All File Changes
v485_base to v486_preview (2025-07-21 to 2025-07-28) v486
Show details
- confs/asia.hg.conf
- lines changed 8, context: html, text, full: html, text
1bb611971263cd3ea1b73ef3e1b1f5eaa28d0a5d Sun Jul 27 01:11:19 2025 -0700
Installing updated hg.conf files from UCSC servers
- confs/euro.hg.conf
- lines changed 8, context: html, text, full: html, text
1bb611971263cd3ea1b73ef3e1b1f5eaa28d0a5d Sun Jul 27 01:11:19 2025 -0700
Installing updated hg.conf files from UCSC servers
- confs/hgwbeta.hg.conf
- lines changed 6, context: html, text, full: html, text
1bb611971263cd3ea1b73ef3e1b1f5eaa28d0a5d Sun Jul 27 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
1bb611971263cd3ea1b73ef3e1b1f5eaa28d0a5d Sun Jul 27 01:11:19 2025 -0700
Installing updated hg.conf files from UCSC servers
- confs/rr.hg.conf
- lines changed 4, context: html, text, full: html, text
1bb611971263cd3ea1b73ef3e1b1f5eaa28d0a5d Sun Jul 27 01:11:19 2025 -0700
Installing updated hg.conf files from UCSC servers
- src/hg/cirm/cdw/lib/cdwPageFooter.h
- lines changed 4, context: html, text, full: html, text
c0382dd8fbd6f817dd6ba8f842fb4d29bf9b7cd9 Tue Jul 22 13:20:52 2025 -0700
Adding link to SSPsyGene Gene spreadsheet on lib/cdwPageFooter.h
- src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html
- lines changed 8, context: html, text, full: html, text
cb132eebcd2484023c6e828e92d63bbc90a42e73 Wed Jul 23 16:29:31 2025 -0700
Shortening AIM2 Yale gene lists to make more readable (Gene1 - Gene20; vs listing all 20)
- src/hg/hgTracks/hgTracks.c
- lines changed 3, context: html, text, full: html, text
6f7f5bac129d59cfb99d47a3f1de118c48e423cd Wed Jul 23 15:25:01 2025 -0700
When mousing over a track, put a gear icon over the grey bar to hint that a context click is available. Put a 'x' icon to the right (or left in revCmp mode) to allow quick hiding of tracks. Both icons are enabled via hg.conf:greyBarIcons, refs #34420
- src/hg/hgc/barChartClick.c
- lines changed 1, context: html, text, full: html, text
6986d502973a4a246506b1b15c515648a2abf483 Mon Jul 21 15:52:33 2025 -0700
Move the hgc init call in the hgTracks popup later so function calls that rely on rendered text will work, refs #36092
- src/hg/htdocs/goldenPath/help/api.html
- lines changed 32, context: html, text, full: html, text
cb718a9f9f9d2c9d43a92a618da91be0de85ed3d Mon Jul 21 16:32:16 2025 -0700
document the findGenome endpoint and reveal the /list/genarkGenomes endpoing function refs #35468
- src/hg/htdocs/goldenPath/help/bedMethyl.html
- lines changed 6, context: html, text, full: html, text
dc786f63faddbd66835ea45a511ea4d5a9587c4f Tue Jul 22 16:51:26 2025 -0700
code review edits, refs #36116
- src/hg/htdocs/goldenPath/newsarch.html
- lines changed 24, context: html, text, full: html, text
b03430ed0a650b5d4f644ed65b0a9e7fac1aeaf4 Wed Jul 23 15:32:36 2025 -0700
Announcing the Bionano track for hg38 and hg19, refs #36033
- lines changed 4, context: html, text, full: html, text
f8ab4521716f62297723211e07e55df0bb660e0f Wed Jul 23 15:46:49 2025 -0700
Making some typo and styling changes, refs #36033
- src/hg/htdocs/indexNews.html
- lines changed 12, context: html, text, full: html, text
b03430ed0a650b5d4f644ed65b0a9e7fac1aeaf4 Wed Jul 23 15:32:36 2025 -0700
Announcing the Bionano track for hg38 and hg19, refs #36033
- src/hg/htdocs/staff.html
- lines changed 22, context: html, text, full: html, text
d6827b00ca2385a0ca07858abf5ffcfc6701694d Mon Jul 28 10:30:05 2025 -0700
Updating team photo, no RM.
- src/hg/htdocs/style/HGStyle.css
- lines changed 33, context: html, text, full: html, text
6f7f5bac129d59cfb99d47a3f1de118c48e423cd Wed Jul 23 15:25:01 2025 -0700
When mousing over a track, put a gear icon over the grey bar to hint that a context click is available. Put a 'x' icon to the right (or left in revCmp mode) to allow quick hiding of tracks. Both icons are enabled via hg.conf:greyBarIcons, refs #34420
- src/hg/js/hgTracks.js
- lines changed 6, context: html, text, full: html, text
6986d502973a4a246506b1b15c515648a2abf483 Mon Jul 21 15:52:33 2025 -0700
Move the hgc init call in the hgTracks popup later so function calls that rely on rendered text will work, refs #36092
- src/hg/js/hgc.js
- lines changed 1, context: html, text, full: html, text
6986d502973a4a246506b1b15c515648a2abf483 Mon Jul 21 15:52:33 2025 -0700
Move the hgc init call in the hgTracks popup later so function calls that rely on rendered text will work, refs #36092
- src/hg/js/jquery.contextmenu.js
- lines changed 0, context: html, text, full: html, text
6f7f5bac129d59cfb99d47a3f1de118c48e423cd Wed Jul 23 15:25:01 2025 -0700
When mousing over a track, put a gear icon over the grey bar to hint that a context click is available. Put a 'x' icon to the right (or left in revCmp mode) to allow quick hiding of tracks. Both icons are enabled via hg.conf:greyBarIcons, refs #34420
- src/hg/js/utils.js
- lines changed 87, context: html, text, full: html, text
6f7f5bac129d59cfb99d47a3f1de118c48e423cd Wed Jul 23 15:25:01 2025 -0700
When mousing over a track, put a gear icon over the grey bar to hint that a context click is available. Put a 'x' icon to the right (or left in revCmp mode) to allow quick hiding of tracks. Both icons are enabled via hg.conf:greyBarIcons, refs #34420
- src/hg/lib/hdb.c
- lines changed 2, context: html, text, full: html, text
fd59292a0d003980626abe2b31de187cd199ce3b Tue Jul 22 11:02:04 2025 -0700
fix a memory trashing bug
- src/hg/makeDb/doc/archaeaAsmHub/archaea.orderList.tsv
- lines changed 754, context: html, text, full: html, text
222404c7253a1bfc6800f8252ca698cc57e1eb0d Tue Jul 22 11:02:54 2025 -0700
adding all "reference" sequences for RefSeq refs #29545
- src/hg/makeDb/doc/asmHubs/commonHtml.pm
- lines changed 11, context: html, text, full: html, text
bd7ad41f40025e2d8d08ea6a001507b935a8ff5d Mon Jul 21 17:39:50 2025 -0700
adding archaea as a new group refs #29545
- src/hg/makeDb/doc/asmHubs/commonNames.py
- lines changed 1, context: html, text, full: html, text
b26ad6e7a08036ee13cd05598e81dbf5111be67d Tue Jul 22 13:22:29 2025 -0700
minimum allowed tracks on bacteria lowered and more categories allow scientific name to come through as the "common name" in the browser for odd categories of archaea and bacteria refs #29545
- src/hg/makeDb/doc/asmHubs/hubIndex.pl
- lines changed 5, context: html, text, full: html, text
bd7ad41f40025e2d8d08ea6a001507b935a8ff5d Mon Jul 21 17:39:50 2025 -0700
adding archaea as a new group refs #29545
- src/hg/makeDb/doc/asmHubs/master.run.list
- lines changed 1, context: html, text, full: html, text
6a00887793c65562b2d7ed2f5abe5feb9dd3a7e3 Mon Jul 21 17:35:20 2025 -0700
adding one per user request refs #29545
- lines changed 16473, context: html, text, full: html, text
222404c7253a1bfc6800f8252ca698cc57e1eb0d Tue Jul 22 11:02:54 2025 -0700
adding all "reference" sequences for RefSeq refs #29545
- lines changed 2, context: html, text, full: html, text
2484a9ced9c4142c547286ce90a8b6d8ee15b262 Wed Jul 23 22:59:17 2025 -0700
adding two per user requests refs #29545
- lines changed 2, context: html, text, full: html, text
61c171c4958f1ea946c88b890e7c2690cbe1b6f7 Thu Jul 24 11:19:33 2025 -0700
adding one for demo purpose for Chris Lee refs #29545
- lines changed 2, context: html, text, full: html, text
e2aceeadccb5811a593e545e1381e210b91d172c Sat Jul 26 22:11:00 2025 -0700
adding one per user request refs #29545
- src/hg/makeDb/doc/asmHubs/verifyOnDownload.sh
- lines changed 1, context: html, text, full: html, text
b26ad6e7a08036ee13cd05598e81dbf5111be67d Tue Jul 22 13:22:29 2025 -0700
minimum allowed tracks on bacteria lowered and more categories allow scientific name to come through as the "common name" in the browser for odd categories of archaea and bacteria refs #29545
- src/hg/makeDb/doc/bacteriaAsmHub/bacteria.orderList.tsv
- lines changed 1, context: html, text, full: html, text
6a00887793c65562b2d7ed2f5abe5feb9dd3a7e3 Mon Jul 21 17:35:20 2025 -0700
adding one per user request refs #29545
- lines changed 15720, context: html, text, full: html, text
222404c7253a1bfc6800f8252ca698cc57e1eb0d Tue Jul 22 11:02:54 2025 -0700
adding all "reference" sequences for RefSeq refs #29545
- src/hg/makeDb/doc/hg19.txt
- lines changed 7, context: html, text, full: html, text
1682d0bc59a928306f37e31bf9ea7d4816873dee Mon Jul 21 16:56:56 2025 -0700
Updating the location of the makedoc for the bionano track, refs #36033
- lines changed 5, context: html, text, full: html, text
e6f620332184dabe9e817555cf9a389af099aecd Thu Jul 24 12:24:17 2025 -0700
Adding pubtator dbsnp makedocs
- lines changed 45, context: html, text, full: html, text
da323191c57c36932ad1751af87b59b71b836501 Fri Jul 25 23:20:00 2025 -0700
fixed issues created by the pain of parsing gene2accession #36073
- src/hg/makeDb/doc/hg38/exomeProbesets.txt
- lines changed 7, context: html, text, full: html, text
1682d0bc59a928306f37e31bf9ea7d4816873dee Mon Jul 21 16:56:56 2025 -0700
Updating the location of the makedoc for the bionano track, refs #36033
- src/hg/makeDb/doc/hg38/genotypeArrays.txt
- lines changed 6, context: html, text, full: html, text
1cfb42e3aebf071c9010146a56fbb4138403ca1d Tue Jul 22 12:19:19 2025 -0700
Moving the makedoc for the Bionano track to the parent text file (genotypeArrays.txt), refs #36033
- src/hg/makeDb/doc/hg38/hg38.txt
- lines changed 4, context: html, text, full: html, text
1682d0bc59a928306f37e31bf9ea7d4816873dee Mon Jul 21 16:56:56 2025 -0700
Updating the location of the makedoc for the bionano track, refs #36033
- lines changed 6, context: html, text, full: html, text
1cfb42e3aebf071c9010146a56fbb4138403ca1d Tue Jul 22 12:19:19 2025 -0700
Moving the makedoc for the Bionano track to the parent text file (genotypeArrays.txt), refs #36033
- src/hg/makeDb/doc/hg38/hgnc.txt
- lines changed 30, context: html, text, full: html, text
da323191c57c36932ad1751af87b59b71b836501 Fri Jul 25 23:20:00 2025 -0700
fixed issues created by the pain of parsing gene2accession #36073
- src/hg/makeDb/doc/hg38/pubtatorDbSnp.txt
- lines changed 4, context: html, text, full: html, text
e6f620332184dabe9e817555cf9a389af099aecd Thu Jul 24 12:24:17 2025 -0700
Adding pubtator dbsnp makedocs
- src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
- lines changed 1, context: html, text, full: html, text
2484a9ced9c4142c547286ce90a8b6d8ee15b262 Wed Jul 23 22:59:17 2025 -0700
adding two per user requests refs #29545
- src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt
- lines changed 3, context: html, text, full: html, text
6a00887793c65562b2d7ed2f5abe5feb9dd3a7e3 Mon Jul 21 17:35:20 2025 -0700
adding one per user request refs #29545
- lines changed 1, context: html, text, full: html, text
afe9c0bb67d2bc258825b17ae65c9a16e820d77e Tue Jul 22 12:12:38 2025 -0700
illegal entry here for GCF_000006175.1 it is over in archaea refs #29545
- src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv
- lines changed 3, context: html, text, full: html, text
6a00887793c65562b2d7ed2f5abe5feb9dd3a7e3 Mon Jul 21 17:35:20 2025 -0700
adding one per user request refs #29545
- src/hg/makeDb/doc/legacyAsmHub/promoted.list
- lines changed 2, context: html, text, full: html, text
054630c640462a38eb3f1cf3d2f6d7003c3ad095 Tue Jul 22 12:18:38 2025 -0700
do not want to have T2T CHM13 exist in GenArk no redmine
- src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
- lines changed 1, context: html, text, full: html, text
2484a9ced9c4142c547286ce90a8b6d8ee15b262 Wed Jul 23 22:59:17 2025 -0700
adding two per user requests refs #29545
- src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv
- lines changed 1, context: html, text, full: html, text
e2aceeadccb5811a593e545e1381e210b91d172c Sat Jul 26 22:11:00 2025 -0700
adding one per user request refs #29545
- src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv
- lines changed 1, context: html, text, full: html, text
222404c7253a1bfc6800f8252ca698cc57e1eb0d Tue Jul 22 11:02:54 2025 -0700
adding all "reference" sequences for RefSeq refs #29545
- src/hg/makeDb/doc/viralAsmHub/viral.orderList.tsv
- lines changed 1, context: html, text, full: html, text
61c171c4958f1ea946c88b890e7c2690cbe1b6f7 Thu Jul 24 11:19:33 2025 -0700
adding one for demo purpose for Chris Lee refs #29545
- src/hg/makeDb/outside/hgnc/hgncToBigBed
- lines changed 374, context: html, text, full: html, text
da323191c57c36932ad1751af87b59b71b836501 Fri Jul 25 23:20:00 2025 -0700
fixed issues created by the pain of parsing gene2accession #36073
- src/hg/makeDb/outside/hgnc/makefile
- lines changed 14, context: html, text, full: html, text
da323191c57c36932ad1751af87b59b71b836501 Fri Jul 25 23:20:00 2025 -0700
fixed issues created by the pain of parsing gene2accession #36073
- src/hg/makeDb/outside/hgnc/tests/expected/hg38Test.bed
- lines changed 120, context: html, text, full: html, text
da323191c57c36932ad1751af87b59b71b836501 Fri Jul 25 23:20:00 2025 -0700
fixed issues created by the pain of parsing gene2accession #36073
- src/hg/makeDb/outside/hgnc/tests/expected/hg38Test.locus_type.filter.txt
- lines changed 1, context: html, text, full: html, text
da323191c57c36932ad1751af87b59b71b836501 Fri Jul 25 23:20:00 2025 -0700
fixed issues created by the pain of parsing gene2accession #36073
- src/hg/makeDb/outside/hgnc/tests/expected/hg38Test.trixin
- lines changed 99, context: html, text, full: html, text
da323191c57c36932ad1751af87b59b71b836501 Fri Jul 25 23:20:00 2025 -0700
fixed issues created by the pain of parsing gene2accession #36073
- src/hg/makeDb/outside/hgnc/tests/expected/hg38Test.unmapped.tsv
- lines changed 3, context: html, text, full: html, text
da323191c57c36932ad1751af87b59b71b836501 Fri Jul 25 23:20:00 2025 -0700
fixed issues created by the pain of parsing gene2accession #36073
- src/hg/makeDb/outside/hgnc/tests/input/hgnc_complete_set.part.txt
- lines changed 102, context: html, text, full: html, text
da323191c57c36932ad1751af87b59b71b836501 Fri Jul 25 23:20:00 2025 -0700
fixed issues created by the pain of parsing gene2accession #36073
- src/hg/makeDb/outside/hgnc/tests/makefile
- lines changed 23, context: html, text, full: html, text
da323191c57c36932ad1751af87b59b71b836501 Fri Jul 25 23:20:00 2025 -0700
fixed issues created by the pain of parsing gene2accession #36073
- src/hg/makeDb/trackDb/human/clinvar.html
- lines changed 60, context: html, text, full: html, text
728d257662efbf3ab935d4d5959078d6c99e3d54 Tue Jul 22 15:37:22 2025 -0700
Updates to the clinvar.html, refs #35750
- src/hg/makeDb/trackDb/human/clinvar.ra
- lines changed 9, context: html, text, full: html, text
cf9d03a1e5d97a366c9d33859fe9ba3c4d86b17b Tue Jun 24 06:28:43 2025 -0700
moving clinvar alpha changes into main clinvar trackDb, refs #35750
- lines changed 1, context: html, text, full: html, text
d6de0450aca838fdec8a96399487850dc09a6452 Thu Jun 26 05:05:49 2025 -0700
adding line decorator.default.bigDataUrl to clinvar track, refs #35750
- lines changed 2, context: html, text, full: html, text
60ba9ea2367f370a97b739b2a32608ae0674f216 Tue Jul 22 13:52:05 2025 -0700
Hiding the ClinVar track decorators by default, refs #35750
- src/hg/makeDb/trackDb/human/clinvarAlpha.html
- lines changed 14, context: html, text, full: html, text
db0c0fec91167570421eaa54d3e88219e35f6c04 Wed Jun 25 12:13:05 2025 -0700
Edits to the clinvar description page, refs #35750
- src/hg/makeDb/trackDb/human/hg19/genotypeArrays.html
- lines changed 10, context: html, text, full: html, text
f386e652ab6429e9c39164b3726a4d23a7ca5b70 Mon Jul 21 17:07:52 2025 -0700
Adding the methods and credits for the Bionano track, refs #36033
- lines changed 1, context: html, text, full: html, text
7b9fe6166c3e9648ea33f12eb12c1e2a77651237 Tue Jul 22 11:16:01 2025 -0700
Updating the header tags to match the other tracks, refs #36033
- lines changed 1, context: html, text, full: html, text
d5814fcd19322db60a01f365b152cb202ed89489 Wed Jul 23 09:53:10 2025 -0700
Making changes from code review, refs #36118
- src/hg/makeDb/trackDb/human/hg19/trackDb.ra
- lines changed 1, context: html, text, full: html, text
70c3ee1d28c4b11d3f3fa544b021ef13930ee795 Mon Jul 21 17:11:28 2025 -0700
Removing the color for the Bionano track since it is no longer needed, refs #36033
- lines changed 1, context: html, text, full: html, text
366647a1f03839959cc28f62c1f8889e83bf823c Tue Jul 22 11:19:52 2025 -0700
Removing the release tags to stage on the RR, refs #36033
- lines changed 1, context: html, text, full: html, text
b03430ed0a650b5d4f644ed65b0a9e7fac1aeaf4 Wed Jul 23 15:32:36 2025 -0700
Announcing the Bionano track for hg38 and hg19, refs #36033
- src/hg/makeDb/trackDb/human/hg38/genotypeArrays.html
- lines changed 10, context: html, text, full: html, text
f386e652ab6429e9c39164b3726a4d23a7ca5b70 Mon Jul 21 17:07:52 2025 -0700
Adding the methods and credits for the Bionano track, refs #36033
- lines changed 1, context: html, text, full: html, text
01275fbbee45b5ffa715fce55bca1ccf6281e05a Mon Jul 21 17:08:50 2025 -0700
Fixing a typo with 'Agilent', no Redmine
- lines changed 1, context: html, text, full: html, text
d5814fcd19322db60a01f365b152cb202ed89489 Wed Jul 23 09:53:10 2025 -0700
Making changes from code review, refs #36118
- src/hg/makeDb/trackDb/human/hg38/trackDb.ra
- lines changed 1, context: html, text, full: html, text
70c3ee1d28c4b11d3f3fa544b021ef13930ee795 Mon Jul 21 17:11:28 2025 -0700
Removing the color for the Bionano track since it is no longer needed, refs #36033
- lines changed 1, context: html, text, full: html, text
366647a1f03839959cc28f62c1f8889e83bf823c Tue Jul 22 11:19:52 2025 -0700
Removing the release tags to stage on the RR, refs #36033
- lines changed 1, context: html, text, full: html, text
b03430ed0a650b5d4f644ed65b0a9e7fac1aeaf4 Wed Jul 23 15:32:36 2025 -0700
Announcing the Bionano track for hg38 and hg19, refs #36033
- src/hg/makeDb/trackDb/human/trackDb.ra
- lines changed 1, context: html, text, full: html, text
70c69f60b5b41a3e4d13998acb8793036ad35445 Thu Jul 24 12:17:48 2025 -0700
Removing the .html from trackDb's html line, refs #35957
- lines changed 1, context: html, text, full: html, text
fd736e33849e54fe10802e3c675564feac322e6d Thu Jul 24 12:30:57 2025 -0700
Capitalizing the V in variants to match the other tracks, refs #35957
- lines changed 1, context: html, text, full: html, text
da323191c57c36932ad1751af87b59b71b836501 Fri Jul 25 23:20:00 2025 -0700
fixed issues created by the pain of parsing gene2accession #36073
- src/hg/makeDb/trackDb/human/varsInPubs.html
- lines changed 2, context: html, text, full: html, text
5ffcdbf56df3d1ef3ba5928d2d9154a32f600b03 Thu Jul 24 12:21:21 2025 -0700
Uncommenting the PubTator3 track for human, refs #35957
- src/hg/utils/automation/doAssemblyHub.pl
- lines changed 1, context: html, text, full: html, text
98bd6fb357fb3c8922e563693f299dd498d9d27f Sat Jul 26 00:42:45 2025 -0700
forgotten testing "head" in the size determination should not be there, no redmine
- src/hg/utils/otto/genArk/pushRR.sh
- lines changed 41, context: html, text, full: html, text
edbbab22e6f1006892ef64cfd0ef7e8ecd78a9c0 Thu Jul 24 21:56:47 2025 -0700
now protecting itself from overrunning if it takes longer than a day refs #34917
- src/hg/utils/otto/otto.crontab
- lines changed 1, context: html, text, full: html, text
618b3efb7efbe710b1766a07f8a63d243f60fa69 Wed Jul 23 14:32:54 2025 -0700
momentarily turn off the GenArk pushRR.sh so it can be lockfile protected from an overrun
- lines changed 3, context: html, text, full: html, text
73003519f1690c2731d6858b759661ad2bfa111c Thu Jul 24 21:58:13 2025 -0700
pushRR script now protecting itself from overrunning if it takes longer than a day refs #34917
- src/hg/utils/otto/pubtatorDbSnp/doUpdate.sh
- lines changed 4, context: html, text, full: html, text
cffc50d83e0e127bb90d6b556a5f5317208d147b Wed Jul 23 09:14:32 2025 -0700
Updated log file name for pubtator db snp
- lines changed 6, context: html, text, full: html, text
0ae810d31ae6ed8919e252d9bfc4f12e486a0d44 Wed Jul 23 09:32:16 2025 -0700
Fixed bugs in doUpdate for pubtatordbsnp
- lines changed 4, context: html, text, full: html, text
0c069cefb4fe5a7ebb25d53279b6a12f9c65c5e1 Wed Jul 23 09:34:26 2025 -0700
Updating output dir
- src/utils/qa/weeklybld/buildEnv.csh
- lines changed 2, context: html, text, full: html, text
989a61f1c67adfe47f0877cab1df7e4381963be4 Mon Jul 28 14:32:11 2025 -0700
v486 preview1, refs #36036
- lines changed: 34293
- files changed: 88