All File Changes

v450_base to v451_preview (2023-06-26 to 2023-07-03) v451

• build/kent-core/makeKentCore
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    c61ce270c06c60383bca4ab6f479665f58402701 Sat Jul 1 00:16:26 2023 -0700
    Fixing git commit instructions in makeKentCore
• src/hg/hgGeneGraph/hgGeneGraph
  • lines changed 27, context: html, text, full: html, text
    ecb21defee4e9278c2d6b80036e2fc7ab1f9f838 Fri Jun 30 06:50:47 2023 -0700
    more fixes for hgGeneGraph, refs #31563
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    0499acf308c6afaf709ab70679c776ab7b1d6b34 Mon Jul 3 03:16:22 2023 -0700
    another py3 fix for hgGeneGraph, refs #31563
• src/hg/htdocs/contacts.html
  • lines changed 53, context: html, text, full: html, text
    a2ee38a7ef81c51a8bc51c8a387b775ddf3d9abe Tue Jun 27 02:11:09 2023 -0700
    changing contacts page a little, refs #31558
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    3db04f35bbb85495c3ea038a0e5ff3020ceb70ca Wed Jun 28 16:00:06 2023 -0700
    Small tweaks to Max's update contacts page, refs #31558
• src/hg/htdocs/goldenPath/help/customTrackText.html
  • lines changed 1, context: html, text, full: html, text
    0db22588a7ff9208f468cbb5a80884703868a26a Tue Jun 27 12:15:23 2023 -0700
    change maxItems default from 250 to 10,000
• src/hg/htdocs/goldenPath/help/trackDb/changes.html
  • lines changed 6, context: html, text, full: html, text
    8143e1b7f4adbcbadc8c3024bd5afa2aafd7c568 Tue Jun 27 14:04:40 2023 -0700
    documenting trackDb default change, refs #31363
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 1, context: html, text, full: html, text
    0db22588a7ff9208f468cbb5a80884703868a26a Tue Jun 27 12:15:23 2023 -0700
    change maxItems default from 250 to 10,000
• src/hg/htdocs/license/index.html
  • lines changed 8, context: html, text, full: html, text
    7e6e9eab801c5347bf2399df9708543289bd3ba2 Wed Jun 28 06:03:13 2023 -0700
    clarified license once more, refs #31575
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    958cbc454e075a59a807d615ca961d25dba3cabb Wed Jun 28 06:04:51 2023 -0700
    more space, refs #31575
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    08b5bd3c672dfca32e2b0600f0e7857e09380cb0 Wed Jun 28 16:40:35 2023 -0700
    Small tweaks to Max's update of the license page, refs #31575
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    2f4bb5487cf1522af8f502de7257e028b2dda0bd Wed Jun 28 16:45:22 2023 -0700
    Adding another line to cite us because why not, refs #31575
• src/hg/lib/trackHub.c
  • lines changed 4, context: html, text, full: html, text
    22c25c30bebc4819a11ed7d2ae4a1c6efe28d388 Mon Jun 26 14:02:58 2023 -0700
    Move check for whether track hub genome name contains to whitespace to after check whether the genome name exists, refs #31545
• src/hg/makeDb/doc/hg38/cactus447.txt
  • lines changed 305, context: html, text, full: html, text
    923cb1e06520e8f302baabded147081a64db5666 Tue Jun 27 14:20:10 2023 -0700
    construction procedure for the 447-way alignment refs #31528
• src/hg/makeDb/doc/hg38/hprc.metaData.tsv
  • lines changed 48, context: html, text, full: html, text
    88671a65c8bff92cbcd7eadf4bac3e9dad9df7d0 Thu Jun 29 12:30:57 2023 -0700
    listings of HPRC meta data from their git pages refs #31561
  • lines changed 4, context: html, text, full: html, text
    0b248354b16bae38d735588644d54244d966dd1a Thu Jun 29 13:13:24 2023 -0700
    adding population and subpopulation descriptions refs #31561
• src/hg/makeDb/doc/hg38/hprcCoverage.txt
  • lines changed 82, context: html, text, full: html, text
    7b9b6f6f3a35a1b35d8cd40c06b6267623b957cd Fri Jun 30 14:30:05 2023 -0700
    adding coverage/complement tracks from the HPRC chainLinks refs #31561
• src/hg/makeDb/doc/hs1/chm13v2.0_CytoBandMapping.csv
  • lines changed 864, context: html, text, full: html, text
    d09cd024d52f43ebc0fca050b1cd2124492f9e86 Fri Jun 30 03:02:53 2023 -0700
    adding csv version of xlsx file, refs #31542
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    88e65f9779f8b327d8131349bf8d7f75e6b5eb5f Mon Jul 3 01:18:53 2023 -0700
    removing csv file again, misunderstanding, refs #31542
• src/hg/makeDb/doc/hs1/chm13v2.0_CytoBandMapping.main.tsv
  • lines changed 863, context: html, text, full: html, text
    58a5e41d3614c5b524255bf2eb9b91840e92cc31 Fri Jun 30 11:35:10 2023 -0700
    export main sheet
• src/hg/makeDb/doc/hs1/chm13v2.0_CytoBandMapping.xlsx
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    59a3fbdf64e44ac8eac50f55e269004e5c09d397 Thu Jun 29 18:27:54 2023 -0700
    added information on how CHM13 cytobands are built
• src/hg/makeDb/doc/hs1/t2t-supplied.txt
  • lines changed 8, context: html, text, full: html, text
    59a3fbdf64e44ac8eac50f55e269004e5c09d397 Thu Jun 29 18:27:54 2023 -0700
    added information on how CHM13 cytobands are built
  • lines changed 1, context: html, text, full: html, text
    58a5e41d3614c5b524255bf2eb9b91840e92cc31 Fri Jun 30 11:35:10 2023 -0700
    export main sheet
• src/hg/makeDb/trackDb/human/hg38/chainNetHprc.html
  • lines changed 57, context: html, text, full: html, text
    739d5df01bb223681bb832826d48c137484034f8 Wed Jun 28 16:32:16 2023 -0700
    beginning to package the HPRC chains as their own track refs #31561
  • lines changed 57, context: html, text, full: html, text
    2045e76bd07314f248db64d6d60b2ab46a1f19f3 Fri Jun 30 11:51:55 2023 -0700
    names changed to chainsHprc refs #31561
• src/hg/makeDb/trackDb/human/hg38/chainNetHprc.ra
  • lines changed 907, context: html, text, full: html, text
    739d5df01bb223681bb832826d48c137484034f8 Wed Jun 28 16:32:16 2023 -0700
    beginning to package the HPRC chains as their own track refs #31561
  • lines changed 91, context: html, text, full: html, text
    4499d20f21a554b50e0e35a208010a31f1aafe42 Thu Jun 29 11:10:27 2023 -0700
    turn on a matrix to control groups of the tracks as one set refs #31561
  • lines changed 377, context: html, text, full: html, text
    bcd1fb8bbdaa113c9da8f9cc87ae48b89c9842e8 Thu Jun 29 14:02:47 2023 -0700
    now with subpopulation groupings although there seems to be no order refs #31561
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    3d7016e97048a97da6d04b9dec3b035aa06205a3 Thu Jun 29 14:40:19 2023 -0700
    attempted ordering of the subpopulations refs #31561
  • lines changed 1, context: html, text, full: html, text
    932e4f0802f70251dd0fd8d74e862675902080e0 Thu Jun 29 14:50:33 2023 -0700
    trying sortOrder subpop=+ only but it does not sort the matrix refs #31561
  • lines changed 996, context: html, text, full: html, text
    2045e76bd07314f248db64d6d60b2ab46a1f19f3 Fri Jun 30 11:51:55 2023 -0700
    names changed to chainsHprc refs #31561
• src/hg/makeDb/trackDb/human/hg38/chainNetHumanExperiment.ra
  • lines changed 9061, context: html, text, full: html, text
    739d5df01bb223681bb832826d48c137484034f8 Wed Jun 28 16:32:16 2023 -0700
    beginning to package the HPRC chains as their own track refs #31561
• src/hg/makeDb/trackDb/human/hg38/chainsHprc.html
  • lines changed 57, context: html, text, full: html, text
    c520a7d55b8fb32a24b5293c7a516d132d97bd54 Fri Jun 30 11:25:10 2023 -0700
    there is nothing about net in this track, should be no mention of net refs #31561
• src/hg/makeDb/trackDb/human/hg38/chainsHprc.ra
  • lines changed 989, context: html, text, full: html, text
    c520a7d55b8fb32a24b5293c7a516d132d97bd54 Fri Jun 30 11:25:10 2023 -0700
    there is nothing about net in this track, should be no mention of net refs #31561
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    f83b9b55ba06b07733ba018859b9a9e2b8960df5 Fri Jun 30 15:53:03 2023 -0700
    adding T2T-CHM13 and add haplotype group refs #31561
• src/hg/makeDb/trackDb/human/hg38/hprcChain.ra
  • lines changed 3, context: html, text, full: html, text
    739d5df01bb223681bb832826d48c137484034f8 Wed Jun 28 16:32:16 2023 -0700
    beginning to package the HPRC chains as their own track refs #31561
• src/hg/makeDb/trackDb/human/hg38/hprcCoverage.ra
  • lines changed 1, context: html, text, full: html, text
    739d5df01bb223681bb832826d48c137484034f8 Wed Jun 28 16:32:16 2023 -0700
    beginning to package the HPRC chains as their own track refs #31561
  • lines changed 59, context: html, text, full: html, text
    7f94d1a000ee66db823bb7749aee3d995bd0a29f Fri Jun 30 14:31:42 2023 -0700
    adding new coverage track refs #31561
• src/hg/makeDb/trackDb/human/hg38/hprcCoverage97.ra
  • lines changed 65, context: html, text, full: html, text
    7f94d1a000ee66db823bb7749aee3d995bd0a29f Fri Jun 30 14:31:42 2023 -0700
    adding new coverage track refs #31561
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    caadfdf9e08221f25f774498ed2706f16ba4724b Fri Jun 30 17:39:50 2023 -0700
    add a complement for this one to compare to the other refs #31561
• src/hg/makeDb/trackDb/human/hg38/trackDb.447way.ra
  • lines changed 2, context: html, text, full: html, text
    5a84569301fd828c42f868c5a3de353fc9b39c29 Fri Jun 30 16:00:20 2023 -0700
    now with the full iRow annotated big file and add species name labels refs #31528
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    2b2c919006aa13c1a98deeb45fd5112a1b8e5422 Mon Jun 26 17:56:58 2023 -0700
    place alpha tag on 447way no redmine
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    739d5df01bb223681bb832826d48c137484034f8 Wed Jun 28 16:32:16 2023 -0700
    beginning to package the HPRC chains as their own track refs #31561
  • lines changed 1, context: html, text, full: html, text
    c520a7d55b8fb32a24b5293c7a516d132d97bd54 Fri Jun 30 11:25:10 2023 -0700
    there is nothing about net in this track, should be no mention of net refs #31561
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    7f94d1a000ee66db823bb7749aee3d995bd0a29f Fri Jun 30 14:31:42 2023 -0700
    adding new coverage track refs #31561
• src/hg/makeDb/trackDb/trackDb.chainNet.primates.ra
  • lines changed 97, context: html, text, full: html, text
    d1c1f4a37a01868c7e3b2b025c8757ce306fe7ef Wed Jun 28 16:12:46 2023 -0700
    adding GCA_011100615.1 crab-eating macaque chain/net no redmine
• src/utils/bigBedToBed/bigBedToBed.c
  • lines changed 56, context: html, text, full: html, text
    e2389e03c44ae29a330fd0234060494246cb41c5 Wed Jun 28 08:12:06 2023 +0200
    now adding the source code change for -bed option to bigBedToBed, refs #31531
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    b033f31366bc4c78ef9567b7a37b450a07669e36 Tue Jun 27 23:15:15 2023 -0700
    fixing unused variable error, was not found by clang on osx, refs #31531
• src/utils/pslMap/pslMap.c
  • lines changed 11, context: html, text, full: html, text
    ca9aa98fe525e6a571de9edb55def7cad009c920 Fri Jun 30 00:20:40 2023 -0700
    add pslMap -check option to check for valid PSLs to aid in debugging
• src/utils/pslMap/usage.txt
  • lines changed 2, context: html, text, full: html, text
    ca9aa98fe525e6a571de9edb55def7cad009c920 Fri Jun 30 00:20:40 2023 -0700
    add pslMap -check option to check for valid PSLs to aid in debugging
• src/utils/qa/hubCheckPublicHubs.sh
  • lines changed 6, context: html, text, full: html, text
    ff0b1e7bb394bd39e8c550fafb2be3c51d19f7b0 Tue Jun 27 10:48:28 2023 -0700
    Adding path for commands, make directory command and month for directory name, refs #29319
• src/utils/qa/makefile
  • lines changed 4, context: html, text, full: html, text
    bb8631233d8dbf5dde5725471f404105637879c7 Tue Jun 27 10:59:11 2023 -0700
    Adding a script for Selenium testing and scripts for hubCheck to find missing description pages/couldnt open errors and draft emails, refs #30817 #29319
• src/utils/qa/qaTestScript.py
  • lines changed 5, context: html, text, full: html, text
    534afa3162012a8cf63a67d2c6f33de49ab901ba Mon Jun 26 16:24:47 2023 -0700
    Adding a tmpdir for the cron, refs #30817
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    c536d4998bee3af0fa1dd8875224ad46e5891804 Tue Jun 27 13:27:35 2023 -0700
    Updating tmpdir for the cron, refs #30817
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    fde199b11dff18a7b716b28dcd2c2d9370bb6624 Thu Jun 29 12:17:37 2023 -0700
    Fixing tmpdir for the cron, refs #30817
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    18e3c53d908be42e7bd8c8e17b2fb260c99128b0 Mon Jul 3 10:39:40 2023 -0700
    v451 preview1, refs #31600
• src/utils/qa/weeklybld/sendLogEmail.pl
  • lines changed 1, context: html, text, full: html, text
    e44910ae7f8158bb03d14b71310c3fc11eb4966e Mon Jun 26 23:26:54 2023 -0700
    sendLogEmail.pl authorFilter contains unwanted newline at end, add chomp statement to remove it, makes shell happy.

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• files changed: 57