All File Changes

v489_preview2 to v489_base (2025-10-06 to 2025-10-13) v489

• confs/asia.hg.conf
  • lines changed 3, context: html, text, full: html, text
    78dcc5273bd7e2d7857122ac41447a98ece84e00 Sun Oct 12 01:11:19 2025 -0700
    Installing updated hg.conf files from UCSC servers
• confs/euro.hg.conf
  • lines changed 3, context: html, text, full: html, text
    78dcc5273bd7e2d7857122ac41447a98ece84e00 Sun Oct 12 01:11:19 2025 -0700
    Installing updated hg.conf files from UCSC servers
• confs/hgwbeta.hg.conf
  • lines changed 3, context: html, text, full: html, text
    78dcc5273bd7e2d7857122ac41447a98ece84e00 Sun Oct 12 01:11:19 2025 -0700
    Installing updated hg.conf files from UCSC servers
• confs/hgwdev.hg.conf
  • lines changed 2, context: html, text, full: html, text
    78dcc5273bd7e2d7857122ac41447a98ece84e00 Sun Oct 12 01:11:19 2025 -0700
    Installing updated hg.conf files from UCSC servers
• confs/rr.hg.conf
  • lines changed 3, context: html, text, full: html, text
    78dcc5273bd7e2d7857122ac41447a98ece84e00 Sun Oct 12 01:11:19 2025 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/hgConvert/hgConvert.c
  • lines changed 168, context: html, text, full: html, text
    eb5c9cd277c2bcd521aa461d06e9d8a32509c1d3 Thu Oct 9 12:17:30 2025 -0700
    make it possible to use a cart variable in addition to an hg.conf variable to turn on quickLift
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 4, context: html, text, full: html, text
    8f0b9b181e4b7be813445c43693a3f666e8b7619 Fri Oct 10 18:57:15 2025 -0700
    Adding API key documentation and updating the CAPTCHA message so people can find it, refs #36428
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 3, context: html, text, full: html, text
    0dc3dba8c97201b69523bbcf01b4c19b17fce05a Fri Oct 10 13:09:38 2025 -0700
    ongoing work on quickLift
• src/hg/hgTracks/decorator.c
  • lines changed 8, context: html, text, full: html, text
    6d15c4259016e2b9bca547840c4edba7f25bdfcd Mon Oct 13 13:35:01 2025 -0700
    Adding plus and X decoration glyphs, and correcting placement for decorating multi-row items, no ticket (request from Max)
• src/hg/hgTracks/gencodeTracks.c
  • lines changed 15, context: html, text, full: html, text
    4f0b12aadc3153194c9b4c81c70adc86d621ff2b Fri Oct 10 12:08:26 2025 -0700
    support genePred in quickLift
• src/hg/hgTracks/hgTracks.c
  • lines changed 10, context: html, text, full: html, text
    0dc3dba8c97201b69523bbcf01b4c19b17fce05a Fri Oct 10 13:09:38 2025 -0700
    ongoing work on quickLift
  • lines changed 4, context: html, text, full: html, text
    71cbef499bd026b90eb7b45db9e0d16eca279e07 Mon Oct 13 08:49:15 2025 -0700
    shortening track mouseover a little, refs #34922
• src/hg/hgTracks/hgTracks.h
  • lines changed 3, context: html, text, full: html, text
    6d15c4259016e2b9bca547840c4edba7f25bdfcd Mon Oct 13 13:35:01 2025 -0700
    Adding plus and X decoration glyphs, and correcting placement for decorating multi-row items, no ticket (request from Max)
• src/hg/hgTracks/imageV2.c
  • lines changed 7, context: html, text, full: html, text
    62918b2049c18475349ce07a72d53dcd742b78df Fri Oct 10 13:00:19 2025 -0700
    Instead of creating the gear icon dynamically on mouseover of the track td/tr, stick them in the html by default but with display:hide, because creating them dynamically causes Chrome to misinterpret the mouseover/mouseleave events
  • lines changed 1, context: html, text, full: html, text
    0dc3dba8c97201b69523bbcf01b4c19b17fce05a Fri Oct 10 13:09:38 2025 -0700
    ongoing work on quickLift
  • lines changed 6, context: html, text, full: html, text
    68137bd66978c21a5d168b5216f07f03caf34f3c Fri Oct 10 15:10:09 2025 -0700
    Also create the 'x' icons with display:none so mouseover/mouseleave and track drag work correctly, refs #34420
• src/hg/hgTracks/quickLiftPull.c
  • lines changed 1, context: html, text, full: html, text
    0dc3dba8c97201b69523bbcf01b4c19b17fce05a Fri Oct 10 13:09:38 2025 -0700
    ongoing work on quickLift
• src/hg/hgTracks/simpleTracks.c
  • lines changed 11, context: html, text, full: html, text
    6d15c4259016e2b9bca547840c4edba7f25bdfcd Mon Oct 13 13:35:01 2025 -0700
    Adding plus and X decoration glyphs, and correcting placement for decorating multi-row items, no ticket (request from Max)
• src/hg/hgc/hgc.c
  • lines changed 64, context: html, text, full: html, text
    4f0b12aadc3153194c9b4c81c70adc86d621ff2b Fri Oct 10 12:08:26 2025 -0700
    support genePred in quickLift
• src/hg/htdocs/FAQ/FAQdownloads.html
  • lines changed 20, context: html, text, full: html, text
    8f0b9b181e4b7be813445c43693a3f666e8b7619 Fri Oct 10 18:57:15 2025 -0700
    Adding API key documentation and updating the CAPTCHA message so people can find it, refs #36428
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 1, context: html, text, full: html, text
    0b3fad1ff43a24d5fe01fe799a32e03fbe1be694 Fri Oct 10 17:09:04 2025 -0700
    Adding an anchor to the format help section of track hubs. Editing the help text for Hub Space, refs #36290
• src/hg/htdocs/goldenPath/help/hubBasics.html
  • lines changed 1, context: html, text, full: html, text
    7786a0b964b3578900801ddcf88447f0fb854a79 Mon Oct 6 19:23:39 2025 -0700
    adding comma based on code review, refs #36478
• src/hg/htdocs/goldenPath/help/posters.html
  • lines changed 1, context: html, text, full: html, text
    8fd94cdce6a24e02b0877a961bda71132df78df1 Tue Oct 7 10:38:40 2025 -0700
    Code review edit: adding some space under each poster, refs #36473
• src/hg/htdocs/goldenPath/mapPlots/RHguide.html
  • lines changed 41, context: html, text, full: html, text
    af4e35aa7eb04608ff105742525a56cd4950f365 Thu Oct 9 17:39:40 2025 -0700
    This page came up in the check for static doc changes. Updating the page. refs #35294
• src/hg/htdocs/images/HubSpaceUpload.png
  • lines changed 0, context: html, text, full: html, text
    e253fa65a4e39fb7f746eebd4a7383f866e57de7 Fri Oct 10 16:37:25 2025 -0700
    Adding an image for hub space documentation, refs #36290
• src/hg/htdocs/inc/hgMyData.html
  • lines changed 40, context: html, text, full: html, text
    0b3fad1ff43a24d5fe01fe799a32e03fbe1be694 Fri Oct 10 17:09:04 2025 -0700
    Adding an anchor to the format help section of track hubs. Editing the help text for Hub Space, refs #36290
  • lines changed 13, context: html, text, full: html, text
    14858883290f91667b6f50ea931e89950e933ba2 Fri Oct 10 17:27:45 2025 -0700
    Moving the 'view selected' and 'delete selected' buttons to the bottom of the table, refs #31058
  • lines changed 4, context: html, text, full: html, text
    0d1298fd78ff70ad5ebd24b2e7d6c7badc899fb4 Fri Oct 10 17:43:49 2025 -0700
    Updating the spacing for the div lines. Editing text for when you select a file, refs #31058
• src/hg/inc/cart.h
  • lines changed 2, context: html, text, full: html, text
    eb5c9cd277c2bcd521aa461d06e9d8a32509c1d3 Thu Oct 9 12:17:30 2025 -0700
    make it possible to use a cart variable in addition to an hg.conf variable to turn on quickLift
• src/hg/inc/quickLift.h
  • lines changed 5, context: html, text, full: html, text
    eb5c9cd277c2bcd521aa461d06e9d8a32509c1d3 Thu Oct 9 12:17:30 2025 -0700
    make it possible to use a cart variable in addition to an hg.conf variable to turn on quickLift
• src/hg/js/hgHubConnect.js
  • lines changed 3, context: html, text, full: html, text
    49a02af9f3ec0cfff74d0dd93da2722a030e4147 Fri Oct 10 10:24:15 2025 -0700
    Fix hgHubConnect tab anchor link detection so urls with the anchor will actually switch to that tab, refs Lou email
• src/hg/js/subCfg.js
  • lines changed 1, context: html, text, full: html, text
    09b2cc42cfd3b47dabe774f5fb4f77eb31c3bed2 Tue Oct 7 05:50:44 2025 -0700
    fixing error message when VCF tree display is part of a composite, refs #36259
• src/hg/js/utils.js
  • lines changed 2, context: html, text, full: html, text
    2b1aedbeabcbd667f019a274104f0ac9b9abedb4 Fri Oct 10 11:32:12 2025 -0700
    Change gear icon event handlers from mouseenter/mouseleave to pointerenter/pointerleave to catch subtle event handler differences between Chrome and Firefox, refs #34420
  • lines changed 9, context: html, text, full: html, text
    62918b2049c18475349ce07a72d53dcd742b78df Fri Oct 10 13:00:19 2025 -0700
    Instead of creating the gear icon dynamically on mouseover of the track td/tr, stick them in the html by default but with display:hide, because creating them dynamically causes Chrome to misinterpret the mouseover/mouseleave events
  • lines changed 10, context: html, text, full: html, text
    68137bd66978c21a5d168b5216f07f03caf34f3c Fri Oct 10 15:10:09 2025 -0700
    Also create the 'x' icons with display:none so mouseover/mouseleave and track drag work correctly, refs #34420
• src/hg/lib/cart.c
  • lines changed 10, context: html, text, full: html, text
    eb5c9cd277c2bcd521aa461d06e9d8a32509c1d3 Thu Oct 9 12:17:30 2025 -0700
    make it possible to use a cart variable in addition to an hg.conf variable to turn on quickLift
  • lines changed 2, context: html, text, full: html, text
    8f0b9b181e4b7be813445c43693a3f666e8b7619 Fri Oct 10 18:57:15 2025 -0700
    Adding API key documentation and updating the CAPTCHA message so people can find it, refs #36428
  • lines changed 1, context: html, text, full: html, text
    a4e6ec39723aef8e1233da1a55a7ad3079ed6592 Fri Oct 10 19:00:34 2025 -0700
    Tweaking the wording to be shorter, refs #36428
• src/hg/lib/hubConnect.c
  • lines changed 3, context: html, text, full: html, text
    0dc3dba8c97201b69523bbcf01b4c19b17fce05a Fri Oct 10 13:09:38 2025 -0700
    ongoing work on quickLift
• src/hg/lib/quickLift.c
  • lines changed 21, context: html, text, full: html, text
    eb5c9cd277c2bcd521aa461d06e9d8a32509c1d3 Thu Oct 9 12:17:30 2025 -0700
    make it possible to use a cart variable in addition to an hg.conf variable to turn on quickLift
• src/hg/lib/trackHub.c
  • lines changed 2, context: html, text, full: html, text
    4f0b12aadc3153194c9b4c81c70adc86d621ff2b Fri Oct 10 12:08:26 2025 -0700
    support genePred in quickLift
  • lines changed 2, context: html, text, full: html, text
    0dc3dba8c97201b69523bbcf01b4c19b17fce05a Fri Oct 10 13:09:38 2025 -0700
    ongoing work on quickLift
• src/hg/makeDb/doc/archaeaAsmHub/archaea.orderList.tsv
  • lines changed 22, context: html, text, full: html, text
    7fbaf4ec666799c553411e1a8c5ae1edeeafa9ba Wed Oct 8 09:08:13 2025 -0700
    RefSeq update and user requests refs #29545
• src/hg/makeDb/doc/asmHubs/README.chromAlias.txt
  • lines changed 82, context: html, text, full: html, text
    26db090072511b54c477fb9824d24aaeae349a13 Mon Oct 13 12:38:56 2025 -0700
    document chromAlias procedure refs #36461
  • lines changed 0, context: html, text, full: html, text
    e69d556b5fda919a0e8e2e31d18d01c8e20d57ba Mon Oct 13 12:39:36 2025 -0700
    document chromAlias procedure refs #36461
• src/hg/makeDb/doc/asmHubs/verifyOnDownload.sh
  • lines changed 1, context: html, text, full: html, text
    1246c62aed3a510683ecb63c27e11ff1fe623140 Wed Oct 8 13:49:50 2025 -0700
    some archaea have slipped to 9 tracks refs #29545
• src/hg/makeDb/doc/bacteriaAsmHub/bacteria.orderList.tsv
  • lines changed 90, context: html, text, full: html, text
    7fbaf4ec666799c553411e1a8c5ae1edeeafa9ba Wed Oct 8 09:08:13 2025 -0700
    RefSeq update and user requests refs #29545
• src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    7fbaf4ec666799c553411e1a8c5ae1edeeafa9ba Wed Oct 8 09:08:13 2025 -0700
    RefSeq update and user requests refs #29545
• src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    7fbaf4ec666799c553411e1a8c5ae1edeeafa9ba Wed Oct 8 09:08:13 2025 -0700
    RefSeq update and user requests refs #29545
• src/hg/makeDb/doc/hprcAsmHub/hprc.orderList.tsv
  • lines changed 20, context: html, text, full: html, text
    36af765196a9d28d87fa6b67045f9fc30dee13bd Fri Oct 10 15:24:36 2025 -0700
    correctly identify haplotype for stray HPRC assemblies refs #35415
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
  • lines changed 7, context: html, text, full: html, text
    7fbaf4ec666799c553411e1a8c5ae1edeeafa9ba Wed Oct 8 09:08:13 2025 -0700
    RefSeq update and user requests refs #29545
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 4, context: html, text, full: html, text
    7fbaf4ec666799c553411e1a8c5ae1edeeafa9ba Wed Oct 8 09:08:13 2025 -0700
    RefSeq update and user requests refs #29545
• src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    7fbaf4ec666799c553411e1a8c5ae1edeeafa9ba Wed Oct 8 09:08:13 2025 -0700
    RefSeq update and user requests refs #29545
• src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv
  • lines changed 20, context: html, text, full: html, text
    36af765196a9d28d87fa6b67045f9fc30dee13bd Fri Oct 10 15:24:36 2025 -0700
    correctly identify haplotype for stray HPRC assemblies refs #35415
• src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv
  • lines changed 7, context: html, text, full: html, text
    7fbaf4ec666799c553411e1a8c5ae1edeeafa9ba Wed Oct 8 09:08:13 2025 -0700
    RefSeq update and user requests refs #29545
• src/hg/makeDb/doc/viralAsmHub/viral.orderList.tsv
  • lines changed 16, context: html, text, full: html, text
    7fbaf4ec666799c553411e1a8c5ae1edeeafa9ba Wed Oct 8 09:08:13 2025 -0700
    RefSeq update and user requests refs #29545
• src/hg/makeDb/trackDb/human/spliceAI.ra
  • lines changed 9, context: html, text, full: html, text
    09b6b14cd006dcf74ed1b2415a58b85f36c5af3d Mon Oct 6 16:18:54 2025 -0700
    removing confusing spliceAIWtDonorPlus track, refs #35100
• src/hg/makeDb/trackDb/human/spliceAIWt.ra
  • lines changed 5, context: html, text, full: html, text
    8bace26a6f90392a326b2d293791e3fc0c5014b0 Mon Oct 6 16:38:22 2025 -0700
    fixing up the splice Ai supertrack html page, refs #35100
  • lines changed 2, context: html, text, full: html, text
    bf697abe808e06b482d49306cfaa852fb905968e Tue Oct 7 16:03:35 2025 -0700
    Updates to the SpliceAI Wildtype description page and updating the shortLabel, refs #35100
• src/hg/makeDb/trackDb/human/spliceImpactSuper.html
  • lines changed 22, context: html, text, full: html, text
    8bace26a6f90392a326b2d293791e3fc0c5014b0 Mon Oct 6 16:38:22 2025 -0700
    fixing up the splice Ai supertrack html page, refs #35100
  • lines changed 32, context: html, text, full: html, text
    bf697abe808e06b482d49306cfaa852fb905968e Tue Oct 7 16:03:35 2025 -0700
    Updates to the SpliceAI Wildtype description page and updating the shortLabel, refs #35100
  • lines changed 5, context: html, text, full: html, text
    994850e59495b20664fd6fb1a74a6f44d7e97731 Wed Oct 8 03:19:07 2025 -0700
    adding credits to spliceAi impact html page, especially Illumina, refs #35100
• src/hg/utils/automation/aliasTextToBed.pl
  • lines changed 1, context: html, text, full: html, text
    076b4ef96b9fc40127c3577cb030585709bf5715 Mon Oct 13 11:10:43 2025 -0700
    adding hprcV2 type of alias refs #36461
• src/hg/utils/otto/genArk/devList.sh
  • lines changed 15, context: html, text, full: html, text
    89a11d909c69766605ea99e1fa2d7e55e2ed6429 Wed Oct 8 16:10:33 2025 -0700
    adding the listing of /gbdb/database/quickLift files refs #34917
• src/hg/utils/otto/genArk/gbDbGenArkList.sh
  • lines changed 31, context: html, text, full: html, text
    96ca3838eddeed315b292153e9c00a176ee3481f Wed Oct 8 16:14:43 2025 -0700
    cron script running on RR machines to make file comparisons for pushing refs #34917
  • lines changed 18, context: html, text, full: html, text
    7176aa3eb099704a9b1372bdc27930f172567d13 Wed Oct 8 16:22:01 2025 -0700
    adding the listing of /gbdb/database/quickLift files refs #34917
  • lines changed 1, context: html, text, full: html, text
    0b85dd107323ffc1151a8162a845a0ae37e389d8 Thu Oct 9 11:46:25 2025 -0700
    remove stray g character that upset a file name refs #34917
• src/lib/verbose.c
  • lines changed 2, context: html, text, full: html, text
    0d277e73867e128d9fb1d2dbf34aabd04b910633 Tue Oct 7 15:47:19 2025 -0700
    removing verbose mode when verbose is 0, refs #36259
• src/product/mirrorManual.txt
  • lines changed 1, context: html, text, full: html, text
    5e80e7e2fae96a82ae0df71b9f493287cfb42a6f Tue Oct 7 09:53:44 2025 -0700
    Code review edit, removing hard link to hgwdev, refs #36473

• lines changed: 932
• files changed: 69