All File Changes

v433_preview to v433_preview2 (2022-06-13 to 2022-06-20) v433

• confs/asia.hg.conf
  • lines changed 1, context: html, text, full: html, text
    81b86b91d4a509911f8780fc7fb42fbb69a84a9c Sun Jun 19 01:11:38 2022 -0700
    Installing updated hg.conf files from UCSC servers
• confs/euro.hg.conf
  • lines changed 1, context: html, text, full: html, text
    81b86b91d4a509911f8780fc7fb42fbb69a84a9c Sun Jun 19 01:11:38 2022 -0700
    Installing updated hg.conf files from UCSC servers
• confs/hgwbeta.hg.conf
  • lines changed 1, context: html, text, full: html, text
    81b86b91d4a509911f8780fc7fb42fbb69a84a9c Sun Jun 19 01:11:38 2022 -0700
    Installing updated hg.conf files from UCSC servers
• confs/rr.hg.conf
  • lines changed 1, context: html, text, full: html, text
    81b86b91d4a509911f8780fc7fb42fbb69a84a9c Sun Jun 19 01:11:38 2022 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/hgGene/hgGeneData/Mouse/mm39/otherOrgs.ra
  • lines changed 1, context: html, text, full: html, text
    dcefe608401f82f186a40894c23e65f2d038fafe Thu Jun 16 15:45:39 2022 -0700
    switch to using danRer11 on mm39
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 8, context: html, text, full: html, text
    73b05663e1f9a56f25cc58a8aab51ff8fa79152b Thu Jun 16 08:18:44 2022 -0700
    changes after code review, refs #29594
• src/hg/hgSession/hgSession.c
  • lines changed 11, context: html, text, full: html, text
    9fb48fcf916f66ad45f316969a25599c82fe385e Tue Jun 14 07:34:25 2022 -0700
    adding copy to clipboard feature to hgSession.c. refs #29586
  • lines changed 5, context: html, text, full: html, text
    30eb9db3aaee5dc558ef4554bc9ffb9bdf2fa048 Thu Jun 16 08:47:49 2022 -0700
    adding more space and longer text to copy button on hgSession, refs
  • lines changed 1, context: html, text, full: html, text
    f659fd55c4d823d84ee4cce89506d639d69780fc Fri Jun 17 01:13:06 2022 -0700
    by popular vote, shortening the button label, to just "Copy". from "Copy to clipboard". seven devs/QA voted for the shorter label. refs #29586
• src/hg/hgTracks/wigTrack.c
  • lines changed 5, context: html, text, full: html, text
    9b26d149e1b358d2ad03390762261baeb2602a7d Wed Jun 15 12:25:10 2022 -0700
    add reverse complement support to sequence logo track
• src/hg/htdocs/goldenPath/help/bigRmsk.html
  • lines changed 1, context: html, text, full: html, text
    bd5a22bd0280053152df31eab38a492434229612 Wed Jun 15 07:35:39 2022 -0700
    Removing link to bigRmskAlign.txt as it doesn't exist yet, and static page cronjob check on beta finds 404 here, no RM
• src/hg/htdocs/goldenPath/help/hgSessionHelp.html
  • lines changed 28, context: html, text, full: html, text
    9ad242daa0aeca97b583975f571641b416c6ee8b Tue Jun 14 07:37:48 2022 -0700
    Adding a section in hgSessionHelp.html#NAR about Public Sessions, and the idea of a gallery for sesions related to a paper, and also more clearly documenting short links and the search term feature for Public Sessions.
• src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html
  • lines changed 5, context: html, text, full: html, text
    569c126e603831fc2fb997b54f98391f42d33a8d Wed Jun 15 07:15:23 2022 -0700
    Adding note about GenArkon Quickstart Assembly Hub page, no RM
• src/hg/htdocs/goldenPath/help/query.html
  • lines changed 3, context: html, text, full: html, text
    eabd99a717cdec9ebced9d5164af445c81af2148 Fri Jun 17 09:44:56 2022 -0700
    Advertising ability to create searcheable track hubs via searchTrix on query page, no RM
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html
  • lines changed 7, context: html, text, full: html, text
    525793509839cc6d231c634ab284ed28bc212955 Mon Jun 13 11:25:47 2022 -0700
    CR changes to paragraph order refs #29553
• src/hg/js/hgHubConnect.js
  • lines changed 4, context: html, text, full: html, text
    73b05663e1f9a56f25cc58a8aab51ff8fa79152b Thu Jun 16 08:18:44 2022 -0700
    changes after code review, refs #29594
• src/hg/js/utils.js
  • lines changed 24, context: html, text, full: html, text
    9fb48fcf916f66ad45f316969a25599c82fe385e Tue Jun 14 07:34:25 2022 -0700
    adding copy to clipboard feature to hgSession.c. refs #29586
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 15, context: html, text, full: html, text
    d9684bba3829df163c18949a621ec2ece43395e9 Wed Jun 15 16:38:07 2022 -0700
    adding 15 assemblies requested by user Corey Lewis refs #29545
• src/hg/makeDb/doc/bigDbSnp.txt
  • lines changed 319, context: html, text, full: html, text
    69087d3a65af31c39337085920e99e5b2db13082 Fri Jun 17 15:05:28 2022 -0700
    Ran the dbsnp pipeline designed by Angie for dbsnp v155. It produces huge bigBed output and I found and fixed a problem encountered on the bedToBigBed. I also tweaked dbSnpJsonToTab to deal with some dbsnp data having multiple study subversions, by ignoring the old datasets and just using the latest one. Added a track description page that has lots of content and counts to update. dbsnp155 is ready for QA on hgwdev. refs #rm27751
• src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv
  • lines changed 15, context: html, text, full: html, text
    c6de7482cb8c620e7ce487dd7f314a534ff16574 Wed Jun 15 16:56:26 2022 -0700
    adding 8 new birds per user Corey Lewis request refs #59545
• src/hg/makeDb/doc/hg38/multiz30way.txt
  • lines changed 35, context: html, text, full: html, text
    363d60920206cd70ab8ec35a67a3e25c03eb8a46 Thu Jun 16 17:36:21 2022 -0700
    add 30way sequence logo on hg38
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 7, context: html, text, full: html, text
    2e01a3ba3ed25c1cbb9939f083e7dbe054d90cc8 Wed Jun 15 16:49:28 2022 -0700
    adding 7 new mammals per user Corey Lewis request refs #59545
• src/hg/makeDb/doc/wuhCor1/varskip.txt
  • lines changed 7, context: html, text, full: html, text
    c384840def0ddb7db7cc22090eeac2687d7869f9 Mon Jun 20 02:15:39 2022 -0700
    adding varskip track to wuhCor1, refs #29617
• src/hg/makeDb/schema/all.joiner
  • lines changed 1, context: html, text, full: html, text
    9edd2ff80ac14453e69eed883fdd7e3118045dcb Tue Jun 14 12:16:46 2022 -0700
    spMrna mrnaID doesn't contain values from the all_mrna table
• src/hg/makeDb/trackDb/human/dbSnp155Composite.html
  • lines changed 755, context: html, text, full: html, text
    69087d3a65af31c39337085920e99e5b2db13082 Fri Jun 17 15:05:28 2022 -0700
    Ran the dbsnp pipeline designed by Angie for dbsnp v155. It produces huge bigBed output and I found and fixed a problem encountered on the bedToBigBed. I also tweaked dbSnpJsonToTab to deal with some dbsnp data having multiple study subversions, by ignoring the old datasets and just using the latest one. Added a track description page that has lots of content and counts to update. dbsnp155 is ready for QA on hgwdev. refs #rm27751
• src/hg/makeDb/trackDb/human/hg38/gtexEqtlHighConf.html
  • lines changed 2, context: html, text, full: html, text
    c9c6267a78f027b37c20341ebd98ebba8d61a917 Fri Jun 17 01:43:32 2022 -0700
    adding note that gtexeqtls has no data on chrX. we should probably move our default gene back to SOD1. no redmine, emails with Matt.
• src/hg/makeDb/trackDb/human/hg38/gtexEqtlHighConf.ra
  • lines changed 3, context: html, text, full: html, text
    c9c6267a78f027b37c20341ebd98ebba8d61a917 Fri Jun 17 01:43:32 2022 -0700
    adding note that gtexeqtls has no data on chrX. we should probably move our default gene back to SOD1. no redmine, emails with Matt.
• src/hg/makeDb/trackDb/human/hg38/multiz100Logo.html
  • lines changed 11, context: html, text, full: html, text
    b187b81900601cb093a96e2159a30d8a94427de9 Thu Jun 16 16:15:39 2022 -0700
    tweaks to support sequence logo
• src/hg/makeDb/trackDb/human/hg38/multiz100Logo.ra
  • lines changed 48, context: html, text, full: html, text
    c774b06085131ad411971985c585fcd5753e8283 Wed Jun 15 11:05:38 2022 -0700
    move multiz100Logo to its own ra file
  • lines changed 5, context: html, text, full: html, text
    b187b81900601cb093a96e2159a30d8a94427de9 Thu Jun 16 16:15:39 2022 -0700
    tweaks to support sequence logo
• src/hg/makeDb/trackDb/human/hg38/multiz30Logo.html
  • lines changed 11, context: html, text, full: html, text
    363d60920206cd70ab8ec35a67a3e25c03eb8a46 Thu Jun 16 17:36:21 2022 -0700
    add 30way sequence logo on hg38
• src/hg/makeDb/trackDb/human/hg38/multiz30Logo.ra
  • lines changed 48, context: html, text, full: html, text
    363d60920206cd70ab8ec35a67a3e25c03eb8a46 Thu Jun 16 17:36:21 2022 -0700
    add 30way sequence logo on hg38
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 32, context: html, text, full: html, text
    96d2b3b695bde3e3f589069c0baf8e3023ff373f Tue Jun 14 12:19:09 2022 -0700
    add multiz100way sequence logo track
  • lines changed 47, context: html, text, full: html, text
    c774b06085131ad411971985c585fcd5753e8283 Wed Jun 15 11:05:38 2022 -0700
    move multiz100Logo to its own ra file
  • lines changed 1, context: html, text, full: html, text
    363d60920206cd70ab8ec35a67a3e25c03eb8a46 Thu Jun 16 17:36:21 2022 -0700
    add 30way sequence logo on hg38
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 162, context: html, text, full: html, text
    69087d3a65af31c39337085920e99e5b2db13082 Fri Jun 17 15:05:28 2022 -0700
    Ran the dbsnp pipeline designed by Angie for dbsnp v155. It produces huge bigBed output and I found and fixed a problem encountered on the bedToBigBed. I also tweaked dbSnpJsonToTab to deal with some dbsnp data having multiple study subversions, by ignoring the old datasets and just using the latest one. Added a track description page that has lots of content and counts to update. dbsnp155 is ready for QA on hgwdev. refs #rm27751
• src/hg/makeDb/trackDb/mouse/mm39/knownGeneVM30.html
  • lines changed 142, context: html, text, full: html, text
    99ed5f3706d24ed4dea3994ef8b001c136605b7e Fri Jun 17 14:57:09 2022 -0700
    added knownGeneVM30.html
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    c384840def0ddb7db7cc22090eeac2687d7869f9 Mon Jun 20 02:15:39 2022 -0700
    adding varskip track to wuhCor1, refs #29617
  • lines changed 2, context: html, text, full: html, text
    d46fddd92b27a8bc673f6a6812dc11170cd24f19 Mon Jun 20 03:36:16 2022 -0700
    updating wuhCor1 resistance track, adding new mutations. refs #28889
• src/hg/makeDb/trackDb/virus/wuhCor1/varskip.html
  • lines changed 41, context: html, text, full: html, text
    c384840def0ddb7db7cc22090eeac2687d7869f9 Mon Jun 20 02:15:39 2022 -0700
    adding varskip track to wuhCor1, refs #29617
• src/hg/makeDb/trackDb/virus/wuhCor1/varskip.ra
  • lines changed 44, context: html, text, full: html, text
    c384840def0ddb7db7cc22090eeac2687d7869f9 Mon Jun 20 02:15:39 2022 -0700
    adding varskip track to wuhCor1, refs #29617
• src/hg/ratStuff/mafCounts/mafCounts.c
  • lines changed 73, context: html, text, full: html, text
    b187b81900601cb093a96e2159a30d8a94427de9 Thu Jun 16 16:15:39 2022 -0700
    tweaks to support sequence logo
• src/hg/snp/dbSnpJsonToTab/dbSnpJsonToTab.c
  • lines changed 54, context: html, text, full: html, text
    69087d3a65af31c39337085920e99e5b2db13082 Fri Jun 17 15:05:28 2022 -0700
    Ran the dbsnp pipeline designed by Angie for dbsnp v155. It produces huge bigBed output and I found and fixed a problem encountered on the bedToBigBed. I also tweaked dbSnpJsonToTab to deal with some dbsnp data having multiple study subversions, by ignoring the old datasets and just using the latest one. Added a track description page that has lots of content and counts to update. dbsnp155 is ready for QA on hgwdev. refs #rm27751
• src/hg/utils/automation/doRepeatMasker.pl
  • lines changed 1, context: html, text, full: html, text
    2ee491feb25f942fad09e7d09e2d7a94ffcd06eb Wed Jun 15 17:12:12 2022 -0700
    can not do the faSize measure in the background since the shell may exit before it is done refs #59545
• src/lib/bbiWrite.c
  • lines changed 1, context: html, text, full: html, text
    69087d3a65af31c39337085920e99e5b2db13082 Fri Jun 17 15:05:28 2022 -0700
    Ran the dbsnp pipeline designed by Angie for dbsnp v155. It produces huge bigBed output and I found and fixed a problem encountered on the bedToBigBed. I also tweaked dbSnpJsonToTab to deal with some dbsnp data having multiple study subversions, by ignoring the old datasets and just using the latest one. Added a track description page that has lots of content and counts to update. dbsnp155 is ready for QA on hgwdev. refs #rm27751
• src/utils/bedToBigBed/bedToBigBed.c
  • lines changed 1, context: html, text, full: html, text
    69087d3a65af31c39337085920e99e5b2db13082 Fri Jun 17 15:05:28 2022 -0700
    Ran the dbsnp pipeline designed by Angie for dbsnp v155. It produces huge bigBed output and I found and fixed a problem encountered on the bedToBigBed. I also tweaked dbSnpJsonToTab to deal with some dbsnp data having multiple study subversions, by ignoring the old datasets and just using the latest one. Added a track description page that has lots of content and counts to update. dbsnp155 is ready for QA on hgwdev. refs #rm27751
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    c28f52a59f239f6ac109647e2cb0f8fe804b2277 Mon Jun 20 10:06:47 2022 -0700
    v433 preview2, refs #29585

• lines changed: 1993
• files changed: 47