All File Changes
v492_preview2 to v492_base (2025-12-08 to 2025-12-15) v492
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- 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