All File Changes

v414_preview to v414_preview2 (2021-04-19 to 2021-04-26) v414

• README
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    fbf84e8ee87a23d03cd554a6979b809873ce2022 Fri Apr 23 18:20:46 2021 -0700
    dummy test , added one line to end. Testing git.
• confs/asia.hg.conf
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    1bbaebad5f5f2e65424a52993f475907447344e9 Sun Apr 25 01:11:43 2021 -0700
    Installing updated hg.conf files from UCSC servers
• confs/euro.hg.conf
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    1bbaebad5f5f2e65424a52993f475907447344e9 Sun Apr 25 01:11:43 2021 -0700
    Installing updated hg.conf files from UCSC servers
• confs/hgwbeta.hg.conf
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    1bbaebad5f5f2e65424a52993f475907447344e9 Sun Apr 25 01:11:43 2021 -0700
    Installing updated hg.conf files from UCSC servers
• confs/rr.hg.conf
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    1bbaebad5f5f2e65424a52993f475907447344e9 Sun Apr 25 01:11:43 2021 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/hgTracks/barChartTrack.c
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    5cf8fec12cc427c0db2889430ea1758dbb7e7087 Tue Feb 9 09:42:18 2021 -0800
    Clipping mark of a magenta stripe at top had got lost, I brought it back.
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    6a7d8c49fb6f2af3b1e24e3d82b76a4068807c2e Wed Feb 10 08:51:43 2021 -0800
    Restored space between bars when zoomed close enough.
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    51d3b8b7b18d2dfc1093a30ef925c97ce8f6b129 Tue Apr 20 15:52:05 2021 -0700
    Commenting the extras structure a little and adding stretchToItem set from trackDb barChartStretchToItem to it. This puts the stretching control under this option, which is off by default for backwards compatibility.
• src/hg/hgTracks/cds.c
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    a35c9adcf9ff3f456c3c6255e3e3fd47d1403f00 Wed Apr 21 20:13:40 2021 -0700
    Check for bigPsl inside getPslCds, so all callers don't have to check first. refs #27312 (Jairo reported bug in note 24)
• src/hg/hgTracks/simpleTracks.c
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    0422c3f37bccbc6aeb2be0b7c6f4f12700601518 Tue Apr 20 08:45:29 2021 -0700
    fixing after code review, refs #27399
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    f29792f0ae08378ca0a90c182525c9fe11011236 Tue Apr 20 08:46:06 2021 -0700
    fixing more after code review, refs #27399
• src/hg/hgc/hgc.c
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    be53362ee8a8222e6a5f8c2fdcdde93b08f337d8 Mon Apr 19 12:12:47 2021 -0700
    remove dependency on global tdb in BigPslAli routines
• src/hg/htdocs/covid19.html
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    cbfd50c1a2cd2caa73d6d48878a2d633dac02a8b Wed Apr 21 10:08:18 2021 -0700
    Addig article about Angie refs #27419
• src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html
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    d308fe7147b78ac8c4e5344c797ccab3f60ef07d Tue Apr 20 12:22:44 2021 -0700
    grammar nit
• src/hg/htdocs/goldenPath/help/multiRegionHelp.html
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    3ee43997901d9226d78f052f521fdaa69c2c2975 Mon Apr 19 17:06:56 2021 -0700
    Updating doc images for MR change, deleting old files too refs #26385
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.html
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    8ebd9d16c2d2055361cc0a5775a32b9ecc25b63c Fri Apr 23 11:49:34 2021 -0700
    Setting the v2 date for trackDbHub back-in-time with git checkout c8b2bf8f976f trackDbHub.v2.html, this corresponds to saying we versioned the doc in the Progress Report before adding bigLolly and vcfPhasedTrio type and allows for changes with Ensembl collaboration refs #26598
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v2.html
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    8ebd9d16c2d2055361cc0a5775a32b9ecc25b63c Fri Apr 23 11:49:34 2021 -0700
    Setting the v2 date for trackDbHub back-in-time with git checkout c8b2bf8f976f trackDbHub.v2.html, this corresponds to saying we versioned the doc in the Progress Report before adding bigLolly and vcfPhasedTrio type and allows for changes with Ensembl collaboration refs #26598
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html
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    8ebd9d16c2d2055361cc0a5775a32b9ecc25b63c Fri Apr 23 11:49:34 2021 -0700
    Setting the v2 date for trackDbHub back-in-time with git checkout c8b2bf8f976f trackDbHub.v2.html, this corresponds to saying we versioned the doc in the Progress Report before adding bigLolly and vcfPhasedTrio type and allows for changes with Ensembl collaboration refs #26598
• src/hg/htdocs/goldenPath/newsarch.html
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    781a03a65743abf875b6eb0398a228ea47187670 Tue Apr 20 11:41:54 2021 -0700
    Fixing a minor typo from code review, refs #27398
• src/hg/htdocs/images/MultiRegionButton.png
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    3ee43997901d9226d78f052f521fdaa69c2c2975 Mon Apr 19 17:06:56 2021 -0700
    Updating doc images for MR change, deleting old files too refs #26385
• src/hg/htdocs/images/MultiRegionConfigurationWindow2.png
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    3ee43997901d9226d78f052f521fdaa69c2c2975 Mon Apr 19 17:06:56 2021 -0700
    Updating doc images for MR change, deleting old files too refs #26385
• src/hg/htdocs/images/MultiRegionMouseHighlighted.png
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    3ee43997901d9226d78f052f521fdaa69c2c2975 Mon Apr 19 17:06:56 2021 -0700
    Updating doc images for MR change, deleting old files too refs #26385
• src/hg/htdocs/images/multiRegionButton.png
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    3ee43997901d9226d78f052f521fdaa69c2c2975 Mon Apr 19 17:06:56 2021 -0700
    Updating doc images for MR change, deleting old files too refs #26385
• src/hg/htdocs/images/multiRegionConfig.png
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    3ee43997901d9226d78f052f521fdaa69c2c2975 Mon Apr 19 17:06:56 2021 -0700
    Updating doc images for MR change, deleting old files too refs #26385
• src/hg/htdocs/images/multiRegionExample.png
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    3ee43997901d9226d78f052f521fdaa69c2c2975 Mon Apr 19 17:06:56 2021 -0700
    Updating doc images for MR change, deleting old files too refs #26385
• src/hg/hubApi/apiUtils.c
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    da0932abedd063b6e9fe087bc26ab9ef53b6cd2e Thu Apr 22 16:43:20 2021 -0700
    make hubApi use the trackDb cache.
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    bcf1004e0ab1faed65f32f2dc399fd539fb5aa34 Sat Apr 24 12:25:03 2021 -0700
    Revert "make hubApi use the trackDb cache." This reverts commit da0932abedd063b6e9fe087bc26ab9ef53b6cd2e.
• src/hg/hubApi/hubApi.c
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    4c2cf4c9629af2fe90989a8f52d6f6bd44049b59 Thu Apr 22 15:34:40 2021 -0700
    get hubApi to use the UDC cache directory defined in hg.conf
• src/hg/hubApi/list.c
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    d186e66432880373f1ed5497ae34dca8cd2f4c1a Thu Apr 22 12:45:31 2021 -0700
    Don't open bigBeds when we're listing tracks, this means no itemCount
• src/hg/inc/trackHub.h
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    da0932abedd063b6e9fe087bc26ab9ef53b6cd2e Thu Apr 22 16:43:20 2021 -0700
    make hubApi use the trackDb cache.
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    bcf1004e0ab1faed65f32f2dc399fd539fb5aa34 Sat Apr 24 12:25:03 2021 -0700
    Revert "make hubApi use the trackDb cache." This reverts commit da0932abedd063b6e9fe087bc26ab9ef53b6cd2e.
• src/hg/lib/hubConnect.c
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    da0932abedd063b6e9fe087bc26ab9ef53b6cd2e Thu Apr 22 16:43:20 2021 -0700
    make hubApi use the trackDb cache.
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    bcf1004e0ab1faed65f32f2dc399fd539fb5aa34 Sat Apr 24 12:25:03 2021 -0700
    Revert "make hubApi use the trackDb cache." This reverts commit da0932abedd063b6e9fe087bc26ab9ef53b6cd2e.
• src/hg/lib/hui.c
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    5cbd092e2deb2869385fc3203282ac6c91337048 Tue Apr 20 10:27:40 2021 -0700
    Allow different messages for each side of a relationship in the relatedTracks section of hgc/hgTrackUi. Enforce two lines per relationship in relatedTracks.ra in order to allow this, refs #25721
• src/hg/lib/trackHub.c
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    da0932abedd063b6e9fe087bc26ab9ef53b6cd2e Thu Apr 22 16:43:20 2021 -0700
    make hubApi use the trackDb cache.
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    bcf1004e0ab1faed65f32f2dc399fd539fb5aa34 Sat Apr 24 12:25:03 2021 -0700
    Revert "make hubApi use the trackDb cache." This reverts commit da0932abedd063b6e9fe087bc26ab9ef53b6cd2e.
• src/hg/makeDb/doc/asmHubs/genArkListToSql.pl
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    e737f6b863c3453482f0b996b469abfc54f618c8 Tue Apr 20 15:01:33 2021 -0700
    script to update hgcentral.genark table refs #23891
• src/hg/makeDb/doc/asmHubs/updateGenArkCentral.sh
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    e737f6b863c3453482f0b996b469abfc54f618c8 Tue Apr 20 15:01:33 2021 -0700
    script to update hgcentral.genark table refs #23891
• src/hg/makeDb/doc/hg19.analysisSet.txt
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    77ceb7f28c14b899e105395b479a29de88c1e419 Mon Apr 19 17:47:52 2021 -0700
    typographical error hg19 analysisSet
• src/hg/makeDb/doc/hg38/cactus241way.txt
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    e1e7a65c65869e5b0d157cd1e992e8c905157524 Sun Apr 25 22:01:45 2021 -0700
    added Zoonomia phylop subtrack
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
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    0a319da1f082fd4638e5c1184c23595191727d20 Wed Apr 21 14:18:09 2021 -0700
    adding pig USMARCv1 refs #27388' mammals.orderList.tsv
• src/hg/makeDb/doc/vgpAsmHub/vgp.alternate.orderList.tsv
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    03bb63f76a33d7627ee06ff553c1182624e21760 Tue Apr 20 14:46:25 2021 -0700
    must be tabs to separate two columns refs #23891
• src/hg/makeDb/doc/vgpAsmHub/vgp.taxId.asmId.class.txt
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    b161e6a018809abcb2122c2b714a150e588092c8 Mon Apr 19 10:16:16 2021 -0700
    correct clade for Barn swallow refs #23891
• src/hg/makeDb/doc/wuhCor1/vaccines.txt
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    cd6dd5e0d6f3ecb908ae665ae1a164d855d7c1be Mon Apr 19 14:52:56 2021 -0700
    Fixing a small typo in the makedoc for the vaccines track on wuhCor1, refs #27312
• src/hg/makeDb/genbank/etc/hgwbeta.dbs
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    777424d7b3e381a1e6ae225ffa4bd816a0f2938f Tue Apr 20 17:05:38 2021 -0700
    Turning on GenBank updates for new assembly, refs #26682
• src/hg/makeDb/trackDb/buildRelatedTracks
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    5cbd092e2deb2869385fc3203282ac6c91337048 Tue Apr 20 10:27:40 2021 -0700
    Allow different messages for each side of a relationship in the relatedTracks section of hgc/hgTrackUi. Enforce two lines per relationship in relatedTracks.ra in order to allow this, refs #25721
• src/hg/makeDb/trackDb/human/cadd.ra
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    9f489fd23ec7d2d33eaf1984d1ba3c0887b75fd4 Tue Apr 20 15:13:53 2021 -0700
    Adding maxWindowSize and related lines to cadd, removing caddAlpha for refs #27079
• src/hg/makeDb/trackDb/human/caddAlpha.ra
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    9f489fd23ec7d2d33eaf1984d1ba3c0887b75fd4 Tue Apr 20 15:13:53 2021 -0700
    Adding maxWindowSize and related lines to cadd, removing caddAlpha for refs #27079
• src/hg/makeDb/trackDb/human/hg19/skinSoleBoldo.ra
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    de9fa7cdbb3b8cebf7184fd272010094eac9be15 Thu Feb 11 14:23:11 2021 -0800
    Fixing coloring on cells I now know to be fibroblasts
• src/hg/makeDb/trackDb/human/hg38/cons241way.html
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    e1e7a65c65869e5b0d157cd1e992e8c905157524 Sun Apr 25 22:01:45 2021 -0700
    added Zoonomia phylop subtrack
• src/hg/makeDb/trackDb/human/hg38/fetalGeneAtlas.html
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    205a8cd7512bebea2bb1a95e7cfa3851592bae2b Tue Feb 9 09:51:06 2021 -0800
    Changed exotic apostrophe in the name of Dr. O'Day to a regular one we have fonts for.
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    210e4758304f7361803be8d215c22632939bb17a Tue Apr 20 15:54:07 2021 -0700
    Adding a little more info to the fetalGeneAtlas description, saying where the colors are coming from.
• src/hg/makeDb/trackDb/human/hg38/muscleDeMicheli.ra
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    63c524015e597095351fade867803ca945d7358e Tue Apr 20 15:55:11 2021 -0700
    Adding labe to barChart.
• src/hg/makeDb/trackDb/human/hg38/singleCellMerged.ra
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    857df74c828da15e22f731b2b7d1dc2bb6dbfdf1 Tue Apr 20 15:50:32 2021 -0700
    Adding barChartStretchToItem setting
• src/hg/makeDb/trackDb/human/hg38/skinSoleBoldo.ra
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    de9fa7cdbb3b8cebf7184fd272010094eac9be15 Thu Feb 11 14:23:11 2021 -0800
    Fixing coloring on cells I now know to be fibroblasts
• src/hg/makeDb/trackDb/human/hg38/trackDb.100way.ra
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    9cd16101edd06afa0989e597659af79f6edfebd1 Mon Apr 19 16:43:39 2021 -0700
    Minor change to viewing range No RM
• src/hg/makeDb/trackDb/human/hg38/trackDb.241way.ra
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    e1e7a65c65869e5b0d157cd1e992e8c905157524 Sun Apr 25 22:01:45 2021 -0700
    added Zoonomia phylop subtrack
• src/hg/makeDb/trackDb/human/trackDb.ra
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    9f489fd23ec7d2d33eaf1984d1ba3c0887b75fd4 Tue Apr 20 15:13:53 2021 -0700
    Adding maxWindowSize and related lines to cadd, removing caddAlpha for refs #27079
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.gliresChainNet.ra
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    ce7546895b7aa6d13e2381da75bd790310f99ce9 Fri Apr 23 17:30:35 2021 -0700
    adding rn7 in this group refs #26682
• src/hg/makeDb/trackDb/rat/rn7/trackDb.ra
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    f11645ab2a00802ea5ae0f4765e185b3f642f107 Mon Apr 19 15:50:00 2021 -0700
    Added mm10 getMatrixLines.csh and mm39 getChainLines.csh output to match the description page, refs #26682
• src/hg/makeDb/trackDb/relatedTracks.ra
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    5cbd092e2deb2869385fc3203282ac6c91337048 Tue Apr 20 10:27:40 2021 -0700
    Allow different messages for each side of a relationship in the relatedTracks section of hgc/hgTrackUi. Enforce two lines per relationship in relatedTracks.ra in order to allow this, refs #25721
• src/hg/makeDb/trackDb/tagTypes.tab
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    857df74c828da15e22f731b2b7d1dc2bb6dbfdf1 Tue Apr 20 15:50:32 2021 -0700
    Adding barChartStretchToItem setting
• src/hg/oneShot/demergeSingle/demergeSingle.c
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    7677f81c25a828d3bb37841d3f1db74eeae60ac3 Mon Feb 22 10:56:17 2021 -0800
    Minimally working better than a 3 line awk/shell script would.
• src/hg/oneShot/demergeSingle/makefile
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    7677f81c25a828d3bb37841d3f1db74eeae60ac3 Mon Feb 22 10:56:17 2021 -0800
    Minimally working better than a 3 line awk/shell script would.
• src/hg/utils/automation/altScaffoldPlacementToBed.pl
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    fcc6591a9eb3db4aeb92d2a6d45e43b689e99896 Wed Apr 21 23:55:56 2021 -0700
    adding mm10 to altScaffoldPlacementToBed.pl so it does not create IDs with sub-version, like hg19.
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    037a404d5b76d3005d0263ef6212066e3073ea4a Fri Apr 23 02:27:58 2021 -0700
    altScaffoldPlacementToBed.pl handle MMCHR scaffold fix on alt for mouse.
• src/hg/utils/otto/sarscov2phylo/gisaidFromChunks.sh
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    d6677c2b706a2424e70bcacd517d8a61f4b39f20 Wed Apr 21 15:09:20 2021 -0700
    Apparently GISAID sequence names can have apostrophes too. Strip out more troublemaking characters.
• src/hg/utils/otto/sarscov2phylo/updatePublicTree.sh
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    6aa3eabbd7f14c3f3260183f0cbbf54e2c176724 Mon Apr 19 15:41:28 2021 -0700
    Oops, fix some paths & typos for gzipping public tree archive files.
• src/utils/faRenameRecords/faRenameRecords.c
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    e507dd065fc544d3d6d6122b72aaaf45693d856f Wed Apr 21 16:39:02 2021 -0700
    Added -pass option to faRenameRecords so that if sequences are not in the oldToNew file, they are passed through (no errAbort).
• src/utils/makefile
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    c09a391e996f239d60171eddbf139b270c8ceba5 Wed Apr 21 16:39:29 2021 -0700
    Adding faRenameRecords to top-level build.
• src/utils/qa/weeklybld/buildEnv.csh
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    e3d961d00c7952e86cc33bf52d2615ce09da7780 Mon Apr 26 10:06:57 2021 -0700
    v414 preview2, refs #27418

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• files changed: 71