All File Changes

v441_preview2 to v441_base (2022-12-05 to 2022-12-12) v441

• confs/hgwdev.hg.conf
  • lines changed 4, context: html, text, full: html, text
    6a49aa53e4507fb6aa617ae4049b300c19ddb53a Sun Dec 11 01:11:21 2022 -0800
    Installing updated hg.conf files from UCSC servers
• src/hg/hgBlat/hgBlat.c
  • lines changed 1, context: html, text, full: html, text
    1530c7795223a21e3210988f1007210cc9c75794 Mon Dec 5 15:12:19 2022 -0800
    unset the dbOverride if the user changed the org
• src/hg/hgCustom/hgCustom.c
  • lines changed 3, context: html, text, full: html, text
    e4454dd58d24395dc584d5f234e8cc5639d95995 Fri Dec 9 04:37:27 2022 -0800
    adding return to current position button, refs #30306
• src/hg/hgTracks/hgTracks.c
  • lines changed 8, context: html, text, full: html, text
    11d274be1e5b4364f49fc810ece1f197eddf0ef8 Fri Dec 9 05:02:05 2022 -0800
    adding option for QA to show any random piece of html on hgTracks, refs #30376
  • lines changed 3, context: html, text, full: html, text
    00f6836e89883c2acbdaa88b3940dd5d6e6123cc Fri Dec 9 14:44:46 2022 -0800
    Comment out javascript references until sources are installed, refs Lou email
  • lines changed 3, context: html, text, full: html, text
    b78b89aa485049961a03103dee5cd488cb271cda Mon Dec 12 09:45:43 2022 -0800
    removing stray includes fixed by Chris previously, no redmine, email to browser-dev
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 10, context: html, text, full: html, text
    f860c06610db309b98e1e629856950eac2177b5e Mon Dec 5 15:40:42 2022 -0800
    Adding the latest GB update to pubs page, no RM.
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    cb452184c990541a6109b6921e19912758534eb3 Mon Dec 12 10:13:49 2022 -0800
    New version number v441
• src/hg/lib/dupTrack.c
  • lines changed 2, context: html, text, full: html, text
    54535926c35c6a44c925a3169773f2506a6e27ca Mon Dec 5 11:56:46 2022 -0800
    check for NULL before checking for dups
• src/hg/makeDb/doc/bosTau4.txt
  • lines changed 26, context: html, text, full: html, text
    7b0c8bb2cb0e36f4b8a3335dfe755586cbdf584f Wed Dec 7 21:32:28 2022 -0800
    liftOver per user request 4 to 9 to 4 refs #30301
• src/hg/makeDb/doc/bosTau9/initialBuild.txt
  • lines changed 26, context: html, text, full: html, text
    7b0c8bb2cb0e36f4b8a3335dfe755586cbdf584f Wed Dec 7 21:32:28 2022 -0800
    liftOver per user request 4 to 9 to 4 refs #30301
• src/hg/makeDb/doc/canFam2.txt
  • lines changed 28, context: html, text, full: html, text
    4e87889264ce4941bd458eaea3190c95d9b682c5 Sun Dec 11 15:23:30 2022 -0800
    liftOver to canFam6 per user request refs #30374
• src/hg/makeDb/doc/canFam6/initialBuild.txt
  • lines changed 26, context: html, text, full: html, text
    97cc4f47f34fca7bebb8bc8733d54a57a8d98839 Fri Dec 9 14:25:51 2022 -0800
    liftOver canFam6 to canFam2 refs #30374
• src/hg/makeDb/doc/dp3.txt
  • lines changed 92, context: html, text, full: html, text
    70415b51bd79ffbe93d0e64a49a73ec73493abf6 Tue Dec 6 21:55:51 2022 -0800
    dp3 vs. droPer1 lastz/chain/net run for user, refs #2567
• src/hg/makeDb/doc/mm39/lastzRuns.txt
  • lines changed 91, context: html, text, full: html, text
    408f7dd97515881a86b62c29955b2ca17926e9bc Tue Dec 6 20:58:44 2022 -0800
    mm 9 v GCA_004027735.1 lastz/chain/net run for user, refs #30097
  • lines changed 189, context: html, text, full: html, text
    271b05ba2f4fa9cc7e587faf606d9ad54e65e2f1 Tue Dec 6 21:33:28 2022 -0800
    Updating and adding mm39 vs. mouse strains lastz/chain/net run for users, refs #30097 #30195
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV41lift37.ra
  • lines changed 1, context: html, text, full: html, text
    4772d4dd4f6f14f6846fee951a33edc232c28b44 Thu Dec 8 12:21:01 2022 -0800
    Setting the previous All GENCODE version to hide for the new version release, refs #29789 #29790 #29791
• src/hg/makeDb/trackDb/human/hg38/cons241way.html
  • lines changed 1, context: html, text, full: html, text
    d5576361bdaea1b1d321434af2417a3da80effd1 Thu Dec 8 16:45:45 2022 -0800
    Fixing the tree model link on the Cactus 241-way track description page, refs #30318
• src/hg/makeDb/trackDb/human/hg38/liftOver.ra
  • lines changed 1, context: html, text, full: html, text
    362732db51c3d5049de34bad53d39c85ea02c76b Tue Dec 6 14:39:51 2022 -0800
    Fix copy-paste bug that messed up hgc's 'Approximate Score within browser window' and 'View DNA sequence alignment details ...' for hg38ToHg19 liftOver chains. sorta refs #30355 MLQ.
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV41.ra
  • lines changed 1, context: html, text, full: html, text
    4772d4dd4f6f14f6846fee951a33edc232c28b44 Thu Dec 8 12:21:01 2022 -0800
    Setting the previous All GENCODE version to hide for the new version release, refs #29789 #29790 #29791
• src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM30.ra
  • lines changed 1, context: html, text, full: html, text
    4772d4dd4f6f14f6846fee951a33edc232c28b44 Thu Dec 8 12:21:01 2022 -0800
    Setting the previous All GENCODE version to hide for the new version release, refs #29789 #29790 #29791
• src/hg/makeDb/trackDb/relatedTracks.ra
  • lines changed 11, context: html, text, full: html, text
    675bc34c80612e44b7a251390d6567611f92a37e Thu Dec 8 03:03:47 2022 -0800
    fixing grc incidents - liftover related links, refs #30355
• src/hg/makeDb/trackDb/wgEncodeGencodeDisplay1.shared.html
  • lines changed 1, context: html, text, full: html, text
    6bcb55e7757cef7074e4182e58be5ad8a1281833 Thu Dec 8 12:09:51 2022 -0800
    Adding a dash (-) for layout consistency in the Transcript ranking section, refs #29789 #29790 #29791
• src/hg/utils/automation/asmHubRepeatMasker.sh
  • lines changed 8, context: html, text, full: html, text
    a074cd2a4d68363db2f1b6381bab63363df0bded Tue Dec 6 13:56:52 2022 -0800
    better detection of rmblastn path with new configuration file and allow chrom.sizes to be found in current directory no redmine
  • lines changed 1, context: html, text, full: html, text
    a3daddc4cea89f18fa40b571bfc97d47ad01b0a8 Tue Dec 6 17:40:27 2022 -0800
    correct variable name no redmine
  • lines changed 1, context: html, text, full: html, text
    88df6e5ecb0ba85dee681e7c461e9c635932ad4f Tue Dec 6 18:19:47 2022 -0800
    correct line break after info statement no redmine
• src/hg/utils/automation/doRepeatMasker.pl
  • lines changed 2, context: html, text, full: html, text
    a074cd2a4d68363db2f1b6381bab63363df0bded Tue Dec 6 13:56:52 2022 -0800
    better detection of rmblastn path with new configuration file and allow chrom.sizes to be found in current directory no redmine
• src/hg/utils/otto/ncbiRefSeq/runUcscDb.sh
  • lines changed 2, context: html, text, full: html, text
    e4e70ace5f9974e20048210f0c1f67ee7e57a6ee Mon Dec 5 23:25:51 2022 -0800
    eliminate the not needed message refs #28331
• src/hg/utils/otto/panelApp/genes.py
  • lines changed 92, context: html, text, full: html, text
    6a1db42395f283de1421bd45e9d245ba2f896005 Wed Dec 7 03:38:42 2022 -0800
    commit panelApp otto changes, refs #30212
• src/hg/utils/otto/panelApp/updatePanelApp
  • lines changed 2, context: html, text, full: html, text
    6a1db42395f283de1421bd45e9d245ba2f896005 Wed Dec 7 03:38:42 2022 -0800
    commit panelApp otto changes, refs #30212
• src/inc/srcVersion.h
  • lines changed 1, context: html, text, full: html, text
    cb452184c990541a6109b6921e19912758534eb3 Mon Dec 12 10:13:49 2022 -0800
    New version number v441
• src/product/ex.hg.conf
  • lines changed 12, context: html, text, full: html, text
    11d274be1e5b4364f49fc810ece1f197eddf0ef8 Fri Dec 9 05:02:05 2022 -0800
    adding option for QA to show any random piece of html on hgTracks, refs #30376
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    84e936fe071918f08b94e05ac78291885d53b0c4 Mon Dec 12 10:12:21 2022 -0800
    v441 final build, refs #30323

• lines changed: 654
• files changed: 33