All File Changes

v463_base to v464_preview (2024-04-01 to 2024-04-08) v464

• confs/asia.hg.conf
  • lines changed 4, context: html, text, full: html, text
    f5580cfac9c9893353d551984015250df67d03ec Sun Apr 7 01:11:22 2024 -0700
    Installing updated hg.conf files from UCSC servers
• confs/euro.hg.conf
  • lines changed 4, context: html, text, full: html, text
    f5580cfac9c9893353d551984015250df67d03ec Sun Apr 7 01:11:22 2024 -0700
    Installing updated hg.conf files from UCSC servers
• confs/hgwdev.hg.conf
  • lines changed 3, context: html, text, full: html, text
    f5580cfac9c9893353d551984015250df67d03ec Sun Apr 7 01:11:22 2024 -0700
    Installing updated hg.conf files from UCSC servers
• confs/rr.hg.conf
  • lines changed 3, context: html, text, full: html, text
    f5580cfac9c9893353d551984015250df67d03ec Sun Apr 7 01:11:22 2024 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/hgCollection/hgCollection.c
  • lines changed 1, context: html, text, full: html, text
    529007412cd0baf453103b61c018f1eaaa23e872 Fri Apr 5 17:09:44 2024 -0700
    make a function static that I used elsewhere for the moment.
• src/hg/hgConvert/hgConvert.c
  • lines changed 43, context: html, text, full: html, text
    2d30d99f5f6d3d6532166a0c70c89d38e6053fb1 Fri Apr 5 16:57:02 2024 -0700
    ongoing work on quickLift
• src/hg/hgGene/hgGene.c
  • lines changed 27, context: html, text, full: html, text
    88003194f390b7e4c5978bcc0cee7df03518203d Thu Apr 4 15:03:12 2024 -0700
    Make collapse/expand buttons on hgGene not do a page refresh each time they are clicked, refs #3216
• src/hg/hgPhyloPlace/phyloPlace.c
  • lines changed 1, context: html, text, full: html, text
    3e0322b8be3a7a96e99fcfc2b69525e042bc0ac2 Mon Apr 1 21:18:03 2024 -0700
    Fixing typo bug that caused pangolin lineage lookup to return the column name instead of the actual lineage value. HT @aviczhl2
• src/hg/hgTracks/exportedDataHubs.c
  • lines changed 8, context: html, text, full: html, text
    2d30d99f5f6d3d6532166a0c70c89d38e6053fb1 Fri Apr 5 16:57:02 2024 -0700
    ongoing work on quickLift
• src/hg/hgTracks/hgTracks.c
  • lines changed 2, context: html, text, full: html, text
    ec4ec036af9e086a93c98700aba30b4d8048385d Wed Apr 3 12:34:02 2024 -0700
    ongoing work on quickLift
  • lines changed 4, context: html, text, full: html, text
    3d3f084876b33513ffa9047d3129c71f628b6ebc Wed Mar 13 16:29:59 2024 -0700
    Show hgc details pages in a dialog on hgTracks. Currently under hg.conf control , refs #33216
  • lines changed 4, context: html, text, full: html, text
    8885686b3723a1a256cb1ff0677ca8a07927bed4 Thu Apr 4 13:24:20 2024 -0700
    Make the hprc table stuff work in an hgc popup, make any javascript that would execute on document ready execute when the pop up is ready, refs #33216
• src/hg/hgc/hgc.c
  • lines changed 16, context: html, text, full: html, text
    ec4ec036af9e086a93c98700aba30b4d8048385d Wed Apr 3 12:34:02 2024 -0700
    ongoing work on quickLift
• src/hg/htdocs/goldenPath/help/bigChain.html
  • lines changed 1, context: html, text, full: html, text
    58902da8c77ee226677e9c56c38d7b6b2b319256 Fri Apr 5 20:34:54 2024 -0700
    update documentation on bigChain to match the code. RM 33430
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 1, context: html, text, full: html, text
    2b5f10644f8fc336b6f73c10967edee119f8e8f3 Mon Apr 1 17:42:56 2024 -0700
    Code review edits, refs #33313
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 5, context: html, text, full: html, text
    2b5f10644f8fc336b6f73c10967edee119f8e8f3 Mon Apr 1 17:42:56 2024 -0700
    Code review edits, refs #33313
• src/hg/htdocs/redmineWidget.html
  • lines changed 0, context: html, text, full: html, text
    ff511ec8e45ac5bdc9df602dfd13eca33d20b0b9 Thu Apr 4 14:14:00 2024 -0700
    Adding execute permission to widget so that the condition will activate on genome-preview, refs email 'Genome-preview htdocs?'
• src/hg/htdocs/style/HGStyle.css
  • lines changed 2, context: html, text, full: html, text
    2d30d99f5f6d3d6532166a0c70c89d38e6053fb1 Fri Apr 5 16:57:02 2024 -0700
    ongoing work on quickLift
• src/hg/inc/exportedDataHubs.h
  • lines changed 3, context: html, text, full: html, text
    2d30d99f5f6d3d6532166a0c70c89d38e6053fb1 Fri Apr 5 16:57:02 2024 -0700
    ongoing work on quickLift
• src/hg/inc/quickLift.h
  • lines changed 2, context: html, text, full: html, text
    2d30d99f5f6d3d6532166a0c70c89d38e6053fb1 Fri Apr 5 16:57:02 2024 -0700
    ongoing work on quickLift
• src/hg/inc/trackHub.h
  • lines changed 3, context: html, text, full: html, text
    2d30d99f5f6d3d6532166a0c70c89d38e6053fb1 Fri Apr 5 16:57:02 2024 -0700
    ongoing work on quickLift
• src/hg/js/hgTracks.js
  • lines changed 211, context: html, text, full: html, text
    3d3f084876b33513ffa9047d3129c71f628b6ebc Wed Mar 13 16:29:59 2024 -0700
    Show hgc details pages in a dialog on hgTracks. Currently under hg.conf control , refs #33216
  • lines changed 51, context: html, text, full: html, text
    8885686b3723a1a256cb1ff0677ca8a07927bed4 Thu Apr 4 13:24:20 2024 -0700
    Make the hprc table stuff work in an hgc popup, make any javascript that would execute on document ready execute when the pop up is ready, refs #33216
• src/hg/js/hgc.js
  • lines changed 19, context: html, text, full: html, text
    8885686b3723a1a256cb1ff0677ca8a07927bed4 Thu Apr 4 13:24:20 2024 -0700
    Make the hprc table stuff work in an hgc popup, make any javascript that would execute on document ready execute when the pop up is ready, refs #33216
• src/hg/js/jquery.contextmenu.js
  • lines changed 3, context: html, text, full: html, text
    3d3f084876b33513ffa9047d3129c71f628b6ebc Wed Mar 13 16:29:59 2024 -0700
    Show hgc details pages in a dialog on hgTracks. Currently under hg.conf control , refs #33216
• src/hg/js/utils.js
  • lines changed 1, context: html, text, full: html, text
    8e55cc2bfc3ea9927df82e542838047413c24531 Mon Apr 1 13:16:59 2024 -0700
    Change timeout for showing a tooltip when one is already visible to be much longer, refs #33301
  • lines changed 15, context: html, text, full: html, text
    83ffc65b0574e8b3bfd7d191548ccde8651670b2 Tue Apr 2 11:28:22 2024 -0700
    Fix tooltip bug, when the user is moving their mouse and triggers a new mouseover event, we need to clear the mousemove event that was checking if they were heading to the tooltip. By clearing this event we prevent the mousemoveTimerHelper function from running, which in this case is mistakenly re-triggering a mouseover event but on the wrong event coordinates, leading to tooltips that are a ways away from where they are supposed to be, refs Max email
  • lines changed 8, context: html, text, full: html, text
    3d3f084876b33513ffa9047d3129c71f628b6ebc Wed Mar 13 16:29:59 2024 -0700
    Show hgc details pages in a dialog on hgTracks. Currently under hg.conf control , refs #33216
• src/hg/lib/exportedDataHubs.c
  • lines changed 36, context: html, text, full: html, text
    2d30d99f5f6d3d6532166a0c70c89d38e6053fb1 Fri Apr 5 16:57:02 2024 -0700
    ongoing work on quickLift
• src/hg/lib/hui.c
  • lines changed 12, context: html, text, full: html, text
    afc8cef2dc4d4178a80bea4b2167364a636e73b8 Thu Apr 4 16:59:08 2024 -0700
    with bigBed labels, if there's only one choice, just let user choose if the label is on or off
• src/hg/lib/quickLift.c
  • lines changed 18, context: html, text, full: html, text
    2d30d99f5f6d3d6532166a0c70c89d38e6053fb1 Fri Apr 5 16:57:02 2024 -0700
    ongoing work on quickLift
• src/hg/lib/trackHub.c
  • lines changed 204, context: html, text, full: html, text
    2d30d99f5f6d3d6532166a0c70c89d38e6053fb1 Fri Apr 5 16:57:02 2024 -0700
    ongoing work on quickLift
• src/hg/lib/varProtein.sql
  • lines changed 2, context: html, text, full: html, text
    70ecc23e4b060c8685f1ebc99f0e8e82f08d59b3 Mon Apr 8 10:56:05 2024 -0700
    Updating lib/varProtein.sql to better match the definition in spDb.sql, refs #32414
• src/hg/makeDb/doc/asmHubs/asmHubs.mk
  • lines changed 41, context: html, text, full: html, text
    cb3cd0e9c5b9006b7d316df7905faa516f880c6b Fri Apr 5 00:33:00 2024 -0700
    sending to both hgdownload1 and hgdownload2 no redmine
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 1, context: html, text, full: html, text
    94811511d710efb3aafb1b0c9d4157752f687d13 Thu Apr 4 13:04:56 2024 -0700
    adding GCF_033978685.1_RoL_Nlum_1.0 fish Nerophis_lumbriciformis per user request, refs #29545
• src/hg/makeDb/doc/asmHubs/sendToHgdownload.sh
  • lines changed 34, context: html, text, full: html, text
    d24e198c451d6458dfbdb2305d8a321ee8ae9010 Wed Apr 3 14:40:12 2024 -0700
    sending to both hgdownload1 and hgdownload2 no redmine
• src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    51d7c08c88b0f6a724a4ae46acdc29d5210b41c3 Thu Apr 4 13:31:58 2024 -0700
    adding Nerophis_lumbriciformis GCF_033978685.1_RoL_Nlum_1.0 worm pipefish (RoL_2023-P1 2023), refs #29545
• src/hg/makeDb/doc/hg38/lastzRuns.txt
  • lines changed 83, context: html, text, full: html, text
    f3728f6e4926c0a472017a514ed67fd29f18ba9f Sun Apr 7 21:48:32 2024 -0700
    hg38 to GCA_023856395.1 lastz/chain/net run for user, refs #33276
• src/hg/makeDb/doc/mm39/lastzRuns.txt
  • lines changed 83, context: html, text, full: html, text
    51e36af6ab42bd9c0f858a4d00cf63bcac0fb4a7 Sun Apr 7 21:45:15 2024 -0700
    mm39 to GCA_921997145.2 lastz/chain/net run for user, refs #33296
• src/hg/makeDb/doc/ucscGenes/hg38.gencodeV45.sh
  • lines changed 2, context: html, text, full: html, text
    c18e69d83c6e7c80bae078cc840389a88e7eafc5 Thu Apr 4 11:40:26 2024 -0700
    Correcting minor typos for knownGeneV45, refs #32414
• src/hg/makeDb/doc/ucscGenes/hg38.gencodeV46.sh
  • lines changed 37, context: html, text, full: html, text
    69a0424ad6e043b05e54bf856d8937577ea2be69 Fri Apr 5 23:28:49 2024 -0700
    makedoc for knownGeneV46, refs #33080
• src/hg/makeDb/doc/ucscGenes/mm39.gencodeVM35.sh
  • lines changed 46, context: html, text, full: html, text
    762ac090a1deaff495eff1a1a5d0cb73e115610d Thu Apr 4 11:49:56 2024 -0700
    Makedoc for knownGeneVM35, refs #33083
• src/hg/makeDb/trackDb/human/hg38/knownGene.alpha.ra
  • lines changed 10, context: html, text, full: html, text
    cde15a4447a67276ca892e129fc34a41bf61d393 Tue Apr 2 13:13:51 2024 -0700
    V46 knownGene trackDb
• src/hg/makeDb/trackDb/human/hg38/knownGeneArchive.ra
  • lines changed 27, context: html, text, full: html, text
    cde15a4447a67276ca892e129fc34a41bf61d393 Tue Apr 2 13:13:51 2024 -0700
    V46 knownGene trackDb
• src/hg/makeDb/trackDb/human/hg38/knownGeneOldV45.html
  • lines changed 10, context: html, text, full: html, text
    5894556e834f259943571c85b8cdb853c96673b6 Fri Apr 5 23:26:29 2024 -0700
    Docs page for knownGeneOldV45, refs #33080
• src/hg/makeDb/trackDb/human/hg38/knownGeneV45.html
  • lines changed 4, context: html, text, full: html, text
    c18e69d83c6e7c80bae078cc840389a88e7eafc5 Thu Apr 4 11:40:26 2024 -0700
    Correcting minor typos for knownGeneV45, refs #32414
• src/hg/makeDb/trackDb/human/hg38/knownGeneV46.html
  • lines changed 164, context: html, text, full: html, text
    cde15a4447a67276ca892e129fc34a41bf61d393 Tue Apr 2 13:13:51 2024 -0700
    V46 knownGene trackDb
  • lines changed 1, context: html, text, full: html, text
    441612acc3c7ca96198cf4dd282b87d05db7f357 Fri Apr 5 23:38:56 2024 -0700
    Updating link for V46 GENCODE build, refs #33080
• src/hg/makeDb/trackDb/mouse/mm39/knownGeneVM35.html
  • lines changed 19, context: html, text, full: html, text
    f63b1ae974eb5edd85aebe6fa80bd5b1cdbd299d Thu Apr 4 11:07:40 2024 -0700
    Minor docs update for knownGeneVM35, refs #33083
• src/utils/qa/checkTableStatusDump.sh
  • lines changed 1, context: html, text, full: html, text
    2b5f10644f8fc336b6f73c10967edee119f8e8f3 Mon Apr 1 17:42:56 2024 -0700
    Code review edits, refs #33313
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    ff3c5184034a318d7e9c854335a73b33c09e00bd Mon Apr 8 11:13:21 2024 -0700
    v464 preview1, refs #33267

• lines changed: 1283
• files changed: 51