All File Changes

v473_base to v474_preview (2024-10-28 to 2024-11-04) v474

• confs/hgwbeta.hg.conf
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    7215dbe7864a919d33e3ec2f5e753751bff63552 Sun Nov 3 01:11:18 2024 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/cgilib/cartEdit6.c
  • lines changed 13, context: html, text, full: html, text
    6452a01362d66b305bfda62b217901d0da0c587f Fri Nov 1 11:00:59 2024 -0700
    add cart rewrite for decipher tracks moving into supertrack
• src/hg/cgilib/cartRewrite.c
  • lines changed 2, context: html, text, full: html, text
    6452a01362d66b305bfda62b217901d0da0c587f Fri Nov 1 11:00:59 2024 -0700
    add cart rewrite for decipher tracks moving into supertrack
• src/hg/cgilib/makefile
  • lines changed 1, context: html, text, full: html, text
    6452a01362d66b305bfda62b217901d0da0c587f Fri Nov 1 11:00:59 2024 -0700
    add cart rewrite for decipher tracks moving into supertrack
• src/hg/hgLiftOver/hgLiftOver.c
  • lines changed 8, context: html, text, full: html, text
    2234e88de4bebfb8e520d1c8c284298d12986477 Wed Oct 30 16:23:05 2024 -0700
    Adding the FAQ link for LiftOver output errors and updating the text in hgLiftOver, refs #34665
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    64377fb8085160f38f0f3b7158ae8c20a33b82df Wed Oct 30 16:32:17 2024 -0700
    Editing the hgLiftOver text, had two 'with', refs #34665
• src/hg/hgTracks/hgTracks.h
  • lines changed 1, context: html, text, full: html, text
    978d826eef9b73e51d9c0642a95b7346a79010d1 Fri Oct 25 13:04:16 2024 -0700
    oops, some include files for setColorWith
• src/hg/hgTracks/wigCommon.h
  • lines changed 1, context: html, text, full: html, text
    978d826eef9b73e51d9c0642a95b7346a79010d1 Fri Oct 25 13:04:16 2024 -0700
    oops, some include files for setColorWith
• src/hg/hgTracks/wigTrack.c
  • lines changed 35, context: html, text, full: html, text
    a1a2113c2f18ce0aa25041a00f114092624d9a94 Thu Oct 24 17:44:28 2024 -0700
    letting users specify a bigBed to color their wiggle
  • lines changed 35, context: html, text, full: html, text
    8bf058e19dd56b134b5def2464f1c648d2845273 Fri Oct 25 13:03:00 2024 -0700
    add setColorWith trackDb variable to set wiggle color with bigBed
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    6cbc11f12e044ca1c29cef76f2c1e1fcabcb54c0 Thu Oct 31 17:02:13 2024 -0700
    don't overwrite the end of the array
• src/hg/htdocs/FAQ/FAQdisplay.html
  • lines changed 57, context: html, text, full: html, text
    5768df48d31274d029a8df6e858444ef0a355801 Tue Oct 29 16:22:07 2024 -0700
    Adding a FAQ for LiftOver output errors, refs #34665
• src/hg/htdocs/FAQ/FAQreleases.html
  • lines changed 41, context: html, text, full: html, text
    c7ff827180db5c246eb48e0b52cec414c44370cb Thu Oct 31 15:51:46 2024 -0700
    Adding examples of how to extract positions using rsIDs or extract rsIDs using a list of positions. Max says it is a commonly asked question so updating our FAQ documentation, refs #34701
• src/hg/htdocs/cite.html
  • lines changed 2, context: html, text, full: html, text
    74c5e052d6546daa0cdf2962b1c1f11961832af5 Tue Oct 29 12:42:40 2024 -0700
    Adding the latest nar paper to the htdoc pages, No RM
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 9, context: html, text, full: html, text
    74c5e052d6546daa0cdf2962b1c1f11961832af5 Tue Oct 29 12:42:40 2024 -0700
    Adding the latest nar paper to the htdoc pages, No RM
• src/hg/inc/hubConnect.h
  • lines changed 3, context: html, text, full: html, text
    3b070db77a829321ba062367c4860adb671ab743 Fri Oct 25 16:50:55 2024 -0700
    put out a better error message if a hub-based assembly disappears. Refs #34611
• src/hg/js/hgTracks.js
  • lines changed 2, context: html, text, full: html, text
    c446beb4b0451f790c0bb8e6bc117afa9106d802 Wed Oct 30 11:43:49 2024 -0700
    Fix for being unable to type in pop-up hgTrackUi fields, refs #34737
• src/hg/js/hui.js
  • lines changed 1, context: html, text, full: html, text
    4f5e9072e59d1fd3744fba80f101e6d3374c552e Thu Oct 31 05:53:34 2024 -0700
    color picker looks like other options, refs #33302
• src/hg/lib/hdb.c
  • lines changed 13, context: html, text, full: html, text
    3b070db77a829321ba062367c4860adb671ab743 Fri Oct 25 16:50:55 2024 -0700
    put out a better error message if a hub-based assembly disappears. Refs #34611
• src/hg/lib/hubConnect.c
  • lines changed 11, context: html, text, full: html, text
    3b070db77a829321ba062367c4860adb671ab743 Fri Oct 25 16:50:55 2024 -0700
    put out a better error message if a hub-based assembly disappears. Refs #34611
• src/hg/lib/hui.c
  • lines changed 2, context: html, text, full: html, text
    4f5e9072e59d1fd3744fba80f101e6d3374c552e Thu Oct 31 05:53:34 2024 -0700
    color picker looks like other options, refs #33302
  • lines changed 1, context: html, text, full: html, text
    28e3b85ba41980664563468e7e22584ba3335917 Thu Oct 31 09:56:58 2024 -0700
    small note to tooltip, refs #33302
• src/hg/lib/jksql.c
  • lines changed 3, context: html, text, full: html, text
    472590df500280dc4e82cf0e9aacd5fad147908b Mon Nov 4 04:52:54 2024 -0800
    fix for mysql8 client libs, refs #34723
• src/hg/lib/trackDbCustom.c
  • lines changed 1, context: html, text, full: html, text
    0a582c905f844663a018e9940ee82ff29f69df50 Sun Nov 3 14:36:52 2024 -0800
    add setColorWith to the list of file types that get macro substution
• src/hg/lib/trackHub.c
  • lines changed 3, context: html, text, full: html, text
    f6b1bdaa2f9c39ba2100187c8f596e71c844d846 Thu Oct 24 17:46:02 2024 -0700
    letting users specify a bigBed to color wiggles
  • lines changed 3, context: html, text, full: html, text
    7bc28d01fc11bfeab43b5a970094fce125cf5193 Fri Oct 25 12:00:25 2024 -0700
    Revert "letting users specify a bigBed to color wiggles" This reverts commit f6b1bdaa2f9c39ba2100187c8f596e71c844d846.
• src/hg/makeDb/doc/asmHubs/asmHubList.pl
  • lines changed 61, context: html, text, full: html, text
    42d19c5cec90202c2b8f520de948905af057fe4e Sun Nov 3 13:07:26 2024 -0800
    switch from counting in genomes.txt and instead use the assemblyList.json and count up clades correctly refs #29545
• src/hg/makeDb/doc/asmHubs/hubIndex.pl
  • lines changed 8, context: html, text, full: html, text
    42d19c5cec90202c2b8f520de948905af057fe4e Sun Nov 3 13:07:26 2024 -0800
    switch from counting in genomes.txt and instead use the assemblyList.json and count up clades correctly refs #29545
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 58, context: html, text, full: html, text
    3bda44abd31a4cb5c19f7d6c0f66d6279bdf4cb7 Fri Nov 1 19:50:21 2024 -0700
    running an update for VGP refs #29545
• src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv
  • lines changed 10, context: html, text, full: html, text
    3bda44abd31a4cb5c19f7d6c0f66d6279bdf4cb7 Fri Nov 1 19:50:21 2024 -0700
    running an update for VGP refs #29545
• src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv
  • lines changed 8, context: html, text, full: html, text
    3bda44abd31a4cb5c19f7d6c0f66d6279bdf4cb7 Fri Nov 1 19:50:21 2024 -0700
    running an update for VGP refs #29545
• src/hg/makeDb/doc/hg38/problematicGIAB.txt
  • lines changed 49, context: html, text, full: html, text
    226f4f99c439d7f22200b0f28bf30a8816442e9d Sun Nov 3 14:21:21 2024 -0800
    Adding the makedocs for the difficult regions from GIAB track, refs #32715
• src/hg/makeDb/doc/hs1/problematicGIAB.txt
  • lines changed 49, context: html, text, full: html, text
    226f4f99c439d7f22200b0f28bf30a8816442e9d Sun Nov 3 14:21:21 2024 -0800
    Adding the makedocs for the difficult regions from GIAB track, refs #32715
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
  • lines changed 4, context: html, text, full: html, text
    3bda44abd31a4cb5c19f7d6c0f66d6279bdf4cb7 Fri Nov 1 19:50:21 2024 -0700
    running an update for VGP refs #29545
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 16, context: html, text, full: html, text
    e9d9c5ac5a0eb1a070918f2a261cf075e1dea1d2 Fri Nov 1 19:51:52 2024 -0700
    running an update for VGP refs #29545
• src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv
  • lines changed 53, context: html, text, full: html, text
    3bda44abd31a4cb5c19f7d6c0f66d6279bdf4cb7 Fri Nov 1 19:50:21 2024 -0700
    running an update for VGP refs #29545
• src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv
  • lines changed 20, context: html, text, full: html, text
    3bda44abd31a4cb5c19f7d6c0f66d6279bdf4cb7 Fri Nov 1 19:50:21 2024 -0700
    running an update for VGP refs #29545
• src/hg/makeDb/trackDb/human/cadd.alpha.ra
  • lines changed 193, context: html, text, full: html, text
    1eb0e356b79b6f723aba17fa155e5d5506e913d8 Sat Nov 2 12:25:19 2024 -0700
    Removing a CADD file that was used to develop the CADD 1.7 track, refs #33940
• src/hg/makeDb/trackDb/human/decipher.alpha.ra
  • lines changed 1, context: html, text, full: html, text
    6452a01362d66b305bfda62b217901d0da0c587f Fri Nov 1 11:00:59 2024 -0700
    add cart rewrite for decipher tracks moving into supertrack
• src/hg/makeDb/trackDb/human/hg38/problematic.html
  • lines changed 2, context: html, text, full: html, text
    ececc21b1205b3589dcf50cbfefaa3626662dfd9 Thu Oct 31 16:45:16 2024 -0700
    Updating the hg38 difficult regions from GIAB to v3.5, refs #32715
• src/hg/makeDb/trackDb/human/hg38/problematic.ra
  • lines changed 4, context: html, text, full: html, text
    1e010b388c8a7854b579399a0b18de8f1f3c8137 Wed Oct 30 11:51:17 2024 -0700
    Code review edits, refs #34676
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    ececc21b1205b3589dcf50cbfefaa3626662dfd9 Thu Oct 31 16:45:16 2024 -0700
    Updating the hg38 difficult regions from GIAB to v3.5, refs #32715
• src/hg/makeDb/trackDb/human/hs1/problematic.html
  • lines changed 37, context: html, text, full: html, text
    9adb8d6f8addb802163d0502f9f1d6094cdd56fc Thu Oct 31 17:05:29 2024 -0700
    Adding the hs1 difficult regions from GIAB track, refs #32715
• src/hg/makeDb/trackDb/human/hs1/problematic.ra
  • lines changed 41, context: html, text, full: html, text
    9adb8d6f8addb802163d0502f9f1d6094cdd56fc Thu Oct 31 17:05:29 2024 -0700
    Adding the hs1 difficult regions from GIAB track, refs #32715
  • lines changed 2, context: html, text, full: html, text
    09225970265680b29424b5bed22971307bde3ed5 Thu Oct 31 17:12:04 2024 -0700
    Editing the hs1 difficult regions from GIAB track, refs #32715
• src/hg/makeDb/trackDb/human/hs1/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    9adb8d6f8addb802163d0502f9f1d6094cdd56fc Thu Oct 31 17:05:29 2024 -0700
    Adding the hs1 difficult regions from GIAB track, refs #32715
• src/hg/utils/automation/HgAutomate.pm
  • lines changed 21, context: html, text, full: html, text
    e69db257480ddc4aae24ca6ae0130c9450abc362 Mon Oct 28 14:07:47 2024 -0700
    do not use /dev/shm as a temporary directory refs #34685
• src/hg/utils/automation/asmHubRepeatMasker.sh
  • lines changed 8, context: html, text, full: html, text
    27300d62d155d9941c226a2c27f3a33b3ea53ed0 Mon Oct 28 14:15:17 2024 -0700
    do not use /dev/shm as a temporary directory refs #34685
• src/hg/utils/automation/doAssemblyHub.pl
  • lines changed 3, context: html, text, full: html, text
    2c6090e8d56e6c6ebf9fe8b1e348713451212743 Mon Oct 28 14:25:14 2024 -0700
    remember to remove the temporary seqList file from /dev/shm refs #34685
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    0fb5e02c75ed9836aecfb3a36987bfb8b5fd73e4 Mon Oct 28 19:37:36 2024 -0700
    temporary set doAugustus to cluster ku until hgcompute issues worked out refs #34685
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    7592170a1f176f724492f264eff0e094cc0bc316 Mon Nov 4 03:54:26 2024 -0800
    upgrade augustus binary and correct use of mktemp refs #34685
• src/hg/utils/automation/doAugustus.pl
  • lines changed 1, context: html, text, full: html, text
    e69db257480ddc4aae24ca6ae0130c9450abc362 Mon Oct 28 14:07:47 2024 -0700
    do not use /dev/shm as a temporary directory refs #34685
  • lines changed 1, context: html, text, full: html, text
    0c126bf17c586c00c15714a69ce874c1423e774f Tue Oct 29 14:56:19 2024 -0700
    indicate which paraHub the cluster job is on refs #34685
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    7592170a1f176f724492f264eff0e094cc0bc316 Mon Nov 4 03:54:26 2024 -0800
    upgrade augustus binary and correct use of mktemp refs #34685
• src/hg/utils/automation/doBlastzChainNet.pl
  • lines changed 8, context: html, text, full: html, text
    e69db257480ddc4aae24ca6ae0130c9450abc362 Mon Oct 28 14:07:47 2024 -0700
    do not use /dev/shm as a temporary directory refs #34685
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    767f1be1b487090edbfa9d3653af4a3192b81b7d Thu Oct 31 15:36:28 2024 -0700
    mistaken bash code in csh script refs #3468
• src/hg/utils/automation/doCpgIslands.pl
  • lines changed 8, context: html, text, full: html, text
    e69db257480ddc4aae24ca6ae0130c9450abc362 Mon Oct 28 14:07:47 2024 -0700
    do not use /dev/shm as a temporary directory refs #34685
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    039188978e9faef534235afda7eb14aee6d6cda9 Tue Oct 29 14:00:02 2024 -0700
    handle the case of empty grep result on part.list refs #34685
• src/hg/utils/automation/doRepeatMasker.pl
  • lines changed 8, context: html, text, full: html, text
    e69db257480ddc4aae24ca6ae0130c9450abc362 Mon Oct 28 14:07:47 2024 -0700
    do not use /dev/shm as a temporary directory refs #34685
  • lines changed 1, context: html, text, full: html, text
    2e584a1c66bae4339bd009372f47e97f0636fe85 Tue Oct 29 15:01:41 2024 -0700
    indicate which paraHub the cluster job is on refs #34685
• src/hg/utils/automation/doRepeatModeler.pl
  • lines changed 1, context: html, text, full: html, text
    dac1dd5605a7a3a9dab41ef36b3859953c454ad2 Tue Oct 29 15:03:43 2024 -0700
    indicate which paraHub the cluster job is on refs #34685
• src/hg/utils/automation/doSameSpeciesLiftOver.pl
  • lines changed 2, context: html, text, full: html, text
    e69db257480ddc4aae24ca6ae0130c9450abc362 Mon Oct 28 14:07:47 2024 -0700
    do not use /dev/shm as a temporary directory refs #34685
• src/hg/utils/automation/doSimpleRepeat.pl
  • lines changed 16, context: html, text, full: html, text
    e69db257480ddc4aae24ca6ae0130c9450abc362 Mon Oct 28 14:07:47 2024 -0700
    do not use /dev/shm as a temporary directory refs #34685
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    5bd057d435611f90f3767e1c5bc9a73a56b62e8b Mon Oct 28 21:11:14 2024 -0700
    adding ram and cpu arguments since this process can work in 4gb with 1cpu refs #34685
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    7b95c46185395e1500ab3a56bd185a11be4b9517 Wed Oct 30 21:17:55 2024 -0700
    not a good idea to use /tmp/ for the simple repeat - that filesystem is way too small for the long running hippos refs #34685
• src/hg/utils/automation/doWindowMasker.pl
  • lines changed 16, context: html, text, full: html, text
    e69db257480ddc4aae24ca6ae0130c9450abc362 Mon Oct 28 14:07:47 2024 -0700
    do not use /dev/shm as a temporary directory refs #34685
• src/hg/utils/otto/ottoCompareGitVsHiveFiles.py
  • lines changed 1, context: html, text, full: html, text
    f25b14a9c7970f227d9a6c2f2b35093585d53589 Tue Oct 29 11:05:36 2024 -0700
    Adding a new file exception for mask.bed, we have a copy committed in the tree for mpxv, but a file with the same name is now used by hgPhyloPlace.
• src/lib/basicBed.c
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    83c50d3af3614ea3832bbea7c95488296d0b392e Mon Nov 4 07:17:51 2024 -0800
    When parsing a BED, the space allocated for expScores should be at least expCount entries, even if that's greater than the number of exons. #12101
• src/lib/bbiRead.c
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    639c013f2f7cd7553674c60372a3208cd85a47be Thu Oct 31 14:14:28 2024 -0700
    fix a bug in calculating summaries with the size of the summaries is more than the number of bases in the region. Refs #26932
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    02ec706d1e86195a8fbc0f5e27a41d32baa66434 Thu Oct 31 14:41:01 2024 -0700
    fix silly typo
• src/lib/psGfx.c
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    bca6edaef4f6d3c6a55282c4414936b624a1b54b Mon Oct 28 12:56:15 2024 -0700
    prevent iconv from bailing just because it can't translate a UTF-8 string
• src/utils/qa/errorLogKeywordSearch.py
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    bbd1e55c6e3053e1bbf28a9fabe36335a9a5f387 Mon Oct 28 16:29:51 2024 -0700
    Adding new cron that counts occurence of various keywords in the error logs, refs #33007
• src/utils/qa/makefile
  • lines changed 1, context: html, text, full: html, text
    bbd1e55c6e3053e1bbf28a9fabe36335a9a5f387 Mon Oct 28 16:29:51 2024 -0700
    Adding new cron that counts occurence of various keywords in the error logs, refs #33007
• src/utils/qa/weeklybld/buildEnv.csh
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    b42c3799fda98ceae0d2e7781b8f191b92f08753 Mon Nov 4 10:20:59 2024 -0800
    v474 preview1, refs #34670

• lines changed: 1230
• files changed: 74