4358f366cfad53 Wed Dec 29 12:45:41 2021 -0800
    updated scripts to tolerate database assemblies in the listings no redmine
• src/hg/makeDb/doc/asmHubs/mkSendList.pl
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    1aa2bfd8c15486f23f6efeec5f4358f366cfad53 Wed Dec 29 12:45:41 2021 -0800
    updated scripts to tolerate database assemblies in the listings no redmine
• src/hg/makeDb/doc/asmHubs/mkSymLinks.pl
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    1aa2bfd8c15486f23f6efeec5f4358f366cfad53 Wed Dec 29 12:45:41 2021 -0800
    updated scripts to tolerate database assemblies in the listings no redmine
• src/hg/makeDb/doc/asmHubs/runBuild
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    efcb7334402bd922fa514a2b967ffa3843dd02db Wed Dec 22 09:17:04 2021 -0800
    adding fungi and specifics for augustus species and rmskSpecies no redmine
• src/hg/makeDb/doc/asmHubs/sendToHgdownload.sh
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    7709543f2b32e708d9c9f39334d452d6c52482f6 Wed Dec 29 12:46:40 2021 -0800
    temporarily turn off push to dynablat machine until more disk space is obtained no redmine
• src/hg/makeDb/doc/asmHubs/trackData.pl
  • lines changed 159, context: html, text, full: html, text
    1aa2bfd8c15486f23f6efeec5f4358f366cfad53 Wed Dec 29 12:45:41 2021 -0800
    updated scripts to tolerate database assemblies in the listings no redmine
• src/hg/makeDb/doc/asmHubs/verifyOnDownload.sh
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    d7d1c06cce94bfb5abced6d45f2f6ad3e2dbd2db Wed Dec 29 12:47:26 2021 -0800
    updated scripts to tolerate database assemblies in the listings no redmine
• src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv
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    7c4e6702ec1521e9ec6808dcd201cb8b80e44693 Fri Dec 31 21:32:21 2021 -0800
    adding five new fish no redmine
• src/hg/makeDb/doc/fungiAsmHub/fungi.orderList.tsv
  • lines changed 12, context: html, text, full: html, text
    b9b0a57e12ac267d701445d9f738f23e2edfa30f Sat Jan 1 15:53:16 2022 -0800
    adding 11 new fungi no redmine
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
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    a6478f571b96b1f4c65eb6c10e9750063d58d9df Thu Jan 6 14:09:20 2022 -0800
    adding new invertebrate assemblies no redmine
• src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv
  • lines changed 53, context: html, text, full: html, text
    cf8389dd02c2c67d1424737f932db4c8b53efd12 Mon Dec 20 15:26:34 2021 -0800
    adding in a number of mammal assemblies from the Zoonomia project most already outdated by same assembly in mammals hub no redmind
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    ce6a8cb8e1eeaa44acef44a163feb17db12bea17 Fri Dec 31 11:09:54 2021 -0800
    updating a couple new primate assemblies no redmine
  • lines changed 2, context: html, text, full: html, text
    42baee4d6187208718981a8cd42d699fe7e34a73 Fri Dec 31 22:07:56 2021 -0800
    a couple outdated mammal assemblies no redmine
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    8a4f3a1b26c3cbba02413ad0c16f9d0a6d2d4c62 Thu Jan 6 14:10:01 2022 -0800
    a couple of plant assemblies aged out no redmine
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
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    5beab349a3b593b600526dd7445c63ebff31d13b Mon Dec 20 21:29:24 2021 -0800
    adding many new hubs for Zoonomia 241-way no redmine
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    3d845ef5b4ab847b7d2b6770f10af29023b09760 Thu Jan 6 14:11:12 2022 -0800
    catching up a few new mammal assemblies no redmine
• src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv
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    6988d80500be7cd9ea274ef1a70b732c37e655c7 Thu Jan 6 14:08:26 2022 -0800
    adding a few new plant assemblies no redmine
• src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv
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    ce6a8cb8e1eeaa44acef44a163feb17db12bea17 Fri Dec 31 11:09:54 2021 -0800
    updating a couple new primate assemblies no redmine
• src/hg/makeDb/doc/zoonomiaAsmHub/zoo241.asmId.sciName.tsv
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    2057fe2ab96405f0107a695de71fa9ea1427b0ec Mon Dec 20 18:34:55 2021 -0800
    recording the translation list no redmine
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    110e0750597f5a80bd93e9bea4312428d9f92182 Wed Dec 29 13:00:08 2021 -0800
    updated to use assembly hubs that do not have database assemblies on the RR no redmine
• src/hg/makeDb/doc/zoonomiaAsmHub/zoonomia.orderList.tsv
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    2d7985fc8afa371efe6ea26acef924216383bd18 Wed Dec 29 12:43:15 2021 -0800
    best correspondence list for all hubs now complete no redmine
• src/hg/makeDb/trackDb/crispr10K.ra
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    7f7100b2f8b8bcd30cae3b9f6003921a0fe697a6 Thu Dec 30 09:54:40 2021 -0800
    crispor.org is broken, use original URL crispor.tefor.net, no redmine
• src/hg/makeDb/trackDb/crisprAll.ra
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    7f7100b2f8b8bcd30cae3b9f6003921a0fe697a6 Thu Dec 30 09:54:40 2021 -0800
    crispor.org is broken, use original URL crispor.tefor.net, no redmine
• src/hg/makeDb/trackDb/human/hg19/trackDb.gnomad.alpha.ra
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    a3b734b314b55f1f78052cf0d0fd91e107f13988 Mon Jan 3 14:59:05 2022 -0800
    Staging fixed gnomAD v2.1.1 track on hg19, refs #28666
• src/hg/makeDb/trackDb/human/hg38/hippocampusAyhan.ra
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    9bd28250f857bd08f2359488cd0116393317b91a Tue Dec 21 12:00:50 2021 -0800
    First cut at parallelizing this. It's going about 3x as fast.
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    043555f1c6f76c2ae2f64a9bac67e21cf5c013f2 Tue Dec 21 14:15:55 2021 -0800
    Adding toothKrivaneck and hippocampusAyhan datasets.
• src/hg/makeDb/trackDb/human/hg38/singleCellMerged.html
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    024b985abff094bf56f3a801de99feca2de48534 Wed Dec 22 16:19:08 2021 -0800
    Second (first meaningful) cut at details html page for singleCellMerged.
• src/hg/makeDb/trackDb/human/hg38/tabulaSapiens.ra
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    67959d02e8546bdfb67db4f45b93fc33e2404281 Thu Dec 23 09:18:12 2021 -0800
    Fixing broken trackDb build from a fault commit, refs build email
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    1a9a95aaa060347e603599778834cfb48cb00f2d Fri Dec 24 12:52:04 2021 -0800
    Getting rid of unused tracks again.
• src/hg/makeDb/trackDb/human/hg38/toothKrivanek.ra
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    9bd28250f857bd08f2359488cd0116393317b91a Tue Dec 21 12:00:50 2021 -0800
    First cut at parallelizing this. It's going about 3x as fast.
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    043555f1c6f76c2ae2f64a9bac67e21cf5c013f2 Tue Dec 21 14:15:55 2021 -0800
    Adding toothKrivaneck and hippocampusAyhan datasets.
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
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    043555f1c6f76c2ae2f64a9bac67e21cf5c013f2 Tue Dec 21 14:15:55 2021 -0800
    Adding toothKrivaneck and hippocampusAyhan datasets.
• src/hg/makeDb/trackDb/mouse/mm10/tabulaMurisSenis.ra
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    90c9cf6af590a7936f3d0522c39716016e5c4f1e Wed Dec 22 21:35:18 2021 -0800
    Making both droplet and facs arms have facets_usual and facets_details views that are both mergable. Cleaned up other relics of pre-mergable tracks from /gbdb.
• src/hg/makeDb/trackDb/trackDb.ra
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    7f7100b2f8b8bcd30cae3b9f6003921a0fe697a6 Thu Dec 30 09:54:40 2021 -0800
    crispor.org is broken, use original URL crispor.tefor.net, no redmine
• src/hg/utils/automation/doAssemblyHub.pl
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    c2d8f10c6d0ce5ebb68e8a76c5d9a2e94ab3dcd8 Tue Dec 28 15:51:34 2021 -0800
    correct ncbiGene procedure and correctly run up unplaced contig assembly when no AGP present no redmine
• src/hg/utils/hubCheck/tests/expected/manyErrors.output.txt
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    130f56eedb67b1614ae7e40564051df1f30efb87 Wed Dec 22 08:47:05 2021 -0800
    Fixing expected test results for hubCheck after some changes to lib/https.c warning messages
• src/hg/utils/otto/sarscov2phylo/getCogUk.sh
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    5b376b2547f4a5018823202b0379aad6a5d06c69 Wed Dec 15 19:27:39 2021 -0800
    The latest nextclade adds quotes around names with spaces; strip those out.
• src/hg/utils/otto/sarscov2phylo/getNcbi.sh
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    5b376b2547f4a5018823202b0379aad6a5d06c69 Wed Dec 15 19:27:39 2021 -0800
    The latest nextclade adds quotes around names with spaces; strip those out.
• src/hg/utils/otto/sarscov2phylo/maskDelta.sh
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    1715fcf5e6c59c033d9f6dfb341e62b1f1b7c629 Tue Dec 7 18:38:36 2021 -0800
    Mask 21846 (S:95) in Delta branch - Cornelius Roemer and Chris Ruis pointed out phylogeny problems it caused.
• src/hg/utils/otto/sarscov2phylo/nextstrain.clade-mutations.tsv
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    f19f9a980f4876f0f26668aa121b59c4ab32a046 Wed Dec 15 19:28:21 2021 -0800
    Tweak 21K (BA.1) and add 21L (BA.2).
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    922009dcce8772c595c868e9d4377d2b12e183da Tue Jan 4 12:08:24 2022 -0800
    Add Omicron label to 21L, add 21M.
• src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv
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    96069858e15c4e236ad4a3645d5a8c6e6ded14d0 Sat Dec 4 19:58:00 2021 -0800
    Mask out C21846T in AY lineages because we're masking 21846 (S:95) in Delta now. Remove AY.9.1 (pango-designation v1.2.104). Fix multiple appearances of 19563 in AY.34.2 path.
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    751eaf324fd6a2759f7771387f353fedb07be52c Mon Dec 6 19:49:28 2021 -0800
    Add new lineages defined in pango-designation release v1.2.105.
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    10670fc04382aaae97374b9a9a4b88c718a3d94f Tue Dec 7 18:36:52 2021 -0800
    Broaden B.1.1.529 and add new sublineages BA.1 (Omicron) and BA.2 ("outlier"/"stealth"/"Decepticron") - pango-designation v1.2.106
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    7ac562b0f61603e3c18438fde92cbe6dea73491a Thu Dec 9 19:26:28 2021 -0800
    Adjusted B.1.1.529, BA.1 and BA.2 after some more pruning/opt/adding. Added AY.124.1, B.1.637.1, B.1.640.{1,2}, renamed AY.97 to AY.5.5 - pango-designation v1.2.108.
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    cd5a3614ba723e948f1631538ab8c90b69959bda Tue Dec 14 11:59:51 2021 -0800
    Mask spurious SNVs at the deletion site found in in Alpha, Beta, Gamma and Omicron. One more tweak to BA.2. Add AY.26.1, AY.122.2; broaden AY.112 and rename old AY.112 to AY.112.1 - pango-designation v1.2.109
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    7114f0d248dde6e60e345364c1da2ec7898accb8 Tue Dec 14 12:28:45 2021 -0800
    Added AY.9.2.2, AY.119.2, AY.4.7, AY.4.8, AY.39.1.2 - pango-designation v1.2.110
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    03ea36ac4bf82b4a87a16a63c34988622e4107ea Tue Dec 14 13:00:18 2021 -0800
    Added AY.128, AY.3.2, AY.43.6, AY.102.1, AY.129, P.1.7.1; broadened AY.25.1, renamed old AY.25.1 to AY.25.1.1 - pango-designation v1.2.111
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    0a52c287f522cbe635e9479e62500b5f565fc381 Tue Dec 14 14:39:40 2021 -0800
    Added BA.3 - pango-designation v1.2.112
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    b49e29d1c9fc2d131e44db1f6f3a742367e8626b Tue Dec 14 17:50:54 2021 -0800
    Add mutations for a few lineages, and tweaking a couple existing ones, to resolve some problems turned up in a comparison between our tree's calls and pango-designation/lineages.csv.
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    ed3af61805a008c200e1f22bede2e7c69a40c4e2 Wed Dec 15 19:26:16 2021 -0800
    More B.1.1.529-tweaking
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    3cdaf3294040294806097ce9d2180f6ea0161056 Thu Dec 16 10:16:33 2021 -0800
    Since masking of 21846 (S:95) in Delta, AY.115 and AY.116 are identical, and whichever is assigned the node first in matUtils annotate wins -- not good. This hasn't been released in pango-designation yet, but since there is already an AY.116.1, AY.115 will be merged into AY.116. Make that change now so we don't produce stochastic output in the meantime.
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    5ec77175f8532e474133e5653257f4878c1e011f Wed Dec 22 15:20:28 2021 -0800
    Forgot to mask several mutations in pango-masked regions in recent new lineages. Another tweak to BA.2 mutations as nodes keep hopping around with new noisy sequences.
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    7685bc792fc8a65570eeb2e24d414a8deaf0958c Tue Jan 4 12:09:38 2022 -0800
    Add some more masked mutations to B.1.1.529 path as new sequences continue to shift around early nodes.
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    bc397b4e29e995996ef9e7f9b2f81c4e6e95002c Tue Jan 4 15:58:52 2022 -0800
    Added BB.1, BB.2, AY.102.2, AY.42.1, AY.39.1.3, AY.130 - pango-designation v1.2.113
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    1ec1f2c96c1afaedea7133c32ff179d19f9c9e09 Tue Jan 4 17:15:17 2022 -0800
    Added AY.127.1, AY.123.1, AY.3.3, AY.46.6.1, AY.33.1 and AY.122.3 - pango-designation v1.2.114
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    d74fcd0feaadd46e7042be0fe1b264a217e7f7e8 Tue Jan 4 17:35:02 2022 -0800
    Added P.1.12.1 - pango-designation v1.2.115
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    25ebd73c41dae62a2a53730e21a619a313b3ca2c Tue Jan 4 17:49:02 2022 -0800
    Added AY.131 - pango-designation v1.2.116
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    8613d8975c3f842db4516d6e127e1a7dd067f71c Tue Jan 4 19:16:05 2022 -0800
    Added AY.4.9 and AY.4.10 - pango-designation v1.2.117
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    a3a2f15ee359565a285a1706f2efe3e41e37d851 Tue Jan 4 19:39:34 2022 -0800
    Added AY.43.7 - pango-designation v1.2.118
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    71bc760d1659f6d6f77ee7ab37f3b1da25d39f93 Tue Jan 4 20:00:48 2022 -0800
    Added AY.132 - pango-designation v1.2.119
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    a7b34fd66d5f96b1fd1c78ff6d1d15b9009cd0a9 Tue Jan 4 20:24:53 2022 -0800
    Added AY.133 - pango-designation v1.2.120 [note: v1.2.121 is just an init.py tweak, no lineage changes]
• src/hg/utils/pslToBigPsl/pslToBigPsl.c
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    e9c1e6b69045a4987f9b1107a5c7ecfcecd8fedf Fri Dec 24 09:33:48 2021 -0800
    do not SEGV on an empty PSL file
• src/inc/srcVersion.h
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    1d27cd7fb6e35a4328ee06a73f1a5b0821956b81 Mon Jan 10 10:35:20 2022 -0800
    New version number v425
• src/lib/https.c
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    dd73399f02fbee0158f6290d292ff1b791e5a2ab Mon Dec 20 22:03:54 2021 -0800
    Adding 2 more domains to the https whitelist
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    a897b8f02645405630003683633d76b6058866e4 Tue Dec 21 23:15:54 2021 -0800
    Adding ability to pass the hostName for logging since self-signed certs sometimes just say localhost and certs with wildcards and multiple hosts also do not tell you exactly which specific host is being used, so now we will know it.
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    bd836d6e847a400c1c8b094c389f61b2f0225bd0 Tue Dec 21 23:38:21 2021 -0800
    Re-arranging initDomainWhiteListHash() to be called by openSslInit() which is better and simpler.
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    a35f8c4d07fb3fac7cfce9c39ce5eed3445415c9 Tue Dec 21 23:47:43 2021 -0800
    Adding some more hostNames to the whitelist for https.c
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    cb5eba1bd7083ea105d91f0e85ce929c37eb73db Wed Jan 5 00:59:47 2022 -0800
    Adding more domains found in CGI logs for the https cert whitelist.
• src/lib/strex.c
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    c01f112aa3087b09f57757246028b93babb2c335 Tue Dec 21 14:10:25 2021 -0800
    Adding new built-in function lookup(string, twoColFile)
• src/lib/strex.doc
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    c9199234bbc31055553ff6303cdaf338bc647f3a Tue Dec 21 14:09:19 2021 -0800
    Fixing typo and documenting new lookup function
• src/product/installer/browserSetup.sh
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    b4bf54cd20fd2d7cf9cd4cc0850e5bd0da714456 Mon Jan 3 07:34:55 2022 -0800
    making sure that success in GBIC does not return non-zero error code, refs #28585
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    4b11c0d2ac51d9055146f415ff9431a9f8d6f026 Tue Jan 4 06:52:03 2022 -0800
    fixing obscure bug in GBIC only visible when re-running the script during debuggin, refs #28585
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    82e124d638bd74bc879bbf919232ecfb21aa2405 Tue Jan 4 08:38:31 2022 -0800
    Updating Dockerfile to Ubuntu 20. This brought up a small bug in GBIC which is fixed now. Also updating the Dockerfile docs. Next step is to build the image on hgwdev with the build and upload the image to Docker hub. refs #28585 and hopefully a new ticket at some point for better Docker support.
• src/product/installer/docker/Dockerfile
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    32e386b71d390a00a3956422f0be6ba6afc321ae Mon Jan 3 07:31:20 2022 -0800
    Improving docker docs and dockerfile, refs #28585
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    be2a07a52c2b582b1fc88c1b5c36ca575500a06c Tue Jan 4 02:31:44 2022 -0800
    fixing dockerfile because phusion seems to use mariadb now, not mysql anymore, refs #28585
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    82e124d638bd74bc879bbf919232ecfb21aa2405 Tue Jan 4 08:38:31 2022 -0800
    Updating Dockerfile to Ubuntu 20. This brought up a small bug in GBIC which is fixed now. Also updating the Dockerfile docs. Next step is to build the image on hgwdev with the build and upload the image to Docker hub. refs #28585 and hopefully a new ticket at some point for better Docker support.
• src/product/installer/docker/README.md
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    32e386b71d390a00a3956422f0be6ba6afc321ae Mon Jan 3 07:31:20 2022 -0800
    Improving docker docs and dockerfile, refs #28585
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    82e124d638bd74bc879bbf919232ecfb21aa2405 Tue Jan 4 08:38:31 2022 -0800
    Updating Dockerfile to Ubuntu 20. This brought up a small bug in GBIC which is fixed now. Also updating the Dockerfile docs. Next step is to build the image on hgwdev with the build and upload the image to Docker hub. refs #28585 and hopefully a new ticket at some point for better Docker support.
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    6c9893e46ce4e4c0e9f256c17081f2f9a21c5156 Wed Jan 5 03:33:56 2022 -0800
    typo in docker readme, no redmine
• src/utils/matrixClusterColumns/matrixClusterColumns.c
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    9bd28250f857bd08f2359488cd0116393317b91a Tue Dec 21 12:00:50 2021 -0800
    First cut at parallelizing this. It's going about 3x as fast.
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    92f77f7bef111331d3c88d14cf98ef2e64c765f8 Tue Dec 21 12:06:48 2021 -0800
    Improved a structure name and removed some debugging. Added some comments.
• src/utils/matrixClusterColumns/speed_notes
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    fee62066b22cf401cc44c8d012b165bc89466d69 Tue Dec 21 14:12:12 2021 -0800
    Just adding some testing notes on speed that record observation parallelization is about 2x as fast on gzipped input, 3x on ungzipped input.
• src/utils/matrixNormalize/tests/makefile
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    22de080373a21b6d801ba6c58d664db3a912e901 Mon Dec 20 13:41:45 2021 -0800
    Adding clean target to matrixNormalize makefile so top of the tree make clean runs
• src/utils/qa/weeklybld/buildEnv.csh
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    dca703d8eaf8665b5bdfd605bf05ee04b1edc326 Mon Jan 10 10:33:22 2022 -0800
    v425 final build, refs #28625

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