All File Changes

v492_preview2 to v492_base (2025-12-08 to 2025-12-15) v492

• confs/hgwdev.hg.conf
  • lines changed 3, context: html, text, full: html, text
    e1523b5227aea27f20f88e28bbc51094ffc05cd3 Sun Dec 14 01:11:15 2025 -0800
    Installing updated hg.conf files from UCSC servers
• docs/tutorials/gatewayTutorial.md
  • lines changed 7, context: html, text, full: html, text
    a8ae510a9dbaa0c7932ad242c50fde2ce19ad552 Mon Dec 8 11:53:20 2025 -0800
    Updating the format of images for the Requesting an Assembly section on gatewayTutorial page, No RM
• src/hg/cgilib/hgSeq.c
  • lines changed 1, context: html, text, full: html, text
    091a7e46fe5e9397ec47ba8aa026a8d400040714 Mon Dec 8 10:08:44 2025 -0800
    Fixes hgTables Sequence output with CDS casing. Bug caused introns to be upper case and has existed since 2002. fixes #34381
• src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html
  • lines changed 7, context: html, text, full: html, text
    373e06aadc70142ac8221261992b2815a343cf1d Wed Dec 10 14:23:46 2025 -0800
    Adding RM references to ADGCs on timeline
  • lines changed 16, context: html, text, full: html, text
    e33ed1d7eddc4a1b4061f48e3cc8c327a2c601fa Mon Dec 15 09:43:23 2025 -0800
    WUSTL Y2 updates, with %% removes old ADGC7_F_18 [columnF,row18] prediction replaced by ADGC7_Y2_B_18 [columnB,row18] colB = 2026-03-31
  • lines changed 9, context: html, text, full: html, text
    e35d7f3e6405e8dbd0be98fca69b24c07a1f7416 Mon Dec 15 10:32:42 2025 -0800
    WUSTL ADGC7 2026-07-01 milestone updates
  • lines changed 13, context: html, text, full: html, text
    b29bb3b6adadce65091e3c091edd8ef8e5123f55 Mon Dec 15 12:36:13 2025 -0800
    WUSTL columnD - 2026-09-30 milestones
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 1, context: html, text, full: html, text
    d6589bfe20c70dee505360cc62ba40dc5bd1b201 Sun Dec 14 11:04:25 2025 -0800
    replacing link to quick start page with link to new hub basics page, refs #28347
• src/hg/hgTracks/hgTracks.c
  • lines changed 3, context: html, text, full: html, text
    c2e17a71f401a89a038d5035dad2232a73a838e5 Thu Dec 11 14:13:34 2025 -0800
    change the info icon for quickLift groups
  • lines changed 1, context: html, text, full: html, text
    f7804728e85be56bd858c33acd2b48bbc97549f1 Thu Dec 11 14:42:01 2025 -0800
    don't put out info link for quickLift groups
  • lines changed 5, context: html, text, full: html, text
    fc24be050fabfb742956996423a0d8d942055c87 Fri Dec 12 15:45:23 2025 -0800
    Updating the text for the QuickLift info icon, refs #36662
• src/hg/hgc/bigBedClick.c
  • lines changed 10, context: html, text, full: html, text
    370cc36518fec8f45d0053dec74a4af6ac7ff0cb Thu Dec 11 09:12:31 2025 -0800
    in bigBed click handling, if the trackDb type has a field number in it make sure it's the same as the one in the bigBed itself, otherwise print an error.
• src/hg/hgc/hgc.c
  • lines changed 6, context: html, text, full: html, text
    370cc36518fec8f45d0053dec74a4af6ac7ff0cb Thu Dec 11 09:12:31 2025 -0800
    in bigBed click handling, if the trackDb type has a field number in it make sure it's the same as the one in the bigBed itself, otherwise print an error.
• src/hg/hgc/togaClick.c
  • lines changed 61, context: html, text, full: html, text
    83dbcadd73270e8b652fb4b5537235ca5727c7fa Mon Dec 8 16:22:38 2025 -0800
    fix the toga click code to use a simple local hideToggle class refs #35776
  • lines changed 9, context: html, text, full: html, text
    bddb262e29ccaea9bdf08d393f81375c66e5abb6 Mon Dec 8 16:29:59 2025 -0800
    fix the toga click code to use a simple local hideToggle class refs #35776
  • lines changed 34, context: html, text, full: html, text
    0be7b604dc94f877a813c77d1caffb6caa5ff267 Wed Dec 10 11:06:58 2025 -0800
    improved prompt tags for the expandable sectios refs #35776
• src/hg/htdocs/goldenPath/help/mirrorManual.html
  • lines changed 20, context: html, text, full: html, text
    ad3fa90ca874db73ed3e9109d468ef3cd5db9797 Mon Dec 15 11:09:30 2025 -0800
    documenting the cloudflare captcha, no redmine, email from Hiram
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.js
  • lines changed 1, context: html, text, full: html, text
    08ca8e04a5140c74052299e34a1d811f9bcf4d3c Thu Dec 11 12:13:19 2025 -0800
    Add message to trackDb hub document search that informs shift+enter can be used to jump backwards, refs #36831
  • lines changed 51, context: html, text, full: html, text
    ca790256fe78136e840f27bd251e932fd0658e0c Thu Dec 11 12:39:30 2025 -0800
    Fix bug in trackDbHub doc search: we were re-doing the search after marking up the first set of found elements, causing multiple highlights for a single match, which made cycling through found elements behave oddly, refs #36831
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 4, context: html, text, full: html, text
    2e2420ea3d541de7576685e24cfdfcd9b692cd4b Wed Dec 10 14:27:52 2025 -0800
    Fixing the tutorial links to point to the new nested file locations, no RM.
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 11, context: html, text, full: html, text
    b5cffe7c7c2d3a421940fac3eb6fe5f5991bd2f6 Sun Dec 14 12:12:47 2025 -0800
    Adding new data portal/dcc publication no refs
• src/hg/htdocs/inc/hgMyData.html
  • lines changed 8, context: html, text, full: html, text
    cc46f6b382a2e5ac7c120b7cf43b35823c396252 Fri Dec 12 16:03:11 2025 -0800
    Updating some help text for Hub Space, refs #36830
• src/hg/htdocs/style/shepherd.css
  • lines changed 2, context: html, text, full: html, text
    6c9fe16ff7d38d10abe491d14cfa21736560a27d Mon Dec 8 12:06:40 2025 -0800
    Adding a comment that the external CSS file was edited by UCSC, refs #36818
• src/hg/hubApi/tests/expected/list22.gz
  • lines changed 0, context: html, text, full: html, text
    aee63b855980c1124d156b36dfe7d0e93c7fe005 Tue Dec 9 18:59:22 2025 -0800
    removing some tests that are likely to change frequently, refs #36463
• src/hg/hubApi/tests/expected/list23.gz
  • lines changed 0, context: html, text, full: html, text
    aee63b855980c1124d156b36dfe7d0e93c7fe005 Tue Dec 9 18:59:22 2025 -0800
    removing some tests that are likely to change frequently, refs #36463
• src/hg/hubApi/tests/expected/list28.gz
  • lines changed 0, context: html, text, full: html, text
    aee63b855980c1124d156b36dfe7d0e93c7fe005 Tue Dec 9 18:59:22 2025 -0800
    removing some tests that are likely to change frequently, refs #36463
• src/hg/hubApi/tests/expected/list29.gz
  • lines changed 0, context: html, text, full: html, text
    aee63b855980c1124d156b36dfe7d0e93c7fe005 Tue Dec 9 18:59:22 2025 -0800
    removing some tests that are likely to change frequently, refs #36463
• src/hg/hubApi/tests/makefile
  • lines changed 34, context: html, text, full: html, text
    aee63b855980c1124d156b36dfe7d0e93c7fe005 Tue Dec 9 18:59:22 2025 -0800
    removing some tests that are likely to change frequently, refs #36463
• src/hg/js/hgTracks.js
  • lines changed 1, context: html, text, full: html, text
    83dbcadd73270e8b652fb4b5537235ca5727c7fa Mon Dec 8 16:22:38 2025 -0800
    fix the toga click code to use a simple local hideToggle class refs #35776
• src/hg/js/hgc.js
  • lines changed 12, context: html, text, full: html, text
    83dbcadd73270e8b652fb4b5537235ca5727c7fa Mon Dec 8 16:22:38 2025 -0800
    fix the toga click code to use a simple local hideToggle class refs #35776
  • lines changed 4, context: html, text, full: html, text
    0be7b604dc94f877a813c77d1caffb6caa5ff267 Wed Dec 10 11:06:58 2025 -0800
    improved prompt tags for the expandable sectios refs #35776
• src/hg/js/tutorials/customTrackTutorial.js
  • lines changed 3, context: html, text, full: html, text
    2b810709f5349a9ba8aad784af59abac2c2c422d Fri Dec 12 15:00:27 2025 -0800
    Writing to the apache log that the tutorial has finished, refs #34354
• src/hg/lib/genarkOrg.sql
  • lines changed 10, context: html, text, full: html, text
    65071c1d6cc890e6ad0d23ab3addc13dac6e3a8b Wed Dec 10 20:34:55 2025 -0800
    document that schema for the hgcentral genarkOrg table refs #36213
• src/hg/lib/liftOver.c
  • lines changed 2, context: html, text, full: html, text
    a02093ad8adb1d4e964ee2d404f3b58eb0840bd1 Tue Dec 9 11:34:41 2025 -0800
    hgLiftOver min match filter with -multiple fixed. It has been allowing too-small regions in the output. Error was in system since 2013. fixes #17501
• src/hg/lib/trackHub.c
  • lines changed 7, context: html, text, full: html, text
    289c4a361a8f5192a4928b05a3a68c05afe7f816 Thu Dec 11 15:50:12 2025 -0800
    Little patch for udc.localDir and trackHub security for local bigDataUrl disallowed for non-local hubUrl. We have to double check the cached trackDb data. fixes #34544
  • lines changed 6, context: html, text, full: html, text
    0542bdef848a41fe04a2e043adaaed8eabbaa748 Fri Dec 12 11:37:02 2025 -0800
    freeMem was crashing for settings values, cannot do that for settings returned from trackDbCache. refs #34544, #36835, #36834
  • lines changed 6, context: html, text, full: html, text
    648f90bb5f2bbbf365a7005a69fdfa82c37057e0 Fri Dec 12 14:57:29 2025 -0800
    Revert "freeMem was crashing for settings values, cannot do that for settings returned from trackDbCache. refs #34544, #36835, #36834" This reverts commit 0542bdef848a41fe04a2e043adaaed8eabbaa748. Brian asked me to revert his for now.
  • lines changed 7, context: html, text, full: html, text
    b1d12cdd8bea10895a0ff1b787f5c0549cb76d7a Fri Dec 12 14:58:02 2025 -0800
    Revert "Little patch for udc.localDir and trackHub security for local bigDataUrl disallowed for non-local hubUrl. We have to double check the cached trackDb data. fixes #34544" This reverts commit 289c4a361a8f5192a4928b05a3a68c05afe7f816. Brian asked me to revert his for now since he is worried about speed. I will have to test the speed impactd and seek other possible solutions.
• src/hg/makeDb/doc/asmHubs/asmHubs.mk
  • lines changed 6, context: html, text, full: html, text
    d4d334d54107b89bcc07cbf4684749ccadee31fe Thu Dec 11 14:20:38 2025 -0800
    only copy groups.txt if it is actually different refs #29545
• src/hg/makeDb/doc/asmHubs/mkGenomes.pl
  • lines changed 1, context: html, text, full: html, text
    f345e1c69072f76c484b0ad82423f059a0fff9df Wed Dec 10 13:35:24 2025 -0800
    do not need the extra print of chromAuthority
• src/hg/makeDb/doc/bacteriaAsmHub/bacteria.orderList.tsv
  • lines changed 3, context: html, text, full: html, text
    3185383caf8fdd492637985e969758f0d8cf2e79 Thu Dec 11 14:12:48 2025 -0800
    adding a couple of user requests refs #29545
• src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    3185383caf8fdd492637985e969758f0d8cf2e79 Thu Dec 11 14:12:48 2025 -0800
    adding a couple of user requests refs #29545
• src/hg/makeDb/doc/hg38/recount3.txt
  • lines changed 20, context: html, text, full: html, text
    0adde15fcc0c841a234ab2ea86a4a8fdbef3d49b Fri Dec 12 01:51:06 2025 -0800
    switch recount3 intron track to color items by splice junction motif #34886
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
  • lines changed 3, context: html, text, full: html, text
    3185383caf8fdd492637985e969758f0d8cf2e79 Thu Dec 11 14:12:48 2025 -0800
    adding a couple of user requests refs #29545
• src/hg/makeDb/doc/mm10.txt
  • lines changed 16, context: html, text, full: html, text
    0adde15fcc0c841a234ab2ea86a4a8fdbef3d49b Fri Dec 12 01:51:06 2025 -0800
    switch recount3 intron track to color items by splice junction motif #34886
• src/hg/makeDb/outside/recount3/build-recount3-tracks
  • lines changed 36, context: html, text, full: html, text
    0adde15fcc0c841a234ab2ea86a4a8fdbef3d49b Fri Dec 12 01:51:06 2025 -0800
    switch recount3 intron track to color items by splice junction motif #34886
• src/hg/makeDb/outside/recount3/junctionsToBed.py
  • lines changed 104, context: html, text, full: html, text
    0adde15fcc0c841a234ab2ea86a4a8fdbef3d49b Fri Dec 12 01:51:06 2025 -0800
    switch recount3 intron track to color items by splice junction motif #34886
• src/hg/makeDb/trackDb/TOGAv2.html
  • lines changed 86, context: html, text, full: html, text
    ad4e4b66fe4aeec66d13d5ce01bbaf03f148c9f8 Fri Dec 12 17:46:52 2025 -0800
    updated text for version 2 refs #35776
• src/hg/makeDb/trackDb/betaGenArk.txt
  • lines changed 1, context: html, text, full: html, text
    7b23fe64bffb549f7a7ade1642d30cf9896c1bfa Wed Dec 10 12:43:29 2025 -0800
    Adding VEuPathDb contrib tracks
• src/hg/makeDb/trackDb/human/hg38/gnomad.ra
  • lines changed 1, context: html, text, full: html, text
    a0f7abd772e0e0b47c4a64ffdc43527b39454ccf Thu Dec 11 21:27:58 2025 -0800
    Updating the data of the gnomAD v4.1 CNV track with the gnomad.v4.1.cnv.all.bed data, refs #36788
• src/hg/makeDb/trackDb/human/hg38/gnomadCNV.html
  • lines changed 3, context: html, text, full: html, text
    a0f7abd772e0e0b47c4a64ffdc43527b39454ccf Thu Dec 11 21:27:58 2025 -0800
    Updating the data of the gnomAD v4.1 CNV track with the gnomad.v4.1.cnv.all.bed data, refs #36788
• src/hg/makeDb/trackDb/human/hg38/mpra.ra
  • lines changed 19, context: html, text, full: html, text
    6b5bd6238e327d0310a64e44771de3868a163af1 Thu Dec 11 07:49:34 2025 -0800
    adding mpra superTrack, ticket will come soon
• src/hg/makeDb/trackDb/human/hg38/recount3.ra
  • lines changed 4, context: html, text, full: html, text
    0adde15fcc0c841a234ab2ea86a4a8fdbef3d49b Fri Dec 12 01:51:06 2025 -0800
    switch recount3 intron track to color items by splice junction motif #34886
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    440c873f9f129e0348e8b13b8d5e1a77e86d5eb2 Tue Dec 9 15:58:31 2025 -0800
    staging ancient hominids track on beta, refs #36586
  • lines changed 1, context: html, text, full: html, text
    731c2874c7868355ac0ed1452d864c1066e24f57 Tue Dec 9 16:36:37 2025 -0800
    making ancient hominids track public, refs #36586
  • lines changed 1, context: html, text, full: html, text
    6b5bd6238e327d0310a64e44771de3868a163af1 Thu Dec 11 07:49:34 2025 -0800
    adding mpra superTrack, ticket will come soon
• src/hg/makeDb/trackDb/mouse/mm10/recount3.ra
  • lines changed 1, context: html, text, full: html, text
    0adde15fcc0c841a234ab2ea86a4a8fdbef3d49b Fri Dec 12 01:51:06 2025 -0800
    switch recount3 intron track to color items by splice junction motif #34886
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.encode3.ra
  • lines changed 1, context: html, text, full: html, text
    82772f6aa95e9126bdc6602690e153fd1b4724c5 Tue Dec 9 09:26:49 2025 -0800
    fixing encode3 screen linkout, no redmine, came up at a workshop
• src/hg/makeDb/trackDb/recount3.html
  • lines changed 1, context: html, text, full: html, text
    0adde15fcc0c841a234ab2ea86a4a8fdbef3d49b Fri Dec 12 01:51:06 2025 -0800
    switch recount3 intron track to color items by splice junction motif #34886
  • lines changed 19, context: html, text, full: html, text
    5ac72ff7faebbfea5a4eb9a16815111d36304462 Fri Dec 12 02:01:42 2025 -0800
    improved formating of recount3 track description
• src/hg/utils/automation/asmHubGatewayPage.pl
  • lines changed 1, context: html, text, full: html, text
    3fc0af6f1eaa0286ec5242b6caf6c3ede1382402 Mon Dec 8 11:58:38 2025 -0800
    correct label on ftp link to NCBI fasta resource per Max request
• src/hg/utils/otto/clinvar/doUpdate.sh
  • lines changed 3, context: html, text, full: html, text
    70793bfbb9eb63bf64c1809dae12476eaa7c2387 Wed Dec 10 02:03:10 2025 -0800
    changes after code review, refs #36822
• src/product/mirrorManual.txt
  • lines changed 15, context: html, text, full: html, text
    ad3fa90ca874db73ed3e9109d468ef3cd5db9797 Mon Dec 15 11:09:30 2025 -0800
    documenting the cloudflare captcha, no redmine, email from Hiram
• src/userApps/README
  • lines changed 12, context: html, text, full: html, text
    4a6bbaefd4ad57f0176334fb017c9aed253c0f4c Thu Dec 11 15:28:52 2025 -0800
    can not use the genome-test.soe.ucsc.edu/kent.git server outside UCSC environment refs #36817
• src/userApps/fetchKentSource.sh
  • lines changed 47, context: html, text, full: html, text
    9431ca8ba35a97885ab78a6a4fa997e05d68fd12 Thu Dec 11 15:26:16 2025 -0800
    can not use the genome-test.soe.ucsc.edu/kent.git server outside UCSC environment refs #36817
• src/utils/qa/checkStaticDocsDiff.py
  • lines changed 17, context: html, text, full: html, text
    5a5d63d41c03e0f384569bd1b18b7c70f1158e69 Mon Dec 8 15:16:22 2025 -0800
    Code review edits, refs #36815
• src/utils/qa/hubPublicAutoUpdate
  • lines changed 8, context: html, text, full: html, text
    71c2a0fed48f58560146832cad1fd6d13e8f15a8 Thu Dec 11 18:33:23 2025 -0800
    Updating the script to stop parsing at genome/track lines to avoid overwriting hub labels, and adding a check for useOneFile to parse genome info from hub.txt instead of genomes.txt, refs #36827

• lines changed: 807
• files changed: 67