All File Changes

v461_preview to v461_preview2 (2024-02-06 to 2024-02-12) v461

• src/hg/altSplice/altSplice/makefile
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    136f7d68b04199b8e0c7d4bf853412eb0d2a7fe9 Wed Feb 7 11:43:37 2024 -0800
    eliminate the extra .dSYM directories from being made on the Mac OSX build no redmine
• src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c
  • lines changed 6, context: html, text, full: html, text
    20bbccc6290369e739ad5f0b0fe877c776f50d42 Wed Feb 7 13:52:36 2024 -0800
    Removing some unused facets. Changing CIRM to SSPsyGene a few places.
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    20ac68188d3fe67b991f5f2ed1e712d5a0a8c2c7 Fri Feb 9 09:38:15 2024 -0800
    Will SSPsyGene V1 Updates.
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    9d4635d2821b3d8a73396728cbd9cd56ad842f7c Fri Feb 9 15:54:43 2024 -0800
    Updated Home and Data Images.
• src/hg/cirm/cdw/lib/cdwNavBar.h
  • lines changed 2, context: html, text, full: html, text
    e9d90ba4e09dcc5de259c8e9faef5644de26172c Wed Feb 7 13:52:00 2024 -0800
    Removing analysis menu.
• src/hg/cirm/cdw/lib/cdwPageFooter.h
  • lines changed 28, context: html, text, full: html, text
    20ac68188d3fe67b991f5f2ed1e712d5a0a8c2c7 Fri Feb 9 09:38:15 2024 -0800
    Will SSPsyGene V1 Updates.
• src/hg/cirm/cdw/lib/cdwPageHeader.h
  • lines changed 24, context: html, text, full: html, text
    20ac68188d3fe67b991f5f2ed1e712d5a0a8c2c7 Fri Feb 9 09:38:15 2024 -0800
    Will SSPsyGene V1 Updates.
• src/hg/cirm/gateway/htdocs/cirmIndex.html
  • lines changed 66, context: html, text, full: html, text
    20ac68188d3fe67b991f5f2ed1e712d5a0a8c2c7 Fri Feb 9 09:38:15 2024 -0800
    Will SSPsyGene V1 Updates.
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    9d4635d2821b3d8a73396728cbd9cd56ad842f7c Fri Feb 9 15:54:43 2024 -0800
    Updated Home and Data Images.
• src/hg/cirm/gateway/htdocs/images/ssPsyGeneLogo.jpg
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    20ac68188d3fe67b991f5f2ed1e712d5a0a8c2c7 Fri Feb 9 09:38:15 2024 -0800
    Will SSPsyGene V1 Updates.
• src/hg/cirm/gateway/htdocs/images/sspsygene_data_portal_data_img.jpg
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    9d4635d2821b3d8a73396728cbd9cd56ad842f7c Fri Feb 9 15:54:43 2024 -0800
    Updated Home and Data Images.
• src/hg/cirm/gateway/htdocs/images/sspsygene_data_portal_home_img.png
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    9d4635d2821b3d8a73396728cbd9cd56ad842f7c Fri Feb 9 15:54:43 2024 -0800
    Updated Home and Data Images.
• src/hg/cirm/gateway/htdocs/inc/footer.html
  • lines changed 31, context: html, text, full: html, text
    20ac68188d3fe67b991f5f2ed1e712d5a0a8c2c7 Fri Feb 9 09:38:15 2024 -0800
    Will SSPsyGene V1 Updates.
• src/hg/cirm/gateway/htdocs/inc/header.html
  • lines changed 30, context: html, text, full: html, text
    20ac68188d3fe67b991f5f2ed1e712d5a0a8c2c7 Fri Feb 9 09:38:15 2024 -0800
    Will SSPsyGene V1 Updates.
• src/hg/cirm/gateway/js/cirmStuff.js
  • lines changed 9, context: html, text, full: html, text
    20ac68188d3fe67b991f5f2ed1e712d5a0a8c2c7 Fri Feb 9 09:38:15 2024 -0800
    Will SSPsyGene V1 Updates.
• src/hg/hgCustom/hgCustom.c
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    39c0270589d31890909cc5d783177ba1d5652d90 Wed Feb 7 09:18:10 2024 -0800
    adding cram as a file format to the hgCustom doc text, thanks to MarkD
• src/hg/hgTracks/bigBedTrack.c
  • lines changed 37, context: html, text, full: html, text
    3e441dc3bb095bff8b39c39347008dba5b8667a2 Thu Feb 8 15:22:11 2024 -0800
    autorecognize the number of fields in a bigBed if the user doesn't specify it in the type field
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    957d66d68b880ec48372643e602e9dbff4326a00 Fri Feb 9 11:32:11 2024 -0800
    if bigBed is specified as type without other words then we don't score filter
• src/hg/hgTracks/hgTracks.c
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    fda9295a0476572b081a2cb78bec28e90cd1d71d Wed Feb 7 07:50:54 2024 -0800
    changes after awesome code review by Braney, many thanks, refs #32977
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    d97534ce6ff21f6eb8e9fbd46827753ffba119b1 Thu Feb 8 15:49:49 2024 -0800
    fix bug that crashes if hgt.trackImgOnly is not in cart
• src/hg/hgTracks/mainMain.c
  • lines changed 3, context: html, text, full: html, text
    37d145c71807801efd9cb02926515c82e84c1c71 Wed Feb 7 10:12:23 2024 -0800
    set up a mechanism to limit memory through an hg.conf variable
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    324c79db532cb487e7b3a377954f0821872a7d07 Thu Feb 8 16:57:37 2024 -0800
    add logging of memory high water mark
• src/hg/hgTracks/simpleTracks.c
  • lines changed 2, context: html, text, full: html, text
    db521cd9c64d7adb1506c50c080d04f9b2d2febf Wed Feb 7 12:37:17 2024 -0800
    do all the exon numbering stuff in squish as well as pack and full
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 8, context: html, text, full: html, text
    a7390e6e986da2db7d0c8b0d56fa5f62b56f273a Wed Feb 7 11:34:11 2024 -0800
    Adding more documentation for the autoScale trackDb setting, refs #32954
• src/hg/htdocs/indexMeetings.html
  • lines changed 8, context: html, text, full: html, text
    ad761daca1aa3a4e0eebcd34aa6316718fa3f871 Thu Feb 8 16:22:47 2024 -0800
    Adding EHG conference meeting and removing USC event meeting, No Redmine
• src/hg/htdocs/template.html
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    f286f99977074d8401a9a0ace1205dbf9c071246 Wed Feb 7 11:42:02 2024 -0800
    Will test change
• src/hg/inc/hgConfig.h
  • lines changed 3, context: html, text, full: html, text
    37d145c71807801efd9cb02926515c82e84c1c71 Wed Feb 7 10:12:23 2024 -0800
    set up a mechanism to limit memory through an hg.conf variable
• src/hg/js/utils.js
  • lines changed 88, context: html, text, full: html, text
    19638d540a2552c4eb732adb5a032d97f45b375c Fri Feb 9 12:05:13 2024 -0800
    Mouseover performance optimization, do not make each mouseover element on page load, instead wait for an actual mouseover event to trigger before adding the mouseover nodes, refs #32997
• src/hg/lib/hgConfig.c
  • lines changed 13, context: html, text, full: html, text
    37d145c71807801efd9cb02926515c82e84c1c71 Wed Feb 7 10:12:23 2024 -0800
    set up a mechanism to limit memory through an hg.conf variable
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 1, context: html, text, full: html, text
    39d2932cf92e953de2750d830cf4e518e64629a0 Fri Feb 9 21:11:26 2024 -0800
    adding a catfish per user request refs #29545
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    5cc31e2eab42d7bcef943e93c6434ff6418ab479 Sun Feb 11 22:17:24 2024 -0800
    adding GRCr8 Norway rat refs #32985
• src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    39d2932cf92e953de2750d830cf4e518e64629a0 Fri Feb 9 21:11:26 2024 -0800
    adding a catfish per user request refs #29545
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    5cc31e2eab42d7bcef943e93c6434ff6418ab479 Sun Feb 11 22:17:24 2024 -0800
    adding GRCr8 Norway rat refs #32985
• src/hg/makeDb/doc/wuhCor1/variantMuts.txt
  • lines changed 220, context: html, text, full: html, text
    6ddff6c56e326c28e1754ffe2f3192139fba920d Tue Feb 6 13:41:15 2024 -0800
    Updated wuhCor1 Variants of Concern track with XBB.1.5.70, HK.3, BA.2.86, and JN.1. refs #32980
• src/hg/makeDb/trackDb/human/hg19/decipher.html
  • lines changed 109, context: html, text, full: html, text
    3f633ca057f47c510741c9b830e1507da11b1ae5 Thu Feb 8 06:00:13 2024 -0800
    discouraging use of the decipher tracks on hg19, refs #32960
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 6, context: html, text, full: html, text
    3f633ca057f47c510741c9b830e1507da11b1ae5 Thu Feb 8 06:00:13 2024 -0800
    discouraging use of the decipher tracks on hg19, refs #32960
• src/hg/makeDb/trackDb/human/hg38/trackDb.447way.ra
  • lines changed 1, context: html, text, full: html, text
    2ea54ead34b68d5632f2210fdca6f28f6bbf428e Thu Feb 8 17:52:56 2024 -0800
    Temporarily hiding these two tracks while they are missing from the download server, no RM.
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    0520c6cb17106664449891a2a0165700939529fa Thu Feb 8 18:08:13 2024 -0800
    Fixing some oops when I tried to hide the big tracks before, this is temporary while we fix the cactus tracks in the download server.
• src/hg/makeDb/trackDb/human/hg38/trackDb.470way.ra
  • lines changed 1, context: html, text, full: html, text
    2ea54ead34b68d5632f2210fdca6f28f6bbf428e Thu Feb 8 17:52:56 2024 -0800
    Temporarily hiding these two tracks while they are missing from the download server, no RM.
  • lines changed 6, context: html, text, full: html, text
    0520c6cb17106664449891a2a0165700939529fa Thu Feb 8 18:08:13 2024 -0800
    Fixing some oops when I tried to hide the big tracks before, this is temporary while we fix the cactus tracks in the download server.
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    0520c6cb17106664449891a2a0165700939529fa Thu Feb 8 18:08:13 2024 -0800
    Fixing some oops when I tried to hide the big tracks before, this is temporary while we fix the cactus tracks in the download server.
• src/hg/makeDb/trackDb/human/hs1/html/mappability.html
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    0bcf6d913dcba4859e18f9d2c708fd339a4438d5 Wed Feb 7 17:33:06 2024 -0800
    Making edits to the mappability.html, refs #32694
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    78474b4414b2f5287a346ad33bee024fd477a6aa Thu Feb 8 12:53:22 2024 -0800
    Updating publication link for mappability.html, refs #32694
• src/hg/makeDb/trackDb/human/jaspar.ra
  • lines changed 1, context: html, text, full: html, text
    1ae2e113e6db2d37f66ccfc3acd88cb8fa146dc0 Wed Feb 7 09:23:22 2024 -0800
    Commenting out the maxItems trackDb setting for jaspar track, refs #32854
• src/hg/makeDb/trackDb/virus/wuhCor1/variantMuts.html
  • lines changed 59, context: html, text, full: html, text
    6ddff6c56e326c28e1754ffe2f3192139fba920d Tue Feb 6 13:41:15 2024 -0800
    Updated wuhCor1 Variants of Concern track with XBB.1.5.70, HK.3, BA.2.86, and JN.1. refs #32980
• src/hg/makeDb/trackDb/virus/wuhCor1/variantMuts.ra
  • lines changed 88, context: html, text, full: html, text
    6ddff6c56e326c28e1754ffe2f3192139fba920d Tue Feb 6 13:41:15 2024 -0800
    Updated wuhCor1 Variants of Concern track with XBB.1.5.70, HK.3, BA.2.86, and JN.1. refs #32980
• src/hg/utils/vcfToBed/vcfToBed.c
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    c5225b06da002ec4b1f5cf3946300d5d43f1cb5d Wed Feb 7 15:43:09 2024 -0800
    Check array is not full when reading INFO tags to keep from a file, refs #32973
• src/inc/portable.h
  • lines changed 4, context: html, text, full: html, text
    37d145c71807801efd9cb02926515c82e84c1c71 Wed Feb 7 10:12:23 2024 -0800
    set up a mechanism to limit memory through an hg.conf variable
• src/lib/osunix.c
  • lines changed 13, context: html, text, full: html, text
    37d145c71807801efd9cb02926515c82e84c1c71 Wed Feb 7 10:12:23 2024 -0800
    set up a mechanism to limit memory through an hg.conf variable
• src/utils/qa/weeklybld/buildEnv.csh
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    9dde45d51ee9403f7ae76a6d6bf737eee5134bcd Mon Feb 12 10:36:02 2024 -0800
    v461 preview2, refs #32981

• lines changed: 919
• files changed: 50