All File Changes

v441_base to v442_preview (2022-12-12 to 2022-12-19) v442

• src/hg/hgGene/pathways.c
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    1ae72fd3072fddf58e2d414b33b4700dd3ad70cf Thu Dec 15 15:49:46 2022 -0800
    Fixing hgGene linkout, refs #30404
• src/hg/hgLiftOver/hgLiftOver.c
  • lines changed 5, context: html, text, full: html, text
    6828d99220ef4549484f1fdb31210aee5451fccd Tue Dec 13 12:28:31 2022 -0800
    link to FAQ from hgLiftOver about dbSNP, refs #30394
• src/hg/hgTracks/bigWarn.c
  • lines changed 14, context: html, text, full: html, text
    3d00d8348e1cb6eafec60cc3d7321f6de7e669be Mon Dec 12 13:09:49 2022 -0800
    be smarter about showing the user error messages
• src/hg/hgTracks/bigWarn.h
  • lines changed 3, context: html, text, full: html, text
    3d00d8348e1cb6eafec60cc3d7321f6de7e669be Mon Dec 12 13:09:49 2022 -0800
    be smarter about showing the user error messages
• src/hg/hgTracks/hgTracks.c
  • lines changed 12, context: html, text, full: html, text
    3d00d8348e1cb6eafec60cc3d7321f6de7e669be Mon Dec 12 13:09:49 2022 -0800
    be smarter about showing the user error messages
  • lines changed 1, context: html, text, full: html, text
    7304ed04d31a495ff186f6c4a1c310080b680c93 Thu Dec 15 10:15:39 2022 -0800
    increase the number of possible highlights to 4096
• src/hg/hgTracks/hgTracks.h
  • lines changed 2, context: html, text, full: html, text
    3d00d8348e1cb6eafec60cc3d7321f6de7e669be Mon Dec 12 13:09:49 2022 -0800
    be smarter about showing the user error messages
• src/hg/hgTracks/simpleTracks.c
  • lines changed 3, context: html, text, full: html, text
    3d00d8348e1cb6eafec60cc3d7321f6de7e669be Mon Dec 12 13:09:49 2022 -0800
    be smarter about showing the user error messages
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 2, context: html, text, full: html, text
    9ce4bce41ca63f215458253ee7ad7a401d42eba0 Fri Dec 16 17:07:31 2022 -0800
    Clarifying when/how to use the autoScale group setting, refs #13428
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 47, context: html, text, full: html, text
    72d24d1ebc8b2e2acfbfe1f6a6dcfb7b223b29a0 Tue Dec 13 16:29:15 2022 -0800
    Announcing the release of All GENCODE for hg38, hg19, and mm39. refs #29789 #29790 #29791
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    72d24d1ebc8b2e2acfbfe1f6a6dcfb7b223b29a0 Tue Dec 13 16:29:15 2022 -0800
    Announcing the release of All GENCODE for hg38, hg19, and mm39. refs #29789 #29790 #29791
• src/hg/htdocs/style/HGStyle.css
  • lines changed 2, context: html, text, full: html, text
    3d00d8348e1cb6eafec60cc3d7321f6de7e669be Mon Dec 12 13:09:49 2022 -0800
    be smarter about showing the user error messages
• src/hg/inc/asmAlias.h
  • lines changed 82, context: html, text, full: html, text
    4c1d2a0a761f1afc9da81243357e462ae14c3756 Thu Dec 15 14:49:26 2022 -0800
    add assembly aliasing to hub connection
• src/hg/inc/grp.h
  • lines changed 1, context: html, text, full: html, text
    3d00d8348e1cb6eafec60cc3d7321f6de7e669be Mon Dec 12 13:09:49 2022 -0800
    be smarter about showing the user error messages
• src/hg/inc/hubConnect.h
  • lines changed 1, context: html, text, full: html, text
    3d00d8348e1cb6eafec60cc3d7321f6de7e669be Mon Dec 12 13:09:49 2022 -0800
    be smarter about showing the user error messages
• src/hg/inc/trackDb.h
  • lines changed 2, context: html, text, full: html, text
    3d00d8348e1cb6eafec60cc3d7321f6de7e669be Mon Dec 12 13:09:49 2022 -0800
    be smarter about showing the user error messages
• src/hg/lib/asmAlias.as
  • lines changed 6, context: html, text, full: html, text
    4c1d2a0a761f1afc9da81243357e462ae14c3756 Thu Dec 15 14:49:26 2022 -0800
    add assembly aliasing to hub connection
• src/hg/lib/asmAlias.c
  • lines changed 185, context: html, text, full: html, text
    4c1d2a0a761f1afc9da81243357e462ae14c3756 Thu Dec 15 14:49:26 2022 -0800
    add assembly aliasing to hub connection
• src/hg/lib/asmAlias.h
  • lines changed 64, context: html, text, full: html, text
    4c1d2a0a761f1afc9da81243357e462ae14c3756 Thu Dec 15 14:49:26 2022 -0800
    add assembly aliasing to hub connection
  • lines changed 64, context: html, text, full: html, text
    325a0ac872093ece144003bb3828c419ff82cc31 Thu Dec 15 16:17:31 2022 -0800
    Remove mistakenly committed asmAlias file, refs build email
• src/hg/lib/asmAlias.sql
  • lines changed 12, context: html, text, full: html, text
    4c1d2a0a761f1afc9da81243357e462ae14c3756 Thu Dec 15 14:49:26 2022 -0800
    add assembly aliasing to hub connection
• src/hg/lib/cart.c
  • lines changed 2, context: html, text, full: html, text
    3d00d8348e1cb6eafec60cc3d7321f6de7e669be Mon Dec 12 13:09:49 2022 -0800
    be smarter about showing the user error messages
• src/hg/lib/hubConnect.c
  • lines changed 22, context: html, text, full: html, text
    3d00d8348e1cb6eafec60cc3d7321f6de7e669be Mon Dec 12 13:09:49 2022 -0800
    be smarter about showing the user error messages
  • lines changed 3, context: html, text, full: html, text
    4c1d2a0a761f1afc9da81243357e462ae14c3756 Thu Dec 15 14:49:26 2022 -0800
    add assembly aliasing to hub connection
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    4c1d2a0a761f1afc9da81243357e462ae14c3756 Thu Dec 15 14:49:26 2022 -0800
    add assembly aliasing to hub connection
• src/hg/lib/trackHub.c
  • lines changed 9, context: html, text, full: html, text
    3d00d8348e1cb6eafec60cc3d7321f6de7e669be Mon Dec 12 13:09:49 2022 -0800
    be smarter about showing the user error messages
• src/hg/lib/web.c
  • lines changed 4, context: html, text, full: html, text
    3d00d8348e1cb6eafec60cc3d7321f6de7e669be Mon Dec 12 13:09:49 2022 -0800
    be smarter about showing the user error messages
  • lines changed 3, context: html, text, full: html, text
    4c1d2a0a761f1afc9da81243357e462ae14c3756 Thu Dec 15 14:49:26 2022 -0800
    add assembly aliasing to hub connection
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 365, context: html, text, full: html, text
    6ec26e523de0fce9e1435744362391c75240affa Thu Dec 15 14:13:09 2022 -0800
    fixup clade specifications to be consistent and add one new build GCF_025331425.1_Radspe1 to test RepeatModeler no redmine
• src/hg/makeDb/doc/fungiAsmHub/fungi.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    a59d996823e2008757817774344f116efe6439f3 Thu Dec 15 15:01:09 2022 -0800
    adding GCF_025331425.1_Radspe1 to test RepeatModeler result no redmine
• src/hg/makeDb/trackDb/human/hg19/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    72d24d1ebc8b2e2acfbfe1f6a6dcfb7b223b29a0 Tue Dec 13 16:29:15 2022 -0800
    Announcing the release of All GENCODE for hg38, hg19, and mm39. refs #29789 #29790 #29791
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV42lift37.ra
  • lines changed 1, context: html, text, full: html, text
    72d24d1ebc8b2e2acfbfe1f6a6dcfb7b223b29a0 Tue Dec 13 16:29:15 2022 -0800
    Announcing the release of All GENCODE for hg38, hg19, and mm39. refs #29789 #29790 #29791
• src/hg/makeDb/trackDb/human/hg38/crossTissueMaps.ra
  • lines changed 20, context: html, text, full: html, text
    8bb3646cbdd34ab8af601f1158654ba460b4e399 Mon Dec 12 16:01:13 2022 -0800
    Stage Gtex immune atlas single nuclei expression track, refs #29954
  • lines changed 1, context: html, text, full: html, text
    acfc868d42deff595de900a2e72b96d31ddb07d7 Mon Dec 12 17:14:48 2022 -0800
    Make gtex single cell barCharts non-configurable by pop up because of a javascript bug, refs #29954
• src/hg/makeDb/trackDb/human/hg38/gtexSingleCell.ra
  • lines changed 140, context: html, text, full: html, text
    8bb3646cbdd34ab8af601f1158654ba460b4e399 Mon Dec 12 16:01:13 2022 -0800
    Stage Gtex immune atlas single nuclei expression track, refs #29954
• src/hg/makeDb/trackDb/human/hg38/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    72d24d1ebc8b2e2acfbfe1f6a6dcfb7b223b29a0 Tue Dec 13 16:29:15 2022 -0800
    Announcing the release of All GENCODE for hg38, hg19, and mm39. refs #29789 #29790 #29791
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    8bb3646cbdd34ab8af601f1158654ba460b4e399 Mon Dec 12 16:01:13 2022 -0800
    Stage Gtex immune atlas single nuclei expression track, refs #29954
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV42.ra
  • lines changed 1, context: html, text, full: html, text
    72d24d1ebc8b2e2acfbfe1f6a6dcfb7b223b29a0 Tue Dec 13 16:29:15 2022 -0800
    Announcing the release of All GENCODE for hg38, hg19, and mm39. refs #29789 #29790 #29791
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    72d24d1ebc8b2e2acfbfe1f6a6dcfb7b223b29a0 Tue Dec 13 16:29:15 2022 -0800
    Announcing the release of All GENCODE for hg38, hg19, and mm39. refs #29789 #29790 #29791
• src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM31.ra
  • lines changed 1, context: html, text, full: html, text
    72d24d1ebc8b2e2acfbfe1f6a6dcfb7b223b29a0 Tue Dec 13 16:29:15 2022 -0800
    Announcing the release of All GENCODE for hg38, hg19, and mm39. refs #29789 #29790 #29791
• src/hg/makeDb/trackDb/wgEncodeGencodeDisplay1.shared.html
  • lines changed 1, context: html, text, full: html, text
    dd4821f6b5e8b5dd02947ee9ebf8eb0b3bedaebb Mon Dec 12 16:24:58 2022 -0800
    Fixing the biotype link for Non-coding transcript categorization section, refs #29789 #29790 #29791
• src/hg/makeDb/trackDb/wgEncodeGencodeDisplayLift1.shared.html
  • lines changed 2, context: html, text, full: html, text
    dd4821f6b5e8b5dd02947ee9ebf8eb0b3bedaebb Mon Dec 12 16:24:58 2022 -0800
    Fixing the biotype link for Non-coding transcript categorization section, refs #29789 #29790 #29791
• src/hg/utils/automation/asmHubRepeatMasker.sh
  • lines changed 3, context: html, text, full: html, text
    967b763f92c9dc4d3e57399de0c875029d828ef1 Tue Dec 13 20:58:42 2022 -0800
    now running the next version of RepeatMasker v4.1.4 refs #29545
• src/hg/utils/automation/doAssemblyHub.pl
  • lines changed 59, context: html, text, full: html, text
    395595f60c883b2344ae20299687563b8ea6e215 Thu Dec 15 14:10:23 2022 -0800
    adding RepeatModeler option no redmine
• src/hg/utils/automation/doRepeatMasker.pl
  • lines changed 34, context: html, text, full: html, text
    967b763f92c9dc4d3e57399de0c875029d828ef1 Tue Dec 13 20:58:42 2022 -0800
    now running the next version of RepeatMasker v4.1.4 refs #29545
• src/hg/utils/automation/doRepeatModeler.pl
  • lines changed 307, context: html, text, full: html, text
    29bf2c22b06f9d457bcd43ef2029bad054542ba8 Thu Dec 15 11:35:24 2022 -0800
    initial version of running RepeatModeler no redmine
  • lines changed 14, context: html, text, full: html, text
    55a4d2f27b5f2be54928d7cc454b062f67045b21 Thu Dec 15 11:53:15 2022 -0800
    correct thru cleanup no redmine
• src/hg/utils/hubCheck/hubCheck.c
  • lines changed 5, context: html, text, full: html, text
    b7733722095dfc93a0e3f8a565bb3cbf3cb9d0d5 Fri Dec 16 16:48:23 2022 -0800
    Improving the hubCheck error when autoScale is found in children tracks, refs #13428
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 4, context: html, text, full: html, text
    76941e47655c4a3f9f6e184c68daf6da5d5defc2 Mon Dec 19 10:14:07 2022 -0800
    v442 preview1, refs #30323

• lines changed: 1529
• files changed: 49