All File Changes

v456_preview to v456_preview2 (2023-10-16 to 2023-10-23) v456

• confs/rr.hg.conf
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    d5be9287b6eb8b1508893cbc6dd8deb066b74bbf Sun Oct 22 01:11:23 2023 -0700
    Installing updated hg.conf files from UCSC servers
• src/browserbox/root/updateBrowser.sh
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    a93a919407cb6f0692c00c122f8dc13335fc9630 Tue Oct 17 09:02:26 2023 -0700
    hiding OMIM track on GBIB to avoid error in offline mode and also adding /gbdb symlink to make sure that v455 doesn't cause trouble on GBIB. refs #32440
• src/hg/cgilib/tests/makefile
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    00842bb1a117e43903667e58f3069f436e5ce667 Tue Oct 17 09:32:22 2023 -0700
    temporarily disable annogrator test because it's dependent on hg19 knownGene, which is in flux
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    530f7f0a464a44dd85350d11de3e6052d6f62031 Tue Oct 17 09:34:04 2023 -0700
    oops... output directory may not exist
• src/hg/das/das.c
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    b39119efb42cec014dfe6cba948bc7717b0176c4 Fri Oct 20 14:10:18 2023 -0700
    Changing the abuse message to point to private ML instead of public, refs #22423
• src/hg/hgTracks/simpleTracks.c
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    41228a755bb4fc38a150e4d5e36c259850968212 Fri Oct 20 06:47:16 2023 -0700
    allow exonNumber on with mouseOver in trackDb, refs #32459
• src/hg/hgc/hgc.c
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    2a941ab53227d6b7aab8ffc9054b71a250e0ea73 Tue Oct 17 03:29:23 2023 -0700
    adding a file that I forgot to commit, found in code review by Jonathan, refs #32312, thanks to Jonathan!
• src/hg/htdocs/goldenPath/help/decorator.html
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    598f280e524d74c7a5baed4051d5d7f5e30d489a Mon Oct 23 01:15:36 2023 -0700
    Adding Max additions and suggestions to the doc page, refs #30237
• src/hg/htdocs/images/runx2.png
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    f0f1d26674dcf8a942a044b3ab1c3ed795eda5c6 Thu Oct 19 15:58:34 2023 -0700
    Adding images for the track decorators doc, refs #30237
• src/hg/htdocs/images/runx2_decorator.png
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    f0f1d26674dcf8a942a044b3ab1c3ed795eda5c6 Thu Oct 19 15:58:34 2023 -0700
    Adding images for the track decorators doc, refs #30237
• src/hg/htdocs/inc/hgSearch.html
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    e19930c1512710a279c277546f07e510ff76e790 Tue Oct 17 10:25:48 2023 -0700
    Fix bug in reflow of hgSearch columns, had incorrect row class on elements that were not supposed to be rows, refs Lou email
• src/hg/hubApi/hubApi.c
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    b39119efb42cec014dfe6cba948bc7717b0176c4 Fri Oct 20 14:10:18 2023 -0700
    Changing the abuse message to point to private ML instead of public, refs #22423
• src/hg/js/utils.js
  • lines changed 13, context: html, text, full: html, text
    a5c5763cfadceb5a8894268830f34a830833aeaa Wed Oct 18 11:44:55 2023 -0700
    Fix mouseover coordinate setting when mousing over the grey bar button on hgTracks to take into the mouse position rather than just the element bounding rectangle, because we can cover as much of the grey button as we want, refs Max email
• src/hg/lib/botDelay.c
  • lines changed 1, context: html, text, full: html, text
    b39119efb42cec014dfe6cba948bc7717b0176c4 Fri Oct 20 14:10:18 2023 -0700
    Changing the abuse message to point to private ML instead of public, refs #22423
• src/hg/lib/chainArrange.as
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    56332b7995bf6075d07d88b04e5675c247725892 Tue Oct 17 16:21:18 2023 -0700
    flesh out the indel tracks
• src/hg/lib/hdb.c
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    e90f9ec1342f152874194ba7a24c21da11c0c868 Tue Oct 17 05:54:55 2023 -0700
    changes after code review, refs #32312
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    f80647089b6f923ae55acb0a802051d4ff9d0881 Wed Oct 18 17:25:07 2023 -0700
    Revert "don't check for data accessibility, just trust trackDb Refs #32299" This reverts commit 4140b3fc69c92c3331daca4f7bf35fafc81a5b1f.
• src/hg/makeDb/doc/asmHubs/master.run.list
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    b4c1c054979edf8f7265d42c5a58c2772f1c7528 Fri Oct 20 19:46:39 2023 -0700
    catching up a few things refs #29545
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    80c57a121c5072b421be2673a512feb1a9f8992c Fri Oct 20 22:54:41 2023 -0700
    a VGP update adding 53 mammals assemblies refs #29545
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    17fb6d25db175a14b2666d4a24e3ef237dc1af5e Fri Oct 20 22:56:38 2023 -0700
    a VGP update adding 25 fish refs #29545
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    d448769dca513fd694e9163e7f08e08bf214efd7 Sat Oct 21 21:16:21 2023 -0700
    VGP update adding three primates refs #29545
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    e6950b5b0062d034313160c0ea365c859ef6fe7a Sat Oct 21 23:00:12 2023 -0700
    VGP update adding 37 vertebrate assemblies refs #29545
• src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv
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    0711fb4f20cd7c35d5ac60edce92c9e8f6742345 Sat Oct 21 20:39:20 2023 -0700
    VGP update adds about 25 fish assemblies refs #29545
• src/hg/makeDb/doc/hg38/cosmicV98.txt
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    cf24bf1f4d870e1b6d2d9067c04ff480cfb469b2 Fri Oct 20 12:54:49 2023 -0700
    Adding an updated cosmic makedoc after a user wrote in with multiple errors found, refs #32430
• src/hg/makeDb/doc/hg38/hg38.txt
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    cf24bf1f4d870e1b6d2d9067c04ff480cfb469b2 Fri Oct 20 12:54:49 2023 -0700
    Adding an updated cosmic makedoc after a user wrote in with multiple errors found, refs #32430
• src/hg/makeDb/doc/hg38/hprcInDel.txt
  • lines changed 37, context: html, text, full: html, text
    56332b7995bf6075d07d88b04e5675c247725892 Tue Oct 17 16:21:18 2023 -0700
    flesh out the indel tracks
• src/hg/makeDb/doc/hg38/hprcRearrange.txt
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    56332b7995bf6075d07d88b04e5675c247725892 Tue Oct 17 16:21:18 2023 -0700
    flesh out the indel tracks
• src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt
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    59ec61092fe573df47f03b7716a6cbdab4c55aab Sat Oct 21 08:06:53 2023 -0700
    VGP update for two assemblies refs #29545
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    5583a49c31ac2f6694d2b91eab44a337d741f42e Sat Oct 21 22:19:25 2023 -0700
    VGP update obsoleted GCA_011100535.1_mCalJac1.pat refs #29545
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    e6950b5b0062d034313160c0ea365c859ef6fe7a Sat Oct 21 23:00:12 2023 -0700
    VGP update adding 37 vertebrate assemblies refs #29545
• src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv
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    59ec61092fe573df47f03b7716a6cbdab4c55aab Sat Oct 21 08:06:53 2023 -0700
    VGP update for two assemblies refs #29545
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    5583a49c31ac2f6694d2b91eab44a337d741f42e Sat Oct 21 22:19:25 2023 -0700
    VGP update obsoleted GCA_011100535.1_mCalJac1.pat refs #29545
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    e6950b5b0062d034313160c0ea365c859ef6fe7a Sat Oct 21 23:00:12 2023 -0700
    VGP update adding 37 vertebrate assemblies refs #29545
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
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    6ee52c28d7494f92b4713f5b00e0250ed957920b Fri Oct 20 22:47:42 2023 -0700
    a VGP update adding 52 new mammal assemblies refs #29545
• src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv
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    d448769dca513fd694e9163e7f08e08bf214efd7 Sat Oct 21 21:16:21 2023 -0700
    VGP update adding three primates refs #29545
• src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv
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    a534a26c5063d4745431d4d4a036d46f6f4e8d84 Thu Oct 19 21:34:42 2023 -0700
    catching up with GCA_004786255.1_Pads_1.0 African bullfrog refs #29545
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    e6950b5b0062d034313160c0ea365c859ef6fe7a Sat Oct 21 23:00:12 2023 -0700
    VGP update adding 37 vertebrate assemblies refs #29545
• src/hg/makeDb/trackDb/human/hg19/prs.ra
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    b6101622d6eb321e249513be1438127287738e1d Wed Oct 18 06:37:32 2023 -0700
    removing BMI PRS as per author request from Niall Lennon, until paper is out, refs #31546
• src/hg/makeDb/trackDb/human/hg19/trackDb.100way.ra
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    14b1f8804bcd230f2252b79b002b23348c354113 Tue Oct 17 15:28:29 2023 -0700
    Reverting some stages phyloP changes #29898 and adding the logoMaf setting back after a fix to the performance issue was put in place, refs #32267
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
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    14b1f8804bcd230f2252b79b002b23348c354113 Tue Oct 17 15:28:29 2023 -0700
    Reverting some stages phyloP changes #29898 and adding the logoMaf setting back after a fix to the performance issue was put in place, refs #32267
• src/hg/makeDb/trackDb/human/hg38/cactus447way.html
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    e978921a28da6c0323b6e0da032378cdb1c1eb4d Mon Oct 16 14:34:33 2023 -0700
    better names_a and -b refs #31528
• src/hg/makeDb/trackDb/human/hg38/hprcArr.ra
  • lines changed 42, context: html, text, full: html, text
    56332b7995bf6075d07d88b04e5675c247725892 Tue Oct 17 16:21:18 2023 -0700
    flesh out the indel tracks
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    176321d68a47d3ddb3ea42be8180804ef6c42a5f Wed Oct 18 12:23:03 2023 -0700
    tiny tweaks to labels for HPRC indel tracks
• src/hg/makeDb/trackDb/human/hg38/trackDb.100way.ra
  • lines changed 1, context: html, text, full: html, text
    14b1f8804bcd230f2252b79b002b23348c354113 Tue Oct 17 15:28:29 2023 -0700
    Reverting some stages phyloP changes #29898 and adding the logoMaf setting back after a fix to the performance issue was put in place, refs #32267
• src/hg/makeDb/trackDb/human/hg38/trackDb.30way.ra
  • lines changed 1, context: html, text, full: html, text
    14b1f8804bcd230f2252b79b002b23348c354113 Tue Oct 17 15:28:29 2023 -0700
    Reverting some stages phyloP changes #29898 and adding the logoMaf setting back after a fix to the performance issue was put in place, refs #32267
• src/hg/makeDb/trackDb/human/hg38/trackDb.447way.ra
  • lines changed 4, context: html, text, full: html, text
    e978921a28da6c0323b6e0da032378cdb1c1eb4d Mon Oct 16 14:34:33 2023 -0700
    better names_a and -b refs #31528
• src/hg/makeDb/trackDb/human/hg38/trackDb.470way.ra
  • lines changed 6, context: html, text, full: html, text
    14b1f8804bcd230f2252b79b002b23348c354113 Tue Oct 17 15:28:29 2023 -0700
    Reverting some stages phyloP changes #29898 and adding the logoMaf setting back after a fix to the performance issue was put in place, refs #32267
• src/hg/makeDb/trackDb/human/hs1/html/hgLiftOver.html
  • lines changed 77, context: html, text, full: html, text
    e6d21fe68e1179e21bbb8b944b35518ff5241160 Fri Oct 20 13:47:28 2023 -0700
    Fixing up liftOver page where we mention for T2T minimap and the UCSC liftOver pipeline, except we never released the UCSC alignments. Refs #32422
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.60way.ra
  • lines changed 4, context: html, text, full: html, text
    14b1f8804bcd230f2252b79b002b23348c354113 Tue Oct 17 15:28:29 2023 -0700
    Reverting some stages phyloP changes #29898 and adding the logoMaf setting back after a fix to the performance issue was put in place, refs #32267
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.35way.ra
  • lines changed 1, context: html, text, full: html, text
    14b1f8804bcd230f2252b79b002b23348c354113 Tue Oct 17 15:28:29 2023 -0700
    Reverting some stages phyloP changes #29898 and adding the logoMaf setting back after a fix to the performance issue was put in place, refs #32267
• src/hg/makeDb/trackDb/tagTypes.tab
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    a6333e7e8be2fbc9c8e3ba3753fa6a25fa8e9c2e Mon Oct 16 12:01:36 2023 -0700
    Adding bigGenePred to the mouseOver support since it works fine, refs #32459
• src/hg/utils/otto/genCC/doGenCC.py
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    76d933ccf24bd1a2a360f9b6a437c2e8445c7583 Wed Oct 18 11:01:51 2023 -0700
    Fixing up a small encoding bug in the GenCC otto job and clarification of the printed message. Refs #31795
• src/hg/utils/otto/sarscov2phylo/includeRecombinants.tsv
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    ae198c06b0f8b1c15ae4f28ce3b4ea6000953695 Mon Oct 23 07:20:00 2023 -0700
    More proposed (& designated) recombinants to exempt from too-many-reversions filter.
• src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv
  • lines changed 12, context: html, text, full: html, text
    d3ab1ece644f987c98b64f9ce8933153de6f1cb5 Mon Oct 16 10:34:15 2023 -0700
    Updated B.1.160 path and added paths for several older lineages that were not annotated correctly. Updated BA.2.86_dropout to cover more seqs. pango-designation release v1.23
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    17657a4a3318325d422492254ae14af3084d5cc7 Mon Oct 23 07:22:20 2023 -0700
    Many new lineages. Still have a backlog to annotate.
• src/product/installer/browserSetup.sh
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    380866bf4dbf6466645034f1ac556923d000243d Tue Oct 17 08:52:17 2023 -0700
    hiding OMIM track, its a default track, but may not be there in offline mode, as we are not allowed to distribute it, refs #32440
• src/utils/bedCollect/bedCollect.c
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    56332b7995bf6075d07d88b04e5675c247725892 Tue Oct 17 16:21:18 2023 -0700
    flesh out the indel tracks
• src/utils/qa/checkHTTPS
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    340225016609062b088f4efd2b6f6c0ad16445d9 Sun Oct 22 23:54:17 2023 -0700
    Adding genomewiki.ucsc.edu to cron for https certificate expiration reminder, refs #32456
• src/utils/qa/qaTestScript.py
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    fca4ac6562d128072aa3e113d40e64ffd4c27133 Thu Oct 19 09:29:43 2023 -0700
    Updating the clicking of items on hgTracks, refs #30817
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    a00d84ab5d48483c624d495fbbe17d158ee9c2eb Mon Oct 23 01:10:28 2023 -0700
    Adding hgCollection with custom tracks test case, refs #32477
• src/utils/qa/weeklybld/buildEnv.csh
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    03026d1c50dad410ff59a9a01edd2409c6762258 Mon Oct 16 09:50:46 2023 -0700
    v456 preview1
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    7cfb6ae85a6c143f0425dd4a79613790df5e1969 Mon Oct 23 09:29:27 2023 -0700
    v456 preview2

• lines changed: 1077
• files changed: 62