All File Changes

v437_base to v438_preview (2022-09-19 to 2022-09-26) v438

• confs/asia.hg.conf
  • lines changed 3, context: html, text, full: html, text
    0ab451f851d95a33047baee2a0f580950032ff7d Sun Sep 25 01:11:28 2022 -0700
    Installing updated hg.conf files from UCSC servers
• confs/euro.hg.conf
  • lines changed 3, context: html, text, full: html, text
    0ab451f851d95a33047baee2a0f580950032ff7d Sun Sep 25 01:11:28 2022 -0700
    Installing updated hg.conf files from UCSC servers
• confs/hgwbeta.hg.conf
  • lines changed 3, context: html, text, full: html, text
    0ab451f851d95a33047baee2a0f580950032ff7d Sun Sep 25 01:11:28 2022 -0700
    Installing updated hg.conf files from UCSC servers
• confs/rr.hg.conf
  • lines changed 4, context: html, text, full: html, text
    0ab451f851d95a33047baee2a0f580950032ff7d Sun Sep 25 01:11:28 2022 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/gar/gar.cgi.pl
  • lines changed 18, context: html, text, full: html, text
    ca81b42b47cd5b6419d87f3b8697a0806ce85e99 Tue Sep 20 11:45:40 2022 -0700
    see if the referer and referDomain can be recorded for possible protection refs #28930
• src/hg/gar/garTable.pl
  • lines changed 116, context: html, text, full: html, text
    afe1592acd7a4dd79f8ca81b390d10113cb6aadc Tue Sep 20 09:40:42 2022 -0700
    more complete accounting of all GenArk and UCSC assemblies to get them into the page refs #28930
• src/hg/gar/garTable.sh
  • lines changed 5, context: html, text, full: html, text
    afe1592acd7a4dd79f8ca81b390d10113cb6aadc Tue Sep 20 09:40:42 2022 -0700
    more complete accounting of all GenArk and UCSC assemblies to get them into the page refs #28930
• src/hg/htdocs/goldenPath/help/barChart.html
  • lines changed 3, context: html, text, full: html, text
    2a702699cb3b42282222e2bb9d0947cb03baac75 Wed Sep 21 18:19:32 2022 -0700
    Made a few minor edits to barChart.html_example7, refs #29984
• src/hg/js/jquery-1.2.6.pack.js
  • lines changed 11, context: html, text, full: html, text
    d0154a86751f1204034bcdb78705ad6107c493f8 Mon Sep 19 13:00:44 2022 -0700
    Removing unused dependency that github dependabot was sending security warnings about. Cross-site scripting (XSS) vulnerability in jQuery before 1.6.3
• src/hg/makeDb/autoSql/recombDenovo.as
  • lines changed 12, context: html, text, full: html, text
    50d9453206becf6203aa41b831cca95ba6b5b58d Thu Sep 22 10:31:16 2022 -0700
    adding decode and 1k Genomes genetic maps, refs #30044
• src/hg/makeDb/autoSql/recombEvents.as
  • lines changed 30, context: html, text, full: html, text
    50d9453206becf6203aa41b831cca95ba6b5b58d Thu Sep 22 10:31:16 2022 -0700
    adding decode and 1k Genomes genetic maps, refs #30044
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 1, context: html, text, full: html, text
    6c04b75f3169885273b9979eb5a00e7841e1600f Sat Sep 24 14:57:58 2022 -0700
    correct the assembly name of GCF_016700215.2 no redmine
• src/hg/makeDb/doc/hg38/recombRate.txt
  • lines changed 91, context: html, text, full: html, text
    50d9453206becf6203aa41b831cca95ba6b5b58d Thu Sep 22 10:31:16 2022 -0700
    adding decode and 1k Genomes genetic maps, refs #30044
• src/hg/makeDb/doc/mpxvRivers/pcrAmplicon.txt
  • lines changed 14, context: html, text, full: html, text
    b0afa1116f373bdcf62511df92dc68ef57d654b2 Tue Sep 20 08:06:55 2022 -0700
    adding makedoc, refs #30012
• src/hg/makeDb/doc/mpxvRivers/pcrPrimers.as
  • lines changed 21, context: html, text, full: html, text
    b0afa1116f373bdcf62511df92dc68ef57d654b2 Tue Sep 20 08:06:55 2022 -0700
    adding makedoc, refs #30012
• src/hg/makeDb/trackDb/TOGAannotation.html
  • lines changed 3, context: html, text, full: html, text
    dc7e4fa869733e45e0abdb1f2b9e4508ef7b802a Tue Sep 20 12:10:34 2022 -0700
    correct bioRxiv reference for the paper in preprint status refs #29982
• src/hg/makeDb/trackDb/ebola/eboVir3/spUniprot.html
  • lines changed 104, context: html, text, full: html, text
    0e520097576e90e86ae8b673b660a4dbd436f5b2 Tue Sep 20 06:36:48 2022 -0700
    removing old spUniprot track and moving into eboVir3, the only assembly that now has a track like this, refs #30023
• src/hg/makeDb/trackDb/ebola/eboVir3/trackDb.ra
  • lines changed 35, context: html, text, full: html, text
    0e520097576e90e86ae8b673b660a4dbd436f5b2 Tue Sep 20 06:36:48 2022 -0700
    removing old spUniprot track and moving into eboVir3, the only assembly that now has a track like this, refs #30023
• src/hg/makeDb/trackDb/human/hg38/gtexSingleCell.ra
  • lines changed 9, context: html, text, full: html, text
    305d1064ad09feb6eb827be31e62be979c56e9f0 Fri Sep 23 16:31:13 2022 -0700
    Updating shortLabel’s for the GTEx Atlas Tracks, refs #29954
• src/hg/makeDb/trackDb/human/hg38/recombRate.ra
  • lines changed 79, context: html, text, full: html, text
    50d9453206becf6203aa41b831cca95ba6b5b58d Thu Sep 22 10:31:16 2022 -0700
    adding decode and 1k Genomes genetic maps, refs #30044
• src/hg/makeDb/trackDb/human/hg38/recombRate2.html
  • lines changed 86, context: html, text, full: html, text
    50d9453206becf6203aa41b831cca95ba6b5b58d Thu Sep 22 10:31:16 2022 -0700
    adding decode and 1k Genomes genetic maps, refs #30044
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    50d9453206becf6203aa41b831cca95ba6b5b58d Thu Sep 22 10:31:16 2022 -0700
    adding decode and 1k Genomes genetic maps, refs #30044
• src/hg/makeDb/trackDb/spUniprot.html
  • lines changed 104, context: html, text, full: html, text
    0e520097576e90e86ae8b673b660a4dbd436f5b2 Tue Sep 20 06:36:48 2022 -0700
    removing old spUniprot track and moving into eboVir3, the only assembly that now has a track like this, refs #30023
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 36, context: html, text, full: html, text
    0e520097576e90e86ae8b673b660a4dbd436f5b2 Tue Sep 20 06:36:48 2022 -0700
    removing old spUniprot track and moving into eboVir3, the only assembly that now has a track like this, refs #30023
• src/hg/makeDb/trackDb/virus/mpxv2022/assembly.html
  • lines changed 33, context: html, text, full: html, text
    3a278e49fbd9fcfcd01d427e68c5a14d85f9be6d Wed Sep 21 10:34:29 2022 -0700
    done with mpxv2022 experiment
• src/hg/makeDb/trackDb/virus/mpxv2022/chainNet.html
  • lines changed 148, context: html, text, full: html, text
    3a278e49fbd9fcfcd01d427e68c5a14d85f9be6d Wed Sep 21 10:34:29 2022 -0700
    done with mpxv2022 experiment
• src/hg/makeDb/trackDb/virus/mpxv2022/cpgIslands.html
  • lines changed 78, context: html, text, full: html, text
    3a278e49fbd9fcfcd01d427e68c5a14d85f9be6d Wed Sep 21 10:34:29 2022 -0700
    done with mpxv2022 experiment
• src/hg/makeDb/trackDb/virus/mpxv2022/description.html
  • lines changed 123, context: html, text, full: html, text
    3a278e49fbd9fcfcd01d427e68c5a14d85f9be6d Wed Sep 21 10:34:29 2022 -0700
    done with mpxv2022 experiment
• src/hg/makeDb/trackDb/virus/mpxv2022/gc5Base.html
  • lines changed 21, context: html, text, full: html, text
    3a278e49fbd9fcfcd01d427e68c5a14d85f9be6d Wed Sep 21 10:34:29 2022 -0700
    done with mpxv2022 experiment
• src/hg/makeDb/trackDb/virus/mpxv2022/ncbiGene.html
  • lines changed 16, context: html, text, full: html, text
    3a278e49fbd9fcfcd01d427e68c5a14d85f9be6d Wed Sep 21 10:34:29 2022 -0700
    done with mpxv2022 experiment
• src/hg/makeDb/trackDb/virus/mpxv2022/pcrAmplicon.html
  • lines changed 57, context: html, text, full: html, text
    3a278e49fbd9fcfcd01d427e68c5a14d85f9be6d Wed Sep 21 10:34:29 2022 -0700
    done with mpxv2022 experiment
• src/hg/makeDb/trackDb/virus/mpxv2022/pcrAmplicon.ra
  • lines changed 8, context: html, text, full: html, text
    3a278e49fbd9fcfcd01d427e68c5a14d85f9be6d Wed Sep 21 10:34:29 2022 -0700
    done with mpxv2022 experiment
• src/hg/makeDb/trackDb/virus/mpxv2022/repeatMasker.html
  • lines changed 261, context: html, text, full: html, text
    3a278e49fbd9fcfcd01d427e68c5a14d85f9be6d Wed Sep 21 10:34:29 2022 -0700
    done with mpxv2022 experiment
• src/hg/makeDb/trackDb/virus/mpxv2022/simpleRepeat.html
  • lines changed 48, context: html, text, full: html, text
    3a278e49fbd9fcfcd01d427e68c5a14d85f9be6d Wed Sep 21 10:34:29 2022 -0700
    done with mpxv2022 experiment
• src/hg/makeDb/trackDb/virus/mpxv2022/tanDups.html
  • lines changed 101, context: html, text, full: html, text
    3a278e49fbd9fcfcd01d427e68c5a14d85f9be6d Wed Sep 21 10:34:29 2022 -0700
    done with mpxv2022 experiment
• src/hg/makeDb/trackDb/virus/mpxv2022/trackDb.ra
  • lines changed 204, context: html, text, full: html, text
    3a278e49fbd9fcfcd01d427e68c5a14d85f9be6d Wed Sep 21 10:34:29 2022 -0700
    done with mpxv2022 experiment
• src/hg/makeDb/trackDb/virus/mpxv2022/windowMasker.html
  • lines changed 38, context: html, text, full: html, text
    3a278e49fbd9fcfcd01d427e68c5a14d85f9be6d Wed Sep 21 10:34:29 2022 -0700
    done with mpxv2022 experiment
• src/hg/makeDb/trackDb/virus/mpxvRivers/pcrAmplicon.html
  • lines changed 33, context: html, text, full: html, text
    b0afa1116f373bdcf62511df92dc68ef57d654b2 Tue Sep 20 08:06:55 2022 -0700
    adding makedoc, refs #30012
  • lines changed 1, context: html, text, full: html, text
    86b923fbff880c67ab64929fb268165579909d11 Sat Sep 24 06:07:16 2022 -0700
    updating sequencing primers track docs for mpx, refs #30012
• src/hg/makeDb/trackDb/virus/mpxvRivers/pcrAmplicon.ra
  • lines changed 20, context: html, text, full: html, text
    b0afa1116f373bdcf62511df92dc68ef57d654b2 Tue Sep 20 08:06:55 2022 -0700
    adding makedoc, refs #30012
  • lines changed 2, context: html, text, full: html, text
    86b923fbff880c67ab64929fb268165579909d11 Sat Sep 24 06:07:16 2022 -0700
    updating sequencing primers track docs for mpx, refs #30012
• src/hg/utils/automation/HgAutomate.pm
  • lines changed 1, context: html, text, full: html, text
    adbcbc19d8a90533fc04a2c6a164786fd10e945b Sat Sep 24 18:42:41 2022 -0700
    and yet one final name change for T2T-CHM13 refs @29982
• src/hg/utils/automation/aliasTextToBed.pl
  • lines changed 2, context: html, text, full: html, text
    98a8fb9dfe585027839a944b73cb84f0a244f0ae Sat Sep 24 18:36:17 2022 -0700
    adding custom category to handle TOGA name changes refs #29982
• src/hg/utils/automation/asmHubChainNetComposite.pl
  • lines changed 1, context: html, text, full: html, text
    7f54f5b04dd45175af6af8ed3d7095c1aefa22b2 Sat Sep 24 18:41:55 2022 -0700
    correctly using dbHost in place of hgwdev refs #29982
• src/hg/utils/automation/asmHubChainNetTrackDb.pl
  • lines changed 12, context: html, text, full: html, text
    980db7f979bf44931256f421017262d2983f6aa1 Sat Sep 24 18:39:43 2022 -0700
    correct blank line after output and get queryDate and queryAsmName up a level so they can be used in all sections refs #29982
• src/hg/utils/automation/asmHubChromAlias.pl
  • lines changed 21, context: html, text, full: html, text
    86fd61c5e8efe6d7ac42baa32b891fc1cf9e61bf Thu Sep 22 13:57:04 2022 -0700
    add the option of using a customNames.tsv file to add arbitrary listings refs #29982
  • lines changed 26, context: html, text, full: html, text
    e0232de768e8056705fd15b8bf908d99d3ea74e8 Sat Sep 24 18:37:56 2022 -0700
    do not fill in names for RefSeq or GenBank if either of those is not defined refs #29982
• src/hg/utils/automation/asmHubTOGA.pl
  • lines changed 184, context: html, text, full: html, text
    ac38533f23605cb72cffcf3017838c9a10dab63e Wed Sep 21 16:06:17 2022 -0700
    now making a track for TOGA annotations refs #29982
• src/hg/utils/automation/asmHubTrackDb.sh
  • lines changed 52, context: html, text, full: html, text
    ac38533f23605cb72cffcf3017838c9a10dab63e Wed Sep 21 16:06:17 2022 -0700
    now making a track for TOGA annotations refs #29982
  • lines changed 2, context: html, text, full: html, text
    a529cabbe6ecc9e1dc9a9321bdfdcc6db1d10318 Sat Sep 24 15:18:10 2022 -0700
    default vis pack for TOGA track refs #29982
• src/test/buildTableDescriptions.pl
  • lines changed 1, context: html, text, full: html, text
    7664f4eb366d491f9b6d90075e7aa36bc86e38f5 Tue Sep 20 16:22:09 2022 -0700
    Exclude curated hubs from list of mysql databases to check (because they're not mysql databases) using the 'hub:' prefix in nibPath.
• src/utils/qa/hubPublicUrlChanger
  • lines changed 14, context: html, text, full: html, text
    f62fa43775a2cddb1a0870e9a3f635e4bb103f71 Mon Sep 19 11:56:09 2022 -0700
    Code review suggestions, changing search variable from label to url and adding hard fail refs #29999
• src/utils/qa/hubSearchUpdate
  • lines changed 2, context: html, text, full: html, text
    f6291e25ed8efac33355465b61bfd1b8855ebc5b Mon Sep 19 10:34:58 2022 -0700
    Reformatted log file additions No RM
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    acc6c5dc9f736a0808b88bcfbe095b3416a27891 Mon Sep 26 10:05:21 2022 -0700
    v438 preview1, refs #29979

• lines changed: 2304
• files changed: 54