All File Changes

v446_preview to v446_preview2 (2023-03-20 to 2023-03-27) v446

• README
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    dab0d2ab7319f42388fbd2d4df014e7234ef906d Thu Mar 23 04:26:30 2023 -0700
    Preview2 week - bugs introduced now will need a build patch to fix Consider commiting next week
• src/hg/hgSession/hgSession.c
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    8fcb2ed43b0ec0060a831894d4cf8eaab95fa466 Thu Mar 23 12:42:04 2023 -0700
    add a mechanism whereby hubStatus id's in a session can be mapped to the local hubStatus id for that hub
• src/hg/hgTracks/hgTracks.c
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    53237d35a239609d588340929dec558b0bcca1c7 Mon Mar 20 12:15:32 2023 -0700
    let users specify the squishyPackPoint
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    546e4b62f9c8abdda3576ce5b9bf8c4b82dc6b4e Tue Mar 21 14:42:01 2023 -0700
    make squishyPack work nicely with Javascript track reorder
• src/hg/hgTracks/imageV2.c
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    546e4b62f9c8abdda3576ce5b9bf8c4b82dc6b4e Tue Mar 21 14:42:01 2023 -0700
    make squishyPack work nicely with Javascript track reorder
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    010882a6948505235ea0516ca085178b70299eb8 Fri Mar 24 15:10:45 2023 -0700
    fix bug in squishyPack if squishy part was empty
• src/hg/hgTracks/imageV2.h
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    546e4b62f9c8abdda3576ce5b9bf8c4b82dc6b4e Tue Mar 21 14:42:01 2023 -0700
    make squishyPack work nicely with Javascript track reorder
• src/hg/hgTracks/simpleTracks.c
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    546e4b62f9c8abdda3576ce5b9bf8c4b82dc6b4e Tue Mar 21 14:42:01 2023 -0700
    make squishyPack work nicely with Javascript track reorder
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    6200a69f0871767cd950526e09448503331e9d51 Thu Mar 23 05:46:57 2023 -0700
    Short match track was invisible, refs #30866
• src/hg/htdocs/FAQ/FAQtracks.html
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    c0a631c93bb41116a873c46ee13c87c5d0806c46 Fri Mar 24 16:18:39 2023 -0700
    Adding new FAQ entry for diagnosing slow hgTracks behavior. Refs #30620
• src/hg/hubApi/apiUtils.c
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    7c04d352647faab3ca7f194dc5f11f764d876ce3 Tue Mar 21 13:44:35 2023 -0700
    adding some chromAlias recognition for some getData functions refs #30544
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    0781f49ccdacd52dd75b0f12dab183e4b4cd25fc Tue Mar 21 15:04:48 2023 -0700
    extend the chromAlias function to the getSequence operation refs #30544
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    7deafd5b94221c04282f275c6d1ccc3b24b53654 Thu Mar 23 14:46:30 2023 -0700
    using bigBedFileOpenAlias in place of bigBedFileOpen supplies alias functions for mixed and match tracks with different naming authorities refs #30544
• src/hg/hubApi/dataApi.h
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    7c04d352647faab3ca7f194dc5f11f764d876ce3 Tue Mar 21 13:44:35 2023 -0700
    adding some chromAlias recognition for some getData functions refs #30544
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    0781f49ccdacd52dd75b0f12dab183e4b4cd25fc Tue Mar 21 15:04:48 2023 -0700
    extend the chromAlias function to the getSequence operation refs #30544
• src/hg/hubApi/getData.c
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    7c04d352647faab3ca7f194dc5f11f764d876ce3 Tue Mar 21 13:44:35 2023 -0700
    adding some chromAlias recognition for some getData functions refs #30544
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    0781f49ccdacd52dd75b0f12dab183e4b4cd25fc Tue Mar 21 15:04:48 2023 -0700
    extend the chromAlias function to the getSequence operation refs #30544
• src/hg/hubApi/tests/expected/chrAlias01.gz
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    7bdaa5393c5e94faf1b70c2018b4d76f1b9951f6 Tue Mar 21 13:41:59 2023 -0700
    adding chrAlias testing refs #30544
• src/hg/hubApi/tests/expected/chrAlias02.gz
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    7bdaa5393c5e94faf1b70c2018b4d76f1b9951f6 Tue Mar 21 13:41:59 2023 -0700
    adding chrAlias testing refs #30544
• src/hg/hubApi/tests/expected/chrAlias03.gz
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    7bdaa5393c5e94faf1b70c2018b4d76f1b9951f6 Tue Mar 21 13:41:59 2023 -0700
    adding chrAlias testing refs #30544
• src/hg/hubApi/tests/expected/chrAlias04.gz
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    7bdaa5393c5e94faf1b70c2018b4d76f1b9951f6 Tue Mar 21 13:41:59 2023 -0700
    adding chrAlias testing refs #30544
• src/hg/hubApi/tests/expected/chrAlias05.gz
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    7bdaa5393c5e94faf1b70c2018b4d76f1b9951f6 Tue Mar 21 13:41:59 2023 -0700
    adding chrAlias testing refs #30544
• src/hg/hubApi/tests/expected/chrAlias06.gz
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    7bdaa5393c5e94faf1b70c2018b4d76f1b9951f6 Tue Mar 21 13:41:59 2023 -0700
    adding chrAlias testing refs #30544
• src/hg/hubApi/tests/expected/chrAlias07.gz
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    0781f49ccdacd52dd75b0f12dab183e4b4cd25fc Tue Mar 21 15:04:48 2023 -0700
    extend the chromAlias function to the getSequence operation refs #30544
• src/hg/hubApi/tests/expected/chrAlias08.gz
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    0781f49ccdacd52dd75b0f12dab183e4b4cd25fc Tue Mar 21 15:04:48 2023 -0700
    extend the chromAlias function to the getSequence operation refs #30544
• src/hg/hubApi/tests/expected/chrAlias09.gz
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    665ee1c57639af150db6841dabd0f1d9634f52ed Wed Mar 22 11:14:10 2023 -0700
    add some tests on hs1 refs #30544
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    ca9bb0fbc8288f6decc353a0d106870fdab1663c Thu Mar 23 15:04:30 2023 -0700
    remember to ignore hub.txt path for different sandboxes refs #30544
• src/hg/hubApi/tests/expected/chrAlias10.gz
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    46671c77d37fb4c642e84a38c53c6494f56223c5 Thu Mar 23 14:47:42 2023 -0700
    using bigBedFileOpenAlias in place of bigBedFileOpen supplies alias functions for mixed and match tracks with different naming authorities refs #30544
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    ca9bb0fbc8288f6decc353a0d106870fdab1663c Thu Mar 23 15:04:30 2023 -0700
    remember to ignore hub.txt path for different sandboxes refs #30544
• src/hg/hubApi/tests/expected/chrAlias11.gz
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    46671c77d37fb4c642e84a38c53c6494f56223c5 Thu Mar 23 14:47:42 2023 -0700
    using bigBedFileOpenAlias in place of bigBedFileOpen supplies alias functions for mixed and match tracks with different naming authorities refs #30544
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    ca9bb0fbc8288f6decc353a0d106870fdab1663c Thu Mar 23 15:04:30 2023 -0700
    remember to ignore hub.txt path for different sandboxes refs #30544
• src/hg/hubApi/tests/expected/err50.gz
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    7bdaa5393c5e94faf1b70c2018b4d76f1b9951f6 Tue Mar 21 13:41:59 2023 -0700
    adding chrAlias testing refs #30544
• src/hg/hubApi/tests/expected/list19.gz
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    665ee1c57639af150db6841dabd0f1d9634f52ed Wed Mar 22 11:14:10 2023 -0700
    add some tests on hs1 refs #30544
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    af9d888d2521227f0df54328fe88f3f85dd15e35 Wed Mar 22 11:27:11 2023 -0700
    remember to have up to date trackDb for best results refs #30544
• src/hg/hubApi/tests/expected/list20.gz
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    665ee1c57639af150db6841dabd0f1d9634f52ed Wed Mar 22 11:14:10 2023 -0700
    add some tests on hs1 refs #30544
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    af9d888d2521227f0df54328fe88f3f85dd15e35 Wed Mar 22 11:27:11 2023 -0700
    remember to have up to date trackDb for best results refs #30544
• src/hg/hubApi/tests/expected/list21.gz
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    665ee1c57639af150db6841dabd0f1d9634f52ed Wed Mar 22 11:14:10 2023 -0700
    add some tests on hs1 refs #30544
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    af9d888d2521227f0df54328fe88f3f85dd15e35 Wed Mar 22 11:27:11 2023 -0700
    remember to have up to date trackDb for best results refs #30544
• src/hg/hubApi/tests/expected/multiTrack01.gz
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    665ee1c57639af150db6841dabd0f1d9634f52ed Wed Mar 22 11:14:10 2023 -0700
    add some tests on hs1 refs #30544
• src/hg/hubApi/tests/expected/multiTrack02.gz
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    46671c77d37fb4c642e84a38c53c6494f56223c5 Thu Mar 23 14:47:42 2023 -0700
    using bigBedFileOpenAlias in place of bigBedFileOpen supplies alias functions for mixed and match tracks with different naming authorities refs #30544
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    ca9bb0fbc8288f6decc353a0d106870fdab1663c Thu Mar 23 15:04:30 2023 -0700
    remember to ignore hub.txt path for different sandboxes refs #30544
• src/hg/hubApi/tests/expected/multiTrack03.gz
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    46671c77d37fb4c642e84a38c53c6494f56223c5 Thu Mar 23 14:47:42 2023 -0700
    using bigBedFileOpenAlias in place of bigBedFileOpen supplies alias functions for mixed and match tracks with different naming authorities refs #30544
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    ca9bb0fbc8288f6decc353a0d106870fdab1663c Thu Mar 23 15:04:30 2023 -0700
    remember to ignore hub.txt path for different sandboxes refs #30544
• src/hg/hubApi/tests/makefile
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    7bdaa5393c5e94faf1b70c2018b4d76f1b9951f6 Tue Mar 21 13:41:59 2023 -0700
    adding chrAlias testing refs #30544
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    255bef7f94a872911184ea049071b1ccbc8983fe Tue Mar 21 13:59:51 2023 -0700
    forgot to reference chrAlias06 refs #30544
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    0781f49ccdacd52dd75b0f12dab183e4b4cd25fc Tue Mar 21 15:04:48 2023 -0700
    extend the chromAlias function to the getSequence operation refs #30544
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    e1a1fb5375a5511bd57e4fb67182e7fa8627b37b Wed Mar 22 11:11:50 2023 -0700
    add some tests on hs1 refs #30544
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    af9d888d2521227f0df54328fe88f3f85dd15e35 Wed Mar 22 11:27:11 2023 -0700
    remember to have up to date trackDb for best results refs #30544
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    46671c77d37fb4c642e84a38c53c6494f56223c5 Thu Mar 23 14:47:42 2023 -0700
    using bigBedFileOpenAlias in place of bigBedFileOpen supplies alias functions for mixed and match tracks with different naming authorities refs #30544
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    3d2b88aa010e09690c6c595a9820f449c6b71ab4 Thu Mar 23 14:48:12 2023 -0700
    using bigBedFileOpenAlias in place of bigBedFileOpen supplies alias functions for mixed and match tracks with different naming authorities refs #30544
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    ca9bb0fbc8288f6decc353a0d106870fdab1663c Thu Mar 23 15:04:30 2023 -0700
    remember to ignore hub.txt path for different sandboxes refs #30544
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    40c3e555affbd16d650932d9ae626443f42bbc5b Thu Mar 23 15:14:49 2023 -0700
    add to the help message refs #30544
• src/hg/inc/chromAlias.h
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    eb4b6546550cba82f0031c043ee4f55bdbec8c30 Tue Mar 21 13:43:21 2023 -0700
    expose chromAliasSetupBb for use in hubApi refs #30544
• src/hg/inc/trackDb.h
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    8f243019c3578964dcdb2872453a67562da78337 Sun Mar 26 13:05:56 2023 -0700
    increment trackDb version so cached versions with a non-cloned errMessage are expired.
• src/hg/js/hgTracks.js
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    e2be82208cc33ab43a11087601a846931e2346a5 Wed Mar 22 15:07:11 2023 -0700
    Change downloads current track data button to a link in the downloads menu, refs #30865
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    f7595f0f13e0f33ba539c28d75fdf4eba7514d93 Fri Mar 24 07:49:58 2023 -0700
    adding warning box if page load is too slow, activated via hg.conf, refs #30591
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    7b4a1f34fd34041843801b922473dc15fa849d3b Fri Mar 24 07:58:22 2023 -0700
    changing contact to internal email address, refs #30591
• src/hg/lib/chromAlias.c
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    eb4b6546550cba82f0031c043ee4f55bdbec8c30 Tue Mar 21 13:43:21 2023 -0700
    expose chromAliasSetupBb for use in hubApi refs #30544
• src/hg/lib/hubConnect.c
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    8fcb2ed43b0ec0060a831894d4cf8eaab95fa466 Thu Mar 23 12:42:04 2023 -0700
    add a mechanism whereby hubStatus id's in a session can be mapped to the local hubStatus id for that hub
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    ac57c34ad3a97779a948f4f716d704c22061c98b Thu Mar 23 13:01:39 2023 -0700
    oops.. need to remove assumesHub cart variable once it has been processed
• src/hg/lib/hui.c
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    53237d35a239609d588340929dec558b0bcca1c7 Mon Mar 20 12:15:32 2023 -0700
    let users specify the squishyPackPoint
• src/hg/lib/trackDbCache.c
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    fc686a6393efdad7e0b20c4e4718c127de80420e Fri Mar 24 17:04:28 2023 -0700
    properly clone the trackDb errMessage pointer for trackDb caching
• src/hg/makeDb/doc/asmHubs/master.run.list
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    de78b5ec01fe83fa8534377e991d83ade368df48 Mon Mar 20 18:08:13 2023 -0700
    catching up 17 NPRC assemblies refs #30508
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    75f69eb021fdf446bc56f02afb6fd9056d7b7361 Wed Mar 22 08:15:56 2023 -0700
    HPRC and addition from user request refs #29545
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    e333353435bde66c659754f02966057bf191b515 Wed Mar 22 15:19:28 2023 -0700
    a couple of assemblies per user request refs #29545
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    8fe411406aaca63524a93f863ff29d0b47d2a631 Sat Mar 25 13:55:56 2023 -0700
    catching up HPRC and a user request refs #30508
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    db54d5b0929f100f355612d2744d9f5643689edb Mon Mar 27 09:58:51 2023 -0700
    HPRC almost done refs #30508
• src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv
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    2386edc9931a5f930ff78dddf751dd96c1d6b43d Wed Mar 22 15:48:32 2023 -0700
    adding one per user request refs #29545
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    ed866720a585eac35edb86496962b06889122c9e Sat Mar 25 17:14:01 2023 -0700
    adding one per user request refs #29545
• src/hg/makeDb/doc/bosTau9/lastzRuns.txt
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    2fd3b8fcf0d2e0e4e2315ddcd66f2a94d8987e74 Tue Mar 21 11:11:06 2023 -0700
    lastz to GCF_003369695.1 refs #30648
• src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv
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    de29d7985da36f9e65d856791f1c99aa487c9364 Wed Mar 22 15:44:10 2023 -0700
    adding a couple per user request refs #29545
• src/hg/makeDb/doc/hprcAsmHub/hprc.orderList.tsv
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    8c663f648d8952a49347e8857309782d9adef067 Mon Mar 20 11:36:41 2023 -0700
    continuing updates refs #30508
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    22bcbc17f3431b952f802716b45082da8500054a Mon Mar 20 11:40:32 2023 -0700
    continuing updates refs #30508
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    3bacf328f27fe1a429d3afbfb48446f3bd8a5bb4 Wed Mar 22 10:00:06 2023 -0700
    catching up HPRC additions refs #30508
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    8a03b43bb5d418295a0fb655ec65277010567694 Wed Mar 22 16:18:38 2023 -0700
    another HPRC to the lot refs #20508
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    33a753e917fa5230b34bcc058b691f02e5871727 Mon Mar 27 10:09:30 2023 -0700
    HPRC almost done refs #30508
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
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    538ed99276c513f39375bfd4b94ad61b2831d368 Wed Mar 22 09:25:29 2023 -0700
    per user request GCF_028408465.1_idAnaLude1.1 Mexican fruit fly (Willacy primary hap 2023) refs #29545
• src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv
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    a2a3bb0fc32b8bcca665243b252d64b75b6f5f7d Mon Mar 20 18:08:56 2023 -0700
    catching up 17 NPRC assemblies refs #30508
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    00a242f29b93e3718825540e0fbf9e446ffb2fb1 Wed Mar 22 09:43:03 2023 -0700
    continue adding HPRC assembly refs #30508
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    9de2ca240f6ad68c544630a86f518051c4f7a0bc Wed Mar 22 16:14:19 2023 -0700
    another HPRC to the lot refs #20508
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    52e73de9b2a157e02e07eaecaba957ce2ce579d2 Mon Mar 27 10:05:00 2023 -0700
    HPRC almost done refs #30508
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
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    2d342c85706fa108decc142314c97c0a0564280b Thu Mar 23 20:10:22 2023 -0700
    Fixing a few typos I spotted in code review. refs #30826
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    942bac0d5922ca1a48939895627f30c068e35ff2 Fri Mar 24 06:26:40 2023 -0700
    changes after code review, refs #30826
• src/hg/makeDb/trackDb/human/hg38/crossTissueMaps.html
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    9ff765e4c69329fb8f7b0b58066454d70104eff5 Thu Mar 23 10:37:52 2023 -0700
    Update gtex cross tissue track description colors, refs #29954
• src/hg/makeDb/trackDb/human/hg38/problematic.html
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    2d342c85706fa108decc142314c97c0a0564280b Thu Mar 23 20:10:22 2023 -0700
    Fixing a few typos I spotted in code review. refs #30826
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.nextstrain.ra
  • lines changed 436, context: html, text, full: html, text
    cd2c57b40633f481b204fdd59b7e1ca212ecd04d Thu Mar 23 20:11:44 2023 -0700
    Updating the very outdated Nextstrain Clade subtrack stanzas.
• src/hg/utils/hubCheck/hubCheck.c
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    6401def272cf75c2bb0f52203cd37f5ca77baa77 Sun Mar 26 09:50:03 2023 -0700
    get hubCheck to use new tdb->errMessage mechanism
• src/hg/utils/hubCheck/tests/expected/noLongLabel.txt
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    6401def272cf75c2bb0f52203cd37f5ca77baa77 Sun Mar 26 09:50:03 2023 -0700
    get hubCheck to use new tdb->errMessage mechanism
• src/hg/utils/hubCheck/tests/input/noLongLabel.txt
  • lines changed 29, context: html, text, full: html, text
    6401def272cf75c2bb0f52203cd37f5ca77baa77 Sun Mar 26 09:50:03 2023 -0700
    get hubCheck to use new tdb->errMessage mechanism
• src/hg/utils/hubCheck/tests/makefile
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    6401def272cf75c2bb0f52203cd37f5ca77baa77 Sun Mar 26 09:50:03 2023 -0700
    get hubCheck to use new tdb->errMessage mechanism
• src/hg/utils/otto/otto.crontab
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    6cfd61454818f94d58f3654237c84ec05d54f4f6 Wed Mar 22 14:17:32 2023 -0700
    Tidying up small amount of otto crontab, no RM.
• src/hg/utils/otto/sarscov2phylo/findDropoutContam.pl
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    613458edda9014ed673838956868f75a9913cf96 Thu Mar 23 13:27:13 2023 -0700
    Omicron persists past 2022, assume it's here for the decade.
• src/hg/utils/otto/sarscov2phylo/includeRecombinants.tsv
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    61b8f5004b8c9249e46f1b87fe9d34c369b97450 Thu Mar 23 13:30:50 2023 -0700
    Adding some sequences for older proposed recombinants that would be removed from the tree by a harsher application of filters otherwise.
• src/hg/utils/otto/sarscov2phylo/makeNewMaskedVcf.sh
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    a5a4f89c3230564550036f73c9821617d3ab4bac Thu Mar 23 13:28:16 2023 -0700
    No idea why I was skipping the first 3 lines of includeRecombinants.tsv rather than just the header line.
• src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv
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    48f4046340295c6795f5bd4491fdbfec1a2c8527 Tue Mar 21 11:40:36 2023 -0700
    New lineages and some corrections: * BA.2_dropout had 21762 and 21846 twice, oops * BS.1.2 was defined too narrowly, should not have required C29642T * BF.7.6 was defined too narrowly, should not have required A2692T and C15540T * CK.2.1.1 needed G2393N (order-shuffling) * XAW apparently got a bunch of new sequences after cleanup and needed quite a few new Ns * XBC needed C22329T (early sequences had Ns and needed to be removed and re-added to impute)
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    f559b66a0d86b81dd0e1254a198132462f45874c Thu Mar 23 13:25:14 2023 -0700
    Another slew of new lineages.
• src/utils/bigGuessDb/bigGuessDb
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    06886baf58cbcece09362bbcf55ab91b18077f69 Tue Mar 21 02:27:55 2023 -0700
    tiny docs change, refs #30316
• src/utils/qa/hubSearchUpdate
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    31900fdb56ea450b3c7e8fdc97f6962b9b757d59 Wed Mar 22 14:00:40 2023 -0700
    Moving up the shebang line, and removing the path which is already included since it runs from a cron environment now, no RM.
• src/utils/qa/weeklybld/buildEnv.csh
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    38307ed780d31a569a48b208e4f60129072af264 Mon Mar 20 10:56:12 2023 -0700
    v446 preview1
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    755d2da01a2148ca733a7e5218aa96f91ea90b19 Mon Mar 27 10:05:52 2023 -0700
    v446 preview2, refs #30851

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