All File Changes
v488_preview2 to v488_base (2025-09-15 to 2025-09-22) v488
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- confs/hgwdev.hg.conf
- lines changed 3, context: html, text, full: html, text
9b9f268d80b9614505e485d08652a617ddef84e0 Sun Sep 21 01:11:16 2025 -0700
Installing updated hg.conf files from UCSC servers
- src/hg/hgHubConnect/hgHubConnect.c
- lines changed 5, context: html, text, full: html, text
1031734c611c941fe2579426d90aa7e5db7c9cc8 Mon Sep 22 12:41:03 2025 -0700
extending hub connect docs a little, refs #35667
- src/hg/hgTables/bam.c
- lines changed 4, context: html, text, full: html, text
c18ab1c5577b32368f3cf24abfe1664567a8420e Mon Sep 22 08:59:48 2025 -0700
generate correct download link for BAMs in /gbdb #36390
- src/hg/hgTables/hic.c
- lines changed 3, context: html, text, full: html, text
03478e629ac21b1dc68b92ae7d993d1a7314cac2 Mon Sep 22 11:15:22 2025 -0700
hgTables needed help finding trackDb for hic custom tracks, refs #36389
- src/hg/hgTables/mainPage.c
- lines changed 10, context: html, text, full: html, text
03478e629ac21b1dc68b92ae7d993d1a7314cac2 Mon Sep 22 11:15:22 2025 -0700
hgTables needed help finding trackDb for hic custom tracks, refs #36389
- src/hg/hgTracks/hgTracks.c
- lines changed 53, context: html, text, full: html, text
0bf3abced28b96f2d93e811421130345c6549d9c Fri Sep 19 16:51:41 2025 -0700
hgTracks cleanup suggested by Max, no rm for it.
- lines changed 2, context: html, text, full: html, text
583265155026a2b9b68d85daeb371147226ff990 Mon Sep 22 12:12:36 2025 -0700
Adding new keyboard shortcut for quick hub connect, refs #35667
- src/hg/htdocs/admin/filePicker.html
- lines changed 8, context: html, text, full: html, text
7e32381bc2152e0bdf4e5be2f46fe033e80cb5d5 Mon Sep 15 17:41:54 2025 -0700
(1) Broadcast a "filePickerReady" message on filePicker.html mode. (2) Make special input mode optional with a config parameter.
- lines changed 6, context: html, text, full: html, text
4eaf56ff3eb90ea8ebcf1697ac3830b8a7b5465f Tue Sep 16 09:32:52 2025 -0700
Handle file picker edge case - picker is open but doesn't have handles for requested files. Also more comments and reformatting.
- src/hg/htdocs/goldenPath/newsarch.html
- lines changed 49, context: html, text, full: html, text
157a2aba6a9a20bd1f995daf6b799f552a20c77c Fri Sep 19 12:56:24 2025 -0700
Announcing the DDG2P track for hg38 and hg19, refs #35054
- src/hg/htdocs/images/newsArchImages/ddg2p.png
- lines changed 0, context: html, text, full: html, text
a9ecb97d353c65a2b0af67447a504a818dfd3252 Fri Sep 19 12:35:37 2025 -0700
Adding the news image for the DDG2P track, refs #35054
- src/hg/htdocs/indexMeetings.html
- lines changed 1, context: html, text, full: html, text
d7a3005936e9074dbf36aa846bef00e8e143dd5e Thu Sep 18 14:06:21 2025 -0700
Removing Poster Gallery link due to more work and updates to the Poster Gallery page, refs #36182
- src/hg/htdocs/indexNews.html
- lines changed 12, context: html, text, full: html, text
157a2aba6a9a20bd1f995daf6b799f552a20c77c Fri Sep 19 12:56:24 2025 -0700
Announcing the DDG2P track for hg38 and hg19, refs #35054
- src/hg/htdocs/staff.html
- lines changed 6, context: html, text, full: html, text
9b6dede9f571a5ea40393b5e1399e978114b741b Fri Sep 19 13:14:24 2025 -0700
Adding the summer 2025 student interns to the staff page, no Redmine
- src/hg/js/ajax.js
- lines changed 1, context: html, text, full: html, text
655bfafe866c38e0e881de53245836b6b5b340b9 Thu Sep 18 12:26:43 2025 -0700
Revert "make sure AJAX called cartDump adds "db" to the URL"
This reverts commit c04c97754729a8477bb1a57b2aaed75dcdb122b6.
- src/hg/js/hgGateway.js
- lines changed 1, context: html, text, full: html, text
38fb5103beda4b0f705574c541b290b8b253e670 Mon Sep 22 12:23:38 2025 -0700
Remove 0-length characters from search strings, refs #36387
- src/hg/js/hgHubConnect.js
- lines changed 19, context: html, text, full: html, text
6f3696eafb4b9006227c1d5f42f8ccd6ecb5705e Thu Sep 18 10:32:02 2025 -0700
Fix tab selection on hgHubConnect to update the url and make the page load the correct tab based on the url, refs Jonathan for the paper
- src/hg/js/hgSearch.js
- lines changed 1, context: html, text, full: html, text
38fb5103beda4b0f705574c541b290b8b253e670 Mon Sep 22 12:23:38 2025 -0700
Remove 0-length characters from search strings, refs #36387
- src/hg/js/hgTracks.js
- lines changed 1, context: html, text, full: html, text
38fb5103beda4b0f705574c541b290b8b253e670 Mon Sep 22 12:23:38 2025 -0700
Remove 0-length characters from search strings, refs #36387
- src/hg/js/igv.min.js
- lines changed 2, context: html, text, full: html, text
7e32381bc2152e0bdf4e5be2f46fe033e80cb5d5 Mon Sep 15 17:41:54 2025 -0700
(1) Broadcast a "filePickerReady" message on filePicker.html mode. (2) Make special input mode optional with a config parameter.
- lines changed 1, context: html, text, full: html, text
1e82a3b6411cc32e625b36911f4949b552ffba3d Mon Sep 15 19:05:40 2025 -0700
Add igv configuration menu to name panel. Also expose igv.js createIcon function
- src/hg/js/igvFileHelper.js
- lines changed 17, context: html, text, full: html, text
7e32381bc2152e0bdf4e5be2f46fe033e80cb5d5 Mon Sep 15 17:41:54 2025 -0700
(1) Broadcast a "filePickerReady" message on filePicker.html mode. (2) Make special input mode optional with a config parameter.
- lines changed 50, context: html, text, full: html, text
1e82a3b6411cc32e625b36911f4949b552ffba3d Mon Sep 15 19:05:40 2025 -0700
Add igv configuration menu to name panel. Also expose igv.js createIcon function
- lines changed 40, context: html, text, full: html, text
a83239e1585aac37a58288c933d2da9f3e4b8c9f Mon Sep 15 20:27:57 2025 -0700
Bug fix -- igv local session was not cleared after removing last track (and consequently igvBrowser.
Move igv configuration menu close to cog icon from where it's invoked
- lines changed 243, context: html, text, full: html, text
4eaf56ff3eb90ea8ebcf1697ac3830b8a7b5465f Tue Sep 16 09:32:52 2025 -0700
Handle file picker edge case - picker is open but doesn't have handles for requested files. Also more comments and reformatting.
- lines changed 3, context: html, text, full: html, text
c2587413555c7cabd82b21c578d5a6f99599e7d7 Tue Sep 16 09:45:03 2025 -0700
Bug -- missing await
- src/hg/js/parallelSegments.js
- lines changed 446, context: html, text, full: html, text
6ec3c94465c621547de374cef3c52db43b9f7bee Sun Sep 21 11:01:16 2025 -0700
playing around with new display mode
- src/hg/lib/fakeCurl.c
- lines changed 4, context: html, text, full: html, text
336f121807d25e8762b218c6e00b03d3ab0aaef1 Mon Sep 22 09:34:47 2025 -0700
Certain free() calls should be freeMem() to match the allocation routine, refs #36389
- src/hg/lib/hui.c
- lines changed 5, context: html, text, full: html, text
cec653ec536e9a536256b3ebddc39be5ef9701c8 Sun Sep 21 23:37:18 2025 -0700
adding spliceAi wt track, refs #35100
- src/hg/lib/straw/cStraw.cpp
- lines changed 12, context: html, text, full: html, text
c2007dd0e1b2b6df27907f5d4678fa9458d0cbc9 Thu Sep 18 22:47:37 2025 -0700
Fix to find normalization options for hic files that don't annotate the first chromosome, refs #36313
- lines changed 3, context: html, text, full: html, text
336f121807d25e8762b218c6e00b03d3ab0aaef1 Mon Sep 22 09:34:47 2025 -0700
Certain free() calls should be freeMem() to match the allocation routine, refs #36389
- src/hg/lib/straw/hReplaceGbdb.h
- lines changed 3, context: html, text, full: html, text
336f121807d25e8762b218c6e00b03d3ab0aaef1 Mon Sep 22 09:34:47 2025 -0700
Certain free() calls should be freeMem() to match the allocation routine, refs #36389
- src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv
- lines changed 1, context: html, text, full: html, text
fb1e22b084def517ed20cc226a7e2e1fd4806abc Fri Sep 19 16:06:08 2025 -0700
RefSeq update adding a couple of new ones refs #29545
- src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv
- lines changed 4, context: html, text, full: html, text
fb1e22b084def517ed20cc226a7e2e1fd4806abc Fri Sep 19 16:06:08 2025 -0700
RefSeq update adding a couple of new ones refs #29545
- src/hg/makeDb/doc/hg38/colorsDb.txt
- lines changed 231, context: html, text, full: html, text
7695dddf01704294850c170907fe7c4607576dc3 Fri Sep 19 15:27:25 2025 -0700
Adding the makedoc for ColorsDb, refs #34120
- src/hg/makeDb/doc/hg38/ddg2p.txt
- lines changed 191, context: html, text, full: html, text
84e874dbd850363c0e7169978dcffc031d8f75f6 Fri Sep 19 12:07:03 2025 -0700
Adding the DDG2P make doc, refs #35054
- src/hg/makeDb/doc/hg38/spliceAI.txt
- lines changed 1, context: html, text, full: html, text
cec653ec536e9a536256b3ebddc39be5ef9701c8 Sun Sep 21 23:37:18 2025 -0700
adding spliceAi wt track, refs #35100
- src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
- lines changed 13, context: html, text, full: html, text
5e3d6a4c37c01514443d2bf6c1632b14cbadf7dd Fri Sep 19 16:28:49 2025 -0700
RefSeq update adding a couple of new ones refs #29545
- src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
- lines changed 4, context: html, text, full: html, text
fb1e22b084def517ed20cc226a7e2e1fd4806abc Fri Sep 19 16:06:08 2025 -0700
RefSeq update adding a couple of new ones refs #29545
- src/hg/makeDb/doc/ucscGenes/mm39.gencodeVM38.sh
- lines changed 52, context: html, text, full: html, text
eae5b1c7579021039d592b5d7f4ce27a166caa89 Wed Sep 17 13:08:05 2025 -0700
Makedoc for VM38 knownGene, refs #36165
- src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv
- lines changed 6, context: html, text, full: html, text
44c4479a850baccdca9e6b239f2899c20d30d941 Fri Sep 19 16:25:14 2025 -0700
RefSeq update adding a couple of new ones refs #29545
- src/hg/makeDb/trackDb/human/decipher.ra
- lines changed 1, context: html, text, full: html, text
696c4a434f69146ba5729acb48572fa193887e9c Fri Sep 19 11:04:56 2025 -0700
Updating the searching for the population CNV file Yesenia wrangled, no Redmine
- lines changed 9, context: html, text, full: html, text
8aae31876e1061cfdae882f5d5e4f7ae9b5534df Fri Sep 19 11:19:50 2025 -0700
Staging the DDG2P track for release, refs #35054
- lines changed 2, context: html, text, full: html, text
a6b27a9e2934c7d1454209d20ff0eddeb4069d47 Fri Sep 19 12:55:49 2025 -0700
Adding pennantIcons for the DDG2P track, refs #35054
- src/hg/makeDb/trackDb/human/decipherContainer.html
- lines changed 63, context: html, text, full: html, text
8aae31876e1061cfdae882f5d5e4f7ae9b5534df Fri Sep 19 11:19:50 2025 -0700
Staging the DDG2P track for release, refs #35054
- lines changed 30, context: html, text, full: html, text
1dee540669a2ac51afa2ebdff3b53e7f3abc7cc2 Fri Sep 19 12:24:43 2025 -0700
Updating the descripiton to match the styling of the other tracks in the composite, refs #35054
- src/hg/makeDb/trackDb/human/hg38/problematic.ra
- lines changed 1, context: html, text, full: html, text
50df9e24774f4e418396a23a107d1cdf8191f880 Fri Sep 19 09:11:15 2025 -0700
Staging the Panmask track on hgwbeta, refs #36293
- src/hg/makeDb/trackDb/human/hg38/spliceAi.ra
- lines changed 38, context: html, text, full: html, text
cec653ec536e9a536256b3ebddc39be5ef9701c8 Sun Sep 21 23:37:18 2025 -0700
adding spliceAi wt track, refs #35100
- src/hg/makeDb/trackDb/human/hg38/trackDb.ra
- lines changed 1, context: html, text, full: html, text
cec653ec536e9a536256b3ebddc39be5ef9701c8 Sun Sep 21 23:37:18 2025 -0700
adding spliceAi wt track, refs #35100
- src/hg/makeDb/trackDb/human/hg38/varFreqs.html
- lines changed 56, context: html, text, full: html, text
9980a96c9edc6ebe150c32d7857a1c5466de8e05 Tue Sep 16 05:15:38 2025 -0700
docs page for mexico biobank, refs #36259
- lines changed 1, context: html, text, full: html, text
c01c8fdded5d12a949f0b97684685aecb9b4cbaf Tue Sep 16 14:14:22 2025 -0700
small change to docs page, as per submitter
- src/hg/makeDb/trackDb/human/spliceAI.html
- lines changed 26, context: html, text, full: html, text
cec653ec536e9a536256b3ebddc39be5ef9701c8 Sun Sep 21 23:37:18 2025 -0700
adding spliceAi wt track, refs #35100
- src/hg/makeDb/trackDb/human/spliceAI.ra
- lines changed 10, context: html, text, full: html, text
cec653ec536e9a536256b3ebddc39be5ef9701c8 Sun Sep 21 23:37:18 2025 -0700
adding spliceAi wt track, refs #35100
- src/hg/makeDb/trackDb/human/spliceAIWt.ra
- lines changed 45, context: html, text, full: html, text
cec653ec536e9a536256b3ebddc39be5ef9701c8 Sun Sep 21 23:37:18 2025 -0700
adding spliceAi wt track, refs #35100
- src/hg/makeDb/trackDb/human/spliceImpactSuper.ra
- lines changed 5, context: html, text, full: html, text
cec653ec536e9a536256b3ebddc39be5ef9701c8 Sun Sep 21 23:37:18 2025 -0700
adding spliceAi wt track, refs #35100
- src/hg/makeDb/trackDb/mouse/mm39/knownGene.alpha.ra
- lines changed 6, context: html, text, full: html, text
476fb549a27985605163e8c58fdfd61ab8ad0abf Wed Sep 17 13:07:10 2025 -0700
VM38 knownGene trackDb
- src/hg/makeDb/trackDb/mouse/mm39/knownGeneArchive.ra
- lines changed 24, context: html, text, full: html, text
0b82b501aff92020f3e79021baaa80bd22e2cc5f Wed Sep 17 13:34:01 2025 -0700
Adding knownGene VM37 to knownGene archive, refs #36165
- src/hg/makeDb/trackDb/mouse/mm39/knownGeneVM38.html
- lines changed 124, context: html, text, full: html, text
476fb549a27985605163e8c58fdfd61ab8ad0abf Wed Sep 17 13:07:10 2025 -0700
VM38 knownGene trackDb
- src/hg/makeDb/trackDb/mouse/mm39/trackDb.ra
- lines changed 2, context: html, text, full: html, text
476fb549a27985605163e8c58fdfd61ab8ad0abf Wed Sep 17 13:07:10 2025 -0700
VM38 knownGene trackDb
- src/hg/utils/automation/asmHubRepeatMasker.sh
- lines changed 9, context: html, text, full: html, text
e1874141e3c52a43cbdd32bcceff60f2a4232807 Mon Sep 15 12:57:55 2025 -0700
fixed rmToTrackHub.pl script from Robert
- src/hg/utils/automation/doBlastzChainNet.pl
- lines changed 17, context: html, text, full: html, text
d82bb72f23414b783c5f3a7158a36002f27270d8 Mon Sep 15 15:24:56 2025 -0700
adding quickLift file creation refs #35575
- lines changed 6, context: html, text, full: html, text
6ddbb235ad633ecb2f7958329710b79fb07ff1c5 Tue Sep 16 11:51:08 2025 -0700
adding the quickLift symlinks to /gbdb/ when database assembly refs #35575
- src/hg/utils/automation/doRepeatMasker.pl
- lines changed 1, context: html, text, full: html, text
67eb161b05397c50dcfb3c7ec1b60654b15d66d2 Mon Sep 15 13:00:04 2025 -0700
fixed rmToTrackHub.pl script from Robert
- lines changed: 1994
- files changed: 63