All File Changes
v494_preview to v494_preview2 (2026-02-12 to 2026-02-09) v494
Show details
- confs/asia.hg.conf
- lines changed 18, context: html, text, full: html, text
5ef143858259d0bbb520098e036beb585d4285fc Sun Feb 8 01:11:19 2026 -0800
Installing updated hg.conf files from UCSC servers
- confs/euro.hg.conf
- lines changed 18, context: html, text, full: html, text
5ef143858259d0bbb520098e036beb585d4285fc Sun Feb 8 01:11:19 2026 -0800
Installing updated hg.conf files from UCSC servers
- confs/hgwbeta.hg.conf
- lines changed 12, context: html, text, full: html, text
5ef143858259d0bbb520098e036beb585d4285fc Sun Feb 8 01:11:19 2026 -0800
Installing updated hg.conf files from UCSC servers
- confs/rr.hg.conf
- lines changed 18, context: html, text, full: html, text
5ef143858259d0bbb520098e036beb585d4285fc Sun Feb 8 01:11:19 2026 -0800
Installing updated hg.conf files from UCSC servers
- docs/hubs/contributedTracks.md
- lines changed 123, context: html, text, full: html, text
e49a713e18b15cfc70cf4248102ddd5c9170db95 Sun Feb 8 16:46:09 2026 -0800
adding Hiram's new page about contributing tracks to GenArk genomes, refs #37043
- lines changed 11, context: html, text, full: html, text
374e1f49a6756a875e4603394686cbb707cd746b Sun Feb 8 16:59:04 2026 -0800
minor tweaks to formatting and wording of some sections, refs #37043
- docs/tutorials/customTrackTutorial.md
- lines changed 3, context: html, text, full: html, text
f2dc21b9a8f9479ce3dce9594f4965ff0347ccf5 Wed Feb 4 11:23:13 2026 -0800
Fixing typos from code review, refs #37057
- src/hg/cartDump/cartDump.c
- lines changed 90, context: html, text, full: html, text
abe6cb020492b82545875d59c570d0a3acc51376 Wed Feb 4 14:41:49 2026 -0800
Adjusting faceted composite cart logic to support tracks that are on
by default, refs #36320
- src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html
- lines changed 4, context: html, text, full: html, text
4018c2a09105ed50b7a8e16e8dbf279f84ede4aa Mon Feb 2 11:54:40 2026 -0800
Marking active milestones (data, not all metadata)
- src/hg/hgCustom/hgCustom.c
- lines changed 6, context: html, text, full: html, text
892ed11dc23adf5ebc35babd5e62993778f3e4b7 Thu Feb 5 10:18:34 2026 -0800
Add some documentation to hgCustom indicating we have hubspace now, refs #37013
- src/hg/hgGateway/hgGateway.html
- lines changed 15, context: html, text, full: html, text
151f0489b9e4fa73bdc22226a7a6354a450fecb2 Wed Feb 4 11:28:20 2026 -0800
Hide species tree by default but put up a link to show it again. Don't put connected assembly hubs into the species tree, instead into their own card section like the recent genomes list, below the recents. refs #34078
- src/hg/hgLiftOver/hgLiftOver.c
- lines changed 2, context: html, text, full: html, text
2ef9156ca98f85bdfd4bc2cc5c48659a042fdca2 Wed Feb 4 11:59:11 2026 -0800
Fix typos from code review, refs #37053
- src/hg/hgTrackUi/hgTrackUi.c
- lines changed 35, context: html, text, full: html, text
abe6cb020492b82545875d59c570d0a3acc51376 Wed Feb 4 14:41:49 2026 -0800
Adjusting faceted composite cart logic to support tracks that are on
by default, refs #36320
- lines changed 25, context: html, text, full: html, text
07c318cffa6769b6a4b650a88a7887ae01de608d Wed Feb 4 20:07:42 2026 -0800
Impose an overall limit on active track count for featured composites,
and allow alternate labels for the data type selectors, refs #36320
- src/hg/hgTracks/hgTracks.c
- lines changed 39, context: html, text, full: html, text
84b2a66056c61f0661676de79e7d710073ba8d5d Tue Feb 3 01:37:38 2026 -0800
adding hub email display to hub error output, refs #36916 and refs #33571
- lines changed 65, context: html, text, full: html, text
9840af33fea8c07d1b0e017cb9ec77d305535f91 Tue Feb 3 13:03:09 2026 -0800
Updates support for Multi-region exon mode knownGene processing. It now correctly handles pseudoGenes checkbox in the track settings, all the trackSets including MANE, and also the commma-separted ID-list filtering. fixes #37060
- lines changed 3, context: html, text, full: html, text
54413ab8e05496303b70ee4349b4e5ada1802147 Wed Feb 4 03:40:06 2026 -0800
adding XSS security fix to hub error printf, refs #36916
- lines changed 4, context: html, text, full: html, text
933728e143b8408db8a44a948ecafe284a1278fb Wed Feb 4 11:05:21 2026 -0800
fixing stray line commited as part of the hub error email commit, refs #36984
- lines changed 1, context: html, text, full: html, text
c33fb727d29ae43ba03df3c1612990a03224f1ca Wed Feb 4 12:59:28 2026 -0800
OR together top level track with subtrack level vis when calculating visible tracks. Otherwise our particular values for squish vs pack cause problems when ANDing togethe visibilities, refs #36609
- lines changed 3, context: html, text, full: html, text
087d1f625866a7716ee70496c8ba95053ee3fbfa Thu Feb 5 11:27:59 2026 -0800
Make the user confirm they actually want to disconnect from a track hub on hgTracks as the button is right next to the refresh button, refs #36704
- lines changed 0, context: html, text, full: html, text
55b9303aff371358646c4310c5201d30afd38cf3 Fri Feb 6 12:34:22 2026 -0800
Fixing typo, refs #36704
- src/hg/hgTracks/hicTrack.c
- lines changed 59, context: html, text, full: html, text
2f6c858cd7d9b2fc0b48f8618bef5e74712c6639 Tue Feb 3 23:16:15 2026 -0800
Hi-C track height in arc mode should match the height of the highest arc, refs #36774
- src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html
- lines changed 141, context: html, text, full: html, text
eac59164411c5ad958720a1135c46e1983389c56 Sun Feb 8 16:25:59 2026 -0800
adding hub.txt and genomes.txt settings to docs, refs #26284
- src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
- lines changed 298, context: html, text, full: html, text
eac59164411c5ad958720a1135c46e1983389c56 Sun Feb 8 16:25:59 2026 -0800
adding hub.txt and genomes.txt settings to docs, refs #26284
- src/hg/htdocs/goldenPath/newsarch.html
- lines changed 21, context: html, text, full: html, text
4031d6e765e1de6a6a612249f5bc9bdca2358eba Tue Feb 3 15:53:31 2026 -0800
Announcing the Visible Tracks and Hub Space features. refs #36290 and #36609
- lines changed 2, context: html, text, full: html, text
e47b01a8f3fa1a5262905e832bf344414247acd3 Tue Feb 3 16:09:47 2026 -0800
Making minor changes to the Visible Tracks announcement, refs #36609
- lines changed 5, context: html, text, full: html, text
3da4d31d4cb64417945af1231cc1f2dc603123fb Tue Feb 3 16:24:53 2026 -0800
Making minor edits to the news announcement for Hub Space, refs #36290
- lines changed 59, context: html, text, full: html, text
e2ca170ffa028279df201ec24efe354cdf351401 Thu Feb 5 13:46:39 2026 -0800
Releasing and announcing the recount3 track, refs #34886
- src/hg/htdocs/images/newsArchImages/HubSpace.png
- lines changed 0, context: html, text, full: html, text
068244c4d1729286a8fc85470993e786647afad2 Tue Feb 3 15:32:39 2026 -0800
Adding a hub space image for the announcement, refs #36290
- src/hg/htdocs/images/newsArchImages/recount3.png
- lines changed 0, context: html, text, full: html, text
e2ca170ffa028279df201ec24efe354cdf351401 Thu Feb 5 13:46:39 2026 -0800
Releasing and announcing the recount3 track, refs #34886
- src/hg/htdocs/inc/globalNavBar.inc
- lines changed 1, context: html, text, full: html, text
2ef9156ca98f85bdfd4bc2cc5c48659a042fdca2 Wed Feb 4 11:59:11 2026 -0800
Fix typos from code review, refs #37053
- src/hg/htdocs/indexNews.html
- lines changed 24, context: html, text, full: html, text
a45ea44564e66440b353183f4a2e00811e6abb78 Wed Feb 4 11:24:30 2026 -0800
Updating the indexNews page with the recent announcements, no Redmine
- lines changed 12, context: html, text, full: html, text
e2ca170ffa028279df201ec24efe354cdf351401 Thu Feb 5 13:46:39 2026 -0800
Releasing and announcing the recount3 track, refs #34886
- src/hg/htdocs/style/HGStyle.css
- lines changed 16, context: html, text, full: html, text
c746ba4328021a2d5245b77790f5262b7814fbbd Wed Feb 4 21:13:22 2026 -0800
UI tweaks for faceted composites, refs #36320
- src/hg/htdocs/style/jWest.css
- lines changed 2, context: html, text, full: html, text
151f0489b9e4fa73bdc22226a7a6354a450fecb2 Wed Feb 4 11:28:20 2026 -0800
Hide species tree by default but put up a link to show it again. Don't put connected assembly hubs into the species tree, instead into their own card section like the recent genomes list, below the recents. refs #34078
- src/hg/hubApi/apiUtils.c
- lines changed 25, context: html, text, full: html, text
e389c29f0255935bc714c66ce7182c4a24427adc Fri Feb 6 12:13:44 2026 -0800
fixes hubApi trackDb cache bug #37064
- src/hg/hubApi/assemblyList.py
- lines changed 3, context: html, text, full: html, text
d8fcb8618a0aed962c050c0914131e618304ced9 Tue Feb 3 14:51:24 2026 -0800
preparing to add the haplotypes column to the table refs #34736
- lines changed 31, context: html, text, full: html, text
fa3849abfc8a9e5ac4f5e44a2f8115701446ca3f Thu Feb 5 15:01:40 2026 -0800
now adding haplotype CSV list when available refs #34736
- src/hg/hubApi/getData.c
- lines changed 1, context: html, text, full: html, text
e389c29f0255935bc714c66ce7182c4a24427adc Fri Feb 6 12:13:44 2026 -0800
fixes hubApi trackDb cache bug #37064
- src/hg/hubApi/list.c
- lines changed 9, context: html, text, full: html, text
e389c29f0255935bc714c66ce7182c4a24427adc Fri Feb 6 12:13:44 2026 -0800
fixes hubApi trackDb cache bug #37064
- src/hg/hubApi/tests/expected/notSup01.gz
- lines changed 0, context: html, text, full: html, text
e389c29f0255935bc714c66ce7182c4a24427adc Fri Feb 6 12:13:44 2026 -0800
fixes hubApi trackDb cache bug #37064
- src/hg/inc/assemblyList.h
- lines changed 3, context: html, text, full: html, text
f445b21b422aaf984db35718cb50611691210803 Tue Feb 3 14:21:32 2026 -0800
adding a haplotypes item to the assemblyList table refs #34736
- src/hg/inc/trackDb.h
- lines changed 1, context: html, text, full: html, text
c8d9cb736828e9b61058516a6c53f155c04db998 Mon Feb 9 06:35:32 2026 -0800
increment TRACKDB_VERSION to account for change in how hubApi was making
broken ones before
- src/hg/js/facetedComposite.js
- lines changed 63, context: html, text, full: html, text
abe6cb020492b82545875d59c570d0a3acc51376 Wed Feb 4 14:41:49 2026 -0800
Adjusting faceted composite cart logic to support tracks that are on
by default, refs #36320
- lines changed 19, context: html, text, full: html, text
07c318cffa6769b6a4b650a88a7887ae01de608d Wed Feb 4 20:07:42 2026 -0800
Impose an overall limit on active track count for featured composites,
and allow alternate labels for the data type selectors, refs #36320
- lines changed 5, context: html, text, full: html, text
c746ba4328021a2d5245b77790f5262b7814fbbd Wed Feb 4 21:13:22 2026 -0800
UI tweaks for faceted composites, refs #36320
- src/hg/js/hgGateway.js
- lines changed 91, context: html, text, full: html, text
151f0489b9e4fa73bdc22226a7a6354a450fecb2 Wed Feb 4 11:28:20 2026 -0800
Hide species tree by default but put up a link to show it again. Don't put connected assembly hubs into the species tree, instead into their own card section like the recent genomes list, below the recents. refs #34078
- src/hg/js/react/lib/makefile
- lines changed 2, context: html, text, full: html, text
27c103ab1324fd5d181b3e82f7ef3364c9f30e1c Mon Feb 2 11:55:02 2026 -0800
Restore react bundle makefile no-op on mirrors. We provide the bundled file anyways, refs Michael Hiller email
- src/hg/js/utils.js
- lines changed 31, context: html, text, full: html, text
98d6d1e479b2f6d1d61596d8fbcea15ac0012383 Tue Feb 3 12:40:07 2026 -0800
bold highlight on the autocomplete menu search results refs #36232
- lines changed 2, context: html, text, full: html, text
456d9958e98e87dcd02185876ad245964ffefa2a Wed Feb 4 12:26:45 2026 -0800
faceted bar charts include their own jquery lib for some reason and when we strip script tags to do hgc popups we didn't catch this one, refs #37014
- src/hg/lib/assemblyList.as
- lines changed 1, context: html, text, full: html, text
f445b21b422aaf984db35718cb50611691210803 Tue Feb 3 14:21:32 2026 -0800
adding a haplotypes item to the assemblyList table refs #34736
- src/hg/lib/assemblyList.c
- lines changed 23, context: html, text, full: html, text
f445b21b422aaf984db35718cb50611691210803 Tue Feb 3 14:21:32 2026 -0800
adding a haplotypes item to the assemblyList table refs #34736
- src/hg/lib/assemblyList.sql
- lines changed 2, context: html, text, full: html, text
f445b21b422aaf984db35718cb50611691210803 Tue Feb 3 14:21:32 2026 -0800
adding a haplotypes item to the assemblyList table refs #34736
- src/hg/lib/web.c
- lines changed 9, context: html, text, full: html, text
96fc33fbab1157d099263deacc579633a044f853 Tue Feb 3 13:24:58 2026 -0800
Adding an info icon to the new species search bar indicating the various operators that can be applied to search words, refs Hiram email
- src/hg/makeDb/doc/hg38/humanMethylationAtlas.txt
- lines changed 7, context: html, text, full: html, text
a328f4122a06272bb3d76a1f8297e8f5f264e70e Thu Feb 5 16:51:06 2026 -0800
First draft of the human methylation atlas track, refs #36826
- lines changed 1, context: html, text, full: html, text
6722ba1af10cd31bf218f24430f54dc3e0f30b39 Thu Feb 5 16:52:32 2026 -0800
Fixing the wrong script link, refs #36826
- src/hg/makeDb/doc/hg38/jaspar.txt
- lines changed 14, context: html, text, full: html, text
7ef879fbbd36899c1f4107701d0e2be658344c0b Wed Feb 4 16:35:54 2026 -0800
Staging the JASPAR 2026 track update, refs #36264
- src/hg/makeDb/doc/hg38/varFreqs.txt
- lines changed 26, context: html, text, full: html, text
f7cf3eee5dc2134d550c6b35b2fb250f65673341 Tue Feb 3 01:55:53 2026 -0800
changes after code review, refs #37059
- src/hg/makeDb/scripts/humanMethylationAtlas/humanMethylationAtlas_setup.py
- lines changed 636, context: html, text, full: html, text
a328f4122a06272bb3d76a1f8297e8f5f264e70e Thu Feb 5 16:51:06 2026 -0800
First draft of the human methylation atlas track, refs #36826
- src/hg/makeDb/trackDb/human/dnaMethylation.html
- lines changed 16, context: html, text, full: html, text
a328f4122a06272bb3d76a1f8297e8f5f264e70e Thu Feb 5 16:51:06 2026 -0800
First draft of the human methylation atlas track, refs #36826
- lines changed 18, context: html, text, full: html, text
60410f74b7cbc4fbad91bcdbe4e0276e44d936ee Fri Feb 6 09:51:04 2026 -0800
Tweaks to the methylation atlas track based on author feedback, refs #36826
- src/hg/makeDb/trackDb/human/hg38/gnomad3Coverage.html
- lines changed 0, context: html, text, full: html, text
f7cf3eee5dc2134d550c6b35b2fb250f65673341 Tue Feb 3 01:55:53 2026 -0800
changes after code review, refs #37059
- src/hg/makeDb/trackDb/human/hg38/gnomad4ExomeCoverage.html
- lines changed 0, context: html, text, full: html, text
f7cf3eee5dc2134d550c6b35b2fb250f65673341 Tue Feb 3 01:55:53 2026 -0800
changes after code review, refs #37059
- src/hg/makeDb/trackDb/human/hg38/recount3.ra
- lines changed 2, context: html, text, full: html, text
603cf4220990cac99c15aec4c7503e8a81e14bb2 Wed Feb 4 15:11:15 2026 -0800
Updating shortLabels/longLabels and updating the text for the donors and acceptors on the minus strand for the recount3 track, refs #34886
- lines changed 1, context: html, text, full: html, text
e2ca170ffa028279df201ec24efe354cdf351401 Thu Feb 5 13:46:39 2026 -0800
Releasing and announcing the recount3 track, refs #34886
- src/hg/makeDb/trackDb/human/hg38/trackDb.ra
- lines changed 1, context: html, text, full: html, text
8b79ead44beee94362c5d55eb601328712444b6b Wed Feb 4 10:05:36 2026 -0800
Staging the recount3 track for hg38 and mm10 on hgwbeta, refs #34886
- lines changed 1, context: html, text, full: html, text
e2ca170ffa028279df201ec24efe354cdf351401 Thu Feb 5 13:46:39 2026 -0800
Releasing and announcing the recount3 track, refs #34886
- src/hg/makeDb/trackDb/human/humanMethylationAtlas.html
- lines changed 185, context: html, text, full: html, text
a328f4122a06272bb3d76a1f8297e8f5f264e70e Thu Feb 5 16:51:06 2026 -0800
First draft of the human methylation atlas track, refs #36826
- lines changed 5, context: html, text, full: html, text
60410f74b7cbc4fbad91bcdbe4e0276e44d936ee Fri Feb 6 09:51:04 2026 -0800
Tweaks to the methylation atlas track based on author feedback, refs #36826
- src/hg/makeDb/trackDb/human/humanMethylationAtlas.ra
- lines changed 49, context: html, text, full: html, text
a328f4122a06272bb3d76a1f8297e8f5f264e70e Thu Feb 5 16:51:06 2026 -0800
First draft of the human methylation atlas track, refs #36826
- lines changed 3, context: html, text, full: html, text
60410f74b7cbc4fbad91bcdbe4e0276e44d936ee Fri Feb 6 09:51:04 2026 -0800
Tweaks to the methylation atlas track based on author feedback, refs #36826
- src/hg/makeDb/trackDb/human/methylationAtlasSignals.ra
- lines changed 3673, context: html, text, full: html, text
a328f4122a06272bb3d76a1f8297e8f5f264e70e Thu Feb 5 16:51:06 2026 -0800
First draft of the human methylation atlas track, refs #36826
- src/hg/makeDb/trackDb/human/phasedVars.html
- lines changed 1, context: html, text, full: html, text
0ad8ff09c2fd60714a21e752b89a955203f9f074 Thu Feb 5 14:35:11 2026 -0800
Adding a missing comma, no redmine
- src/hg/makeDb/trackDb/human/trackDb.ra
- lines changed 1, context: html, text, full: html, text
a0c54bf7aecca671af8fa6063e129e7524302ca3 Tue Feb 3 09:23:29 2026 -0800
Code review edits, refs #37054
- lines changed 11, context: html, text, full: html, text
a328f4122a06272bb3d76a1f8297e8f5f264e70e Thu Feb 5 16:51:06 2026 -0800
First draft of the human methylation atlas track, refs #36826
- src/hg/makeDb/trackDb/human/varFreqs.html
- lines changed 3, context: html, text, full: html, text
f7cf3eee5dc2134d550c6b35b2fb250f65673341 Tue Feb 3 01:55:53 2026 -0800
changes after code review, refs #37059
- lines changed 30, context: html, text, full: html, text
9cfd62d70caa8a7ce7610fcd55c1cf2cc6ef942b Wed Feb 4 10:52:00 2026 -0800
Making lines less than 100 characters. Fixing typos from code review, refs #37057
- src/hg/makeDb/trackDb/jaspar.html
- lines changed 22, context: html, text, full: html, text
7ef879fbbd36899c1f4107701d0e2be658344c0b Wed Feb 4 16:35:54 2026 -0800
Staging the JASPAR 2026 track update, refs #36264
- src/hg/makeDb/trackDb/jaspar.ra
- lines changed 16, context: html, text, full: html, text
7ef879fbbd36899c1f4107701d0e2be658344c0b Wed Feb 4 16:35:54 2026 -0800
Staging the JASPAR 2026 track update, refs #36264
- src/hg/makeDb/trackDb/mouse/mm10/recount3.ra
- lines changed 1, context: html, text, full: html, text
603cf4220990cac99c15aec4c7503e8a81e14bb2 Wed Feb 4 15:11:15 2026 -0800
Updating shortLabels/longLabels and updating the text for the donors and acceptors on the minus strand for the recount3 track, refs #34886
- lines changed 1, context: html, text, full: html, text
e2ca170ffa028279df201ec24efe354cdf351401 Thu Feb 5 13:46:39 2026 -0800
Releasing and announcing the recount3 track, refs #34886
- src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
- lines changed 1, context: html, text, full: html, text
8b79ead44beee94362c5d55eb601328712444b6b Wed Feb 4 10:05:36 2026 -0800
Staging the recount3 track for hg38 and mm10 on hgwbeta, refs #34886
- lines changed 1, context: html, text, full: html, text
e2ca170ffa028279df201ec24efe354cdf351401 Thu Feb 5 13:46:39 2026 -0800
Releasing and announcing the recount3 track, refs #34886
- src/hg/makeDb/trackDb/recount3.html
- lines changed 1, context: html, text, full: html, text
a0c54bf7aecca671af8fa6063e129e7524302ca3 Tue Feb 3 09:23:29 2026 -0800
Code review edits, refs #37054
- lines changed 3, context: html, text, full: html, text
9fa317264c94a28d9e803669c0547d494bca93f4 Wed Feb 4 09:51:06 2026 -0800
Adding a sentence about the tracks available for hg38 and mm10, refs #34886
- lines changed 2, context: html, text, full: html, text
603cf4220990cac99c15aec4c7503e8a81e14bb2 Wed Feb 4 15:11:15 2026 -0800
Updating shortLabels/longLabels and updating the text for the donors and acceptors on the minus strand for the recount3 track, refs #34886
- lines changed 1, context: html, text, full: html, text
22039ac84d886676950d2726f1c8ff2e57f890a4 Wed Feb 4 20:53:31 2026 -0800
update recount3 color coding descrption to make it a more obvious
- src/hg/utils/hubClone/hubClone.c
- lines changed 227, context: html, text, full: html, text
cf3b8d0618e5ea5763b9968a68601055973e4a2f Tue Feb 3 15:12:57 2026 -0800
Add a checker to see if a file URL can be opened (otherwise hubClone just fails on it), and an optional flag that forces it to continue regardless of missing trackDb.txt files. Refs #36264
- src/inc/common.h
- lines changed 7, context: html, text, full: html, text
54413ab8e05496303b70ee4349b4e5ada1802147 Wed Feb 4 03:40:06 2026 -0800
adding XSS security fix to hub error printf, refs #36916
- src/lib/common.c
- lines changed 12, context: html, text, full: html, text
54413ab8e05496303b70ee4349b4e5ada1802147 Wed Feb 4 03:40:06 2026 -0800
adding XSS security fix to hub error printf, refs #36916
- src/product/installer/browserSetup.sh
- lines changed 3, context: html, text, full: html, text
552381034beaa60ce74d45d768bdf344be0af152 Tue Feb 3 02:11:42 2026 -0800
moving gbic back to beta branch, refs #33781
- lines changed: 6438
- files changed: 91