All File Changes

v472_base to v473_preview (2024-10-07 to 2024-10-14) v473

• src/hg/hgCustom/hgCustom.c
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    1e45128f219d904e99ce298a19e1a43de8f2aa34 Fri Oct 11 12:19:07 2024 -0700
    Updating the text on hgCustom to be more clear on how to update the custom track data from a URL, refs #9452
• src/hg/hgTables/mainPage.c
  • lines changed 5, context: html, text, full: html, text
    df9e09f635d122d0247e6a60dea6d5f0a4ac21b4 Mon Oct 14 05:17:47 2024 -0700
    changes after code review, refs #34582
• src/hg/hgTracks/hgTracks.c
  • lines changed 2, context: html, text, full: html, text
    5999c3385b96ef26b00b63d38808099ad142538d Tue Oct 8 14:33:07 2024 -0700
    fix some problems with what happens after the 32K image is exceeded.
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    623a441bd4af274051b4a397c08e503b6caf2db2 Tue Oct 8 15:06:15 2024 -0700
    Revert "fix some problems with what happens after the 32K image is exceeded." This reverts commit 5999c3385b96ef26b00b63d38808099ad142538d.
  • lines changed 2, context: html, text, full: html, text
    96dd2f204c981155353837647734bc62b96ef85a Tue Oct 8 15:10:15 2024 -0700
    some big* tracks can't wiggle. Causes a problem with images over 32k
• src/hg/hgTracks/simpleTracks.c
  • lines changed 4, context: html, text, full: html, text
    5999c3385b96ef26b00b63d38808099ad142538d Tue Oct 8 14:33:07 2024 -0700
    fix some problems with what happens after the 32K image is exceeded.
  • lines changed 4, context: html, text, full: html, text
    623a441bd4af274051b4a397c08e503b6caf2db2 Tue Oct 8 15:06:15 2024 -0700
    Revert "fix some problems with what happens after the 32K image is exceeded." This reverts commit 5999c3385b96ef26b00b63d38808099ad142538d.
  • lines changed 5, context: html, text, full: html, text
    96dd2f204c981155353837647734bc62b96ef85a Tue Oct 8 15:10:15 2024 -0700
    some big* tracks can't wiggle. Causes a problem with images over 32k
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 23, context: html, text, full: html, text
    8f153131c8eb2c2b898d79e0e79c61c8f1d4798e Tue Oct 8 15:58:50 2024 -0700
    Staging the news announcement for ClinGen CSpec track and tweaking the caps of the label. Refs #33794
  • lines changed 18, context: html, text, full: html, text
    6f3b1f2f5fc0b7ce851ef203da26bb2236a6b83a Fri Oct 11 18:08:39 2024 -0700
    Announcing the release of the CADD 1.7 track, refs #33940
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    9f34fe132f7d27aaceea910f96d3f9035b1a56e1 Fri Oct 11 20:21:00 2024 -0700
    Small grammar fix for the CADD 1.7 track announcement, refs #33940
• src/hg/htdocs/indexNews.html
  • lines changed 19, context: html, text, full: html, text
    8f153131c8eb2c2b898d79e0e79c61c8f1d4798e Tue Oct 8 15:58:50 2024 -0700
    Staging the news announcement for ClinGen CSpec track and tweaking the caps of the label. Refs #33794
• src/hg/inc/hui.h
  • lines changed 3, context: html, text, full: html, text
    df9e09f635d122d0247e6a60dea6d5f0a4ac21b4 Mon Oct 14 05:17:47 2024 -0700
    changes after code review, refs #34582
• src/hg/js/hgTracks.js
  • lines changed 2, context: html, text, full: html, text
    723c7a46c87ed42f8510ed1bf35a3a8890f93609 Fri Oct 11 03:08:30 2024 -0700
    adapting the text a little of the tutorial box, and removing the close button, feedback from Ana und a few users, refs #34604
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    f77216da64ee5a4ff6463b0c42f2fc0189c7cb40 Fri Oct 11 05:58:32 2024 -0700
    changes after code review, address case when top track is not ruler track, refs #34582
  • lines changed 8, context: html, text, full: html, text
    1e3353d3a833c0ec77c70af59add06074220bade Mon Oct 14 04:55:18 2024 -0700
    default on OK button when enter is clicked on track ui dialog box, refs #8833
  • lines changed 5, context: html, text, full: html, text
    66a35c991bbf610b2599802b906c53e84b10237f Mon Oct 14 10:17:09 2024 -0700
    Disable download track data in window function for gbibs, refs #33692
• src/hg/js/utils.js
  • lines changed 11, context: html, text, full: html, text
    723c7a46c87ed42f8510ed1bf35a3a8890f93609 Fri Oct 11 03:08:30 2024 -0700
    adapting the text a little of the tutorial box, and removing the close button, feedback from Ana und a few users, refs #34604
• src/hg/lib/hui.c
  • lines changed 12, context: html, text, full: html, text
    df9e09f635d122d0247e6a60dea6d5f0a4ac21b4 Mon Oct 14 05:17:47 2024 -0700
    changes after code review, refs #34582
• src/hg/lib/sqlProg.c
  • lines changed 2, context: html, text, full: html, text
    d829dea2e62664b38796d495ca6851fa0c2dfdc3 Mon Oct 14 05:10:52 2024 -0700
    changes after code review, refs #34582
• src/hg/makeDb/doc/asmHubs/commonNames.py
  • lines changed 7, context: html, text, full: html, text
    eaf7b44ce9439f1fca4764dfba18de5131995ce4 Wed Oct 9 12:54:21 2024 -0700
    fixup apicomplexans tsetse fly and tunicate
  • lines changed 19, context: html, text, full: html, text
    68207fb5ba1960173ec5460bce40789997c80e19 Wed Oct 9 16:11:26 2024 -0700
    fixup some common names and allow only 10 tracks on a fungi refs #29545
• src/hg/makeDb/doc/asmHubs/lastzRuns.txt
  • lines changed 165, context: html, text, full: html, text
    9393c53b555592fba153dd1608281eb68867bb89 Wed Oct 9 11:32:59 2024 -0700
    Two chains built for refs #34516
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 107, context: html, text, full: html, text
    3f5be310b86e62995312281f6521bb237c820967 Wed Oct 9 14:53:34 2024 -0700
    RefSeq update adding 106 assemblies refs #29545
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    3afb4b5cb1585d3cca8f524fc60cc9ef2fd3f5e3 Thu Oct 10 09:07:11 2024 -0700
    adding one per user request refs #29545
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    a5b706624d390eed8e3f0bb2e43baabdeb66769f Sat Oct 12 21:57:37 2024 -0700
    adding a couple per user request refs #29545
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    769e3448e21276ba591278c1394afcfccbbb08f8 Sat Oct 12 23:16:20 2024 -0700
    adding 4 viral sequences per user request refs #29545
• src/hg/makeDb/doc/asmHubs/verifyOnDownload.sh
  • lines changed 4, context: html, text, full: html, text
    68207fb5ba1960173ec5460bce40789997c80e19 Wed Oct 9 16:11:26 2024 -0700
    fixup some common names and allow only 10 tracks on a fungi refs #29545
• src/hg/makeDb/doc/bacteriaAsmHub/bacteria.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    3afb4b5cb1585d3cca8f524fc60cc9ef2fd3f5e3 Thu Oct 10 09:07:11 2024 -0700
    adding one per user request refs #29545
  • lines changed 1, context: html, text, full: html, text
    a5b706624d390eed8e3f0bb2e43baabdeb66769f Sat Oct 12 21:57:37 2024 -0700
    adding a couple per user request refs #29545
• src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv
  • lines changed 14, context: html, text, full: html, text
    3f5be310b86e62995312281f6521bb237c820967 Wed Oct 9 14:53:34 2024 -0700
    RefSeq update adding 106 assemblies refs #29545
• src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv
  • lines changed 15, context: html, text, full: html, text
    3f5be310b86e62995312281f6521bb237c820967 Wed Oct 9 14:53:34 2024 -0700
    RefSeq update adding 106 assemblies refs #29545
• src/hg/makeDb/doc/fungiAsmHub/fungi.orderList.tsv
  • lines changed 35, context: html, text, full: html, text
    3f5be310b86e62995312281f6521bb237c820967 Wed Oct 9 14:53:34 2024 -0700
    RefSeq update adding 106 assemblies refs #29545
• src/hg/makeDb/doc/hg19.txt
  • lines changed 20, context: html, text, full: html, text
    9b06248769177714d1104ed0a8915e3641bd38cd Wed Oct 9 15:00:21 2024 -0700
    Adding and updating the CADD 1.7 track wrangled by Jeltje, refs #33940
• src/hg/makeDb/doc/hg38/cadd.txt
  • lines changed 18, context: html, text, full: html, text
    9b06248769177714d1104ed0a8915e3641bd38cd Wed Oct 9 15:00:21 2024 -0700
    Adding and updating the CADD 1.7 track wrangled by Jeltje, refs #33940
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 10, context: html, text, full: html, text
    3f5be310b86e62995312281f6521bb237c820967 Wed Oct 9 14:53:34 2024 -0700
    RefSeq update adding 106 assemblies refs #29545
• src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv
  • lines changed 4, context: html, text, full: html, text
    3f5be310b86e62995312281f6521bb237c820967 Wed Oct 9 14:53:34 2024 -0700
    RefSeq update adding 106 assemblies refs #29545
• src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    a5b706624d390eed8e3f0bb2e43baabdeb66769f Sat Oct 12 21:57:37 2024 -0700
    adding a couple per user request refs #29545
• src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv
  • lines changed 11, context: html, text, full: html, text
    3f5be310b86e62995312281f6521bb237c820967 Wed Oct 9 14:53:34 2024 -0700
    RefSeq update adding 106 assemblies refs #29545
• src/hg/makeDb/doc/viralAsmHub/viral.orderList.tsv
  • lines changed 4, context: html, text, full: html, text
    769e3448e21276ba591278c1394afcfccbbb08f8 Sat Oct 12 23:16:20 2024 -0700
    adding 4 viral sequences per user request refs #29545
• src/hg/makeDb/trackDb/human/cadd.alpha.ra
  • lines changed 193, context: html, text, full: html, text
    7766e881ce9fa7ece509263fd71ecf8459e8c4ac Wed Oct 9 16:12:57 2024 -0700
    Adding release tag for the CADD 1.7 track, refs #33940
• src/hg/makeDb/trackDb/human/cadd.ra
  • lines changed 99, context: html, text, full: html, text
    9b06248769177714d1104ed0a8915e3641bd38cd Wed Oct 9 15:00:21 2024 -0700
    Adding and updating the CADD 1.7 track wrangled by Jeltje, refs #33940
  • lines changed 99, context: html, text, full: html, text
    7766e881ce9fa7ece509263fd71ecf8459e8c4ac Wed Oct 9 16:12:57 2024 -0700
    Adding release tag for the CADD 1.7 track, refs #33940
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    a4646d25fdd147ff2982abcc104ea9cb89ff12e0 Thu Oct 10 10:41:22 2024 -0700
    Making CADD 1.7 its own superTrack and changing the CADD superTrack name to 1.6. Originally had both in one superTrack but caused issues. Changed the caddSuper.html back to its previous 1.6 version and made a caddSuper1_7.html. Refs #33940
• src/hg/makeDb/trackDb/human/cadd1_7.ra
  • lines changed 100, context: html, text, full: html, text
    a4646d25fdd147ff2982abcc104ea9cb89ff12e0 Thu Oct 10 10:41:22 2024 -0700
    Making CADD 1.7 its own superTrack and changing the CADD superTrack name to 1.6. Originally had both in one superTrack but caused issues. Changed the caddSuper.html back to its previous 1.6 version and made a caddSuper1_7.html. Refs #33940
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    8ff015c68ded2a52d8b09d7dff5197e949c43630 Fri Oct 11 14:27:29 2024 -0700
    Adding missing html page for the CADD 1.7 track and the mouseOverFunction noAverage setting, refs #33940
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    6f3b1f2f5fc0b7ce851ef203da26bb2236a6b83a Fri Oct 11 18:08:39 2024 -0700
    Announcing the release of the CADD 1.7 track, refs #33940
• src/hg/makeDb/trackDb/human/caddSuper.html
  • lines changed 70, context: html, text, full: html, text
    9b06248769177714d1104ed0a8915e3641bd38cd Wed Oct 9 15:00:21 2024 -0700
    Adding and updating the CADD 1.7 track wrangled by Jeltje, refs #33940
  • lines changed 70, context: html, text, full: html, text
    a4646d25fdd147ff2982abcc104ea9cb89ff12e0 Thu Oct 10 10:41:22 2024 -0700
    Making CADD 1.7 its own superTrack and changing the CADD superTrack name to 1.6. Originally had both in one superTrack but caused issues. Changed the caddSuper.html back to its previous 1.6 version and made a caddSuper1_7.html. Refs #33940
• src/hg/makeDb/trackDb/human/caddSuper1_7.html
  • lines changed 194, context: html, text, full: html, text
    a4646d25fdd147ff2982abcc104ea9cb89ff12e0 Thu Oct 10 10:41:22 2024 -0700
    Making CADD 1.7 its own superTrack and changing the CADD superTrack name to 1.6. Originally had both in one superTrack but caused issues. Changed the caddSuper.html back to its previous 1.6 version and made a caddSuper1_7.html. Refs #33940
• src/hg/makeDb/trackDb/human/clinGen.html
  • lines changed 22, context: html, text, full: html, text
    1b1fe488b3bcf3f500a719d757b2b0a98e911f64 Tue Oct 8 14:42:36 2024 -0700
    Releasing ClinGen CSpec track and adding it to otto, refs #33794
• src/hg/makeDb/trackDb/human/hg38/problematic.html
  • lines changed 37, context: html, text, full: html, text
    d2661193cffea99200bdf3993b515e11a130bec0 Sun Oct 13 16:09:46 2024 -0700
    Adding GIAB difficult regions track to the problematic regions super track, refs #32715
• src/hg/makeDb/trackDb/human/hg38/problematic.ra
  • lines changed 45, context: html, text, full: html, text
    d2661193cffea99200bdf3993b515e11a130bec0 Sun Oct 13 16:09:46 2024 -0700
    Adding GIAB difficult regions track to the problematic regions super track, refs #32715
• src/hg/makeDb/trackDb/human/spliceAI.ra
  • lines changed 0, context: html, text, full: html, text
    92f18bb5221ed3ad9ccdb0b6fa0b58f30354cf1f Mon Oct 14 02:38:21 2024 -0700
    Mouseover was missing a space, no RM.
• src/hg/makeDb/trackDb/human/trackDb.clinGen.ra
  • lines changed 12, context: html, text, full: html, text
    1b1fe488b3bcf3f500a719d757b2b0a98e911f64 Tue Oct 8 14:42:36 2024 -0700
    Releasing ClinGen CSpec track and adding it to otto, refs #33794
  • lines changed 1, context: html, text, full: html, text
    8f153131c8eb2c2b898d79e0e79c61c8f1d4798e Tue Oct 8 15:58:50 2024 -0700
    Staging the news announcement for ClinGen CSpec track and tweaking the caps of the label. Refs #33794
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    7766e881ce9fa7ece509263fd71ecf8459e8c4ac Wed Oct 9 16:12:57 2024 -0700
    Adding release tag for the CADD 1.7 track, refs #33940
  • lines changed 3, context: html, text, full: html, text
    a4646d25fdd147ff2982abcc104ea9cb89ff12e0 Thu Oct 10 10:41:22 2024 -0700
    Making CADD 1.7 its own superTrack and changing the CADD superTrack name to 1.6. Originally had both in one superTrack but caused issues. Changed the caddSuper.html back to its previous 1.6 version and made a caddSuper1_7.html. Refs #33940
• src/hg/utils/otto/clinGen/makeClinGenCspec.sh
  • lines changed 212, context: html, text, full: html, text
    1b1fe488b3bcf3f500a719d757b2b0a98e911f64 Tue Oct 8 14:42:36 2024 -0700
    Releasing ClinGen CSpec track and adding it to otto, refs #33794
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    75bea92d3554ea57e4ace4af908b074c01832e63 Wed Oct 9 13:42:03 2024 -0700
    Adding UTF language var for the cronjob.
• src/hg/utils/otto/otto.crontab
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    1b1fe488b3bcf3f500a719d757b2b0a98e911f64 Tue Oct 8 14:42:36 2024 -0700
    Releasing ClinGen CSpec track and adding it to otto, refs #33794
• src/utils/qa/weeklybld/buildEnv.csh
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    c72aa3cd0289471121ccc7a1b408dd1412f7153c Mon Oct 14 11:08:34 2024 -0700
    v473 preview1
• src/utils/qa/weeklybld/sendLogEmail.pl
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    08ef87f3fa31c9d7fe72600eb76e2db776c1dcbc Tue Oct 8 10:59:16 2024 -0700
    sendmail wants -f to be a single address, no ticket

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• files changed: 63