All File Changes

v490_preview2 to v490_base (2025-10-27 to 2025-11-03) v490

• confs/asia.hg.conf
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    a08a9818f9218719b5a3f360a45dd6f481cf946e Sun Nov 2 01:11:20 2025 -0700
    Installing updated hg.conf files from UCSC servers
• confs/euro.hg.conf
  • lines changed 5, context: html, text, full: html, text
    a08a9818f9218719b5a3f360a45dd6f481cf946e Sun Nov 2 01:11:20 2025 -0700
    Installing updated hg.conf files from UCSC servers
• confs/hgwdev.hg.conf
  • lines changed 1, context: html, text, full: html, text
    a08a9818f9218719b5a3f360a45dd6f481cf946e Sun Nov 2 01:11:20 2025 -0700
    Installing updated hg.conf files from UCSC servers
• confs/rr.hg.conf
  • lines changed 1, context: html, text, full: html, text
    a08a9818f9218719b5a3f360a45dd6f481cf946e Sun Nov 2 01:11:20 2025 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/cgilib/cartEdit9.c
  • lines changed 4, context: html, text, full: html, text
    e41ac82366f030f13c148d7dadb62d04255ffcb4 Wed Oct 29 14:39:33 2025 -0700
    Remove debugging printfs, refs #36599
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    19e5eb84fda6b765410726d439ab366dce141e94 Wed Oct 29 16:07:50 2025 -0700
    For the ddg2p cart rewrite, only turn on the new g2p container super track is the decipher supertrack was on previously
  • lines changed 9, context: html, text, full: html, text
    32002acf29fb049b3d52133778569d3583150b81 Thu Oct 30 12:28:02 2025 -0700
    Fix up ddg2p cart rewrite to instead move the track to a single g2p track not in any super track, refs #36529
• src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html
  • lines changed 7, context: html, text, full: html, text
    a4ff8fa3139e52d36188b26841fb2a362b1d700b Fri Oct 31 13:00:45 2025 -0700
    Adding links to jump to dates in milestones in Google Docs of each ADGCs on SSPsyGene milestones for quicker reference
• src/hg/hgBlat/hgBlat.c
  • lines changed 4, context: html, text, full: html, text
    ae63ce55185746c5fabb2ead8cc20215faada36d Mon Nov 3 08:03:14 2025 -0800
    adding ancient dna track, refs #36592
• src/hg/hgConvert/hgConvert.c
  • lines changed 2, context: html, text, full: html, text
    c5a3038a516922f245b5964b021326598782b684 Tue Oct 28 13:58:44 2025 -0700
    Code review edits, refs #36601
  • lines changed 1, context: html, text, full: html, text
    f2560d1931f0c4f135608db9618d5871f2c2f98a Tue Oct 28 14:04:36 2025 -0700
    Fixing a sentence, refs #35536
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    57bbece80601cd19b99c32f2126aba136d3fc83c Tue Oct 28 16:16:06 2025 -0700
    Code review suggestion from Jairo, refs #36601
• src/hg/hgGateway/hgGateway.html
  • lines changed 1, context: html, text, full: html, text
    ae63ce55185746c5fabb2ead8cc20215faada36d Mon Nov 3 08:03:14 2025 -0800
    adding ancient dna track, refs #36592
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 3, context: html, text, full: html, text
    bde796b26325a6444222f693b5e0374a07de1dc9 Wed Oct 29 15:35:11 2025 -0700
    Adding a link to the docs page for the CAPTCHA on hgHubConnect. No RM.
• src/hg/hgHubConnect/trackHubWizard.c
  • lines changed 1, context: html, text, full: html, text
    c6205c84da7c9f650587fca703ff83fddf8db693 Fri Oct 31 16:25:53 2025 -0700
    Do not send the async request to get hubSpace ui state on page load if the user is not logged in, refs Max discussion
• src/hg/hgTracks/bigBedTrack.c
  • lines changed 31, context: html, text, full: html, text
    ff70fc9c934dd856c7ba5c723f2cdcc3568ad09e Mon Nov 3 15:20:19 2025 -0800
    one path for bigBed, bigPs, bigGenePred, bigDbSNp. refs #19984
  • lines changed 31, context: html, text, full: html, text
    cd6fddde0007623ebbc749201b748dfa24c47b91 Mon Nov 3 15:23:58 2025 -0800
    Revert "one path for bigBed, bigPs, bigGenePred, bigDbSNp. refs #19984" This reverts commit ff70fc9c934dd856c7ba5c723f2cdcc3568ad09e.
• src/hg/hgTracks/hgTracks.c
  • lines changed 23, context: html, text, full: html, text
    ee8b9b26531c6606398b89ef86aa72469ab92bd5 Tue Oct 28 09:29:27 2025 -0700
    adding new info icon to group and making the hide group button do a refresh, refs #36610
  • lines changed 1, context: html, text, full: html, text
    80732564dd5c43725740eaa0c39760e3c89507af Wed Oct 29 07:53:00 2025 -0700
    fixing null exception, refs #36610
  • lines changed 1, context: html, text, full: html, text
    6f8c0b12e680d6205ed80331ef89fa686f710195 Thu Oct 30 16:36:55 2025 -0700
    small group bar fix, refs #36610
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    ae63ce55185746c5fabb2ead8cc20215faada36d Mon Nov 3 08:03:14 2025 -0800
    adding ancient dna track, refs #36592
• src/hg/hgTracks/mainMain.c
  • lines changed 1, context: html, text, full: html, text
    ae63ce55185746c5fabb2ead8cc20215faada36d Mon Nov 3 08:03:14 2025 -0800
    adding ancient dna track, refs #36592
• src/hg/hgTracks/simpleTracks.c
  • lines changed 1, context: html, text, full: html, text
    ff70fc9c934dd856c7ba5c723f2cdcc3568ad09e Mon Nov 3 15:20:19 2025 -0800
    one path for bigBed, bigPs, bigGenePred, bigDbSNp. refs #19984
  • lines changed 1, context: html, text, full: html, text
    cd6fddde0007623ebbc749201b748dfa24c47b91 Mon Nov 3 15:23:58 2025 -0800
    Revert "one path for bigBed, bigPs, bigGenePred, bigDbSNp. refs #19984" This reverts commit ff70fc9c934dd856c7ba5c723f2cdcc3568ad09e.
• src/hg/hgc/hgc.c
  • lines changed 8, context: html, text, full: html, text
    ff70fc9c934dd856c7ba5c723f2cdcc3568ad09e Mon Nov 3 15:20:19 2025 -0800
    one path for bigBed, bigPs, bigGenePred, bigDbSNp. refs #19984
  • lines changed 8, context: html, text, full: html, text
    cd6fddde0007623ebbc749201b748dfa24c47b91 Mon Nov 3 15:23:58 2025 -0800
    Revert "one path for bigBed, bigPs, bigGenePred, bigDbSNp. refs #19984" This reverts commit ff70fc9c934dd856c7ba5c723f2cdcc3568ad09e.
• src/hg/htdocs/covid19.html
  • lines changed 1, context: html, text, full: html, text
    c5a3038a516922f245b5964b021326598782b684 Tue Oct 28 13:58:44 2025 -0700
    Code review edits, refs #36601
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 1, context: html, text, full: html, text
    14fcdb708c646677f8cbe059bf6d76d8a4f5b2d6 Wed Oct 29 11:04:46 2025 -0700
    added a dash to the allowed chars list. refs #19482, #30010
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 64, context: html, text, full: html, text
    c15a59c6ddc7428025519ec671af0a7d4649d7be Thu Oct 30 16:50:26 2025 -0700
    Releasing the new GENCODE Known Gene tracks V49, v49lift37, and VM38, refs #36169 #36167 #36165
• src/hg/htdocs/images/encode4cCREs.png
  • lines changed 0, context: html, text, full: html, text
    8a3f24f0e70e94dc4812283bbd60c715651d6c46 Mon Nov 3 14:50:27 2025 -0800
    Staging the ENCODE4 cCREs track. Next step is asking for feedback from the authors, refs #34923
• src/hg/htdocs/images/encode4cCREsBiosampleSpectrum.png
  • lines changed 0, context: html, text, full: html, text
    8a3f24f0e70e94dc4812283bbd60c715651d6c46 Mon Nov 3 14:50:27 2025 -0800
    Staging the ENCODE4 cCREs track. Next step is asking for feedback from the authors, refs #34923
• src/hg/htdocs/inc/hgMyData.html
  • lines changed 7, context: html, text, full: html, text
    cca4a9fb899c51231734d36d06774fe61eeaa7c2 Tue Oct 28 10:25:41 2025 -0700
    Adding a note for users to contact us with any feedback on the Hub Space page, refs #36290
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    c15a59c6ddc7428025519ec671af0a7d4649d7be Thu Oct 30 16:50:26 2025 -0700
    Releasing the new GENCODE Known Gene tracks V49, v49lift37, and VM38, refs #36169 #36167 #36165
• src/hg/htdocs/maintenance.html
  • lines changed 19, context: html, text, full: html, text
    dda3eb3d495822ace30e65e2ba1c89cc98ea6be9 Thu Oct 30 11:21:52 2025 -0700
    Adding Bluesky to the page and some other updates, No RM
• src/hg/htdocs/robots.rr.txt
  • lines changed 6, context: html, text, full: html, text
    876352800cfcb9d40ed5f7abd8b7816bb8c8b9af Fri Oct 31 14:38:33 2025 -0700
    Tweaking the bots we are blocking based on a new attempt to be more AI/crawl friendly (hoping china bots still stay out), refs #36635
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    1dac24e8ba58bf264f7683f8e0dccc37e1e2a695 Fri Oct 31 14:43:52 2025 -0700
    Experimenting with removing the bot delay, which most companies don't respect anyways (including Google), although allegedly anthropic and bing do. Will bring back if we have issues. Refs #36635
• src/hg/htdocs/robots.txt
  • lines changed 3, context: html, text, full: html, text
    300adfc08c5b5c7ee7510b47eb3a069884f17bfb Tue Oct 28 10:26:49 2025 -0700
    Letting claude into dev so I can share URLs for hubs and data, no RM.
• src/hg/htdocs/style/HGStyle.css
  • lines changed 17, context: html, text, full: html, text
    ae63ce55185746c5fabb2ead8cc20215faada36d Mon Nov 3 08:03:14 2025 -0800
    adding ancient dna track, refs #36592
• src/hg/htdocs/style/autocomplete.css
  • lines changed 1, context: html, text, full: html, text
    ae63ce55185746c5fabb2ead8cc20215faada36d Mon Nov 3 08:03:14 2025 -0800
    adding ancient dna track, refs #36592
• src/hg/inc/bigBedFilter.h
  • lines changed 1, context: html, text, full: html, text
    850b9b7d97d7a0fc1ea8f5357132b95aba4dda37 Tue Oct 28 14:30:19 2025 -0700
    forgot to commit a file in last commit
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    46fb9137d79ec3fafc731fbf896e5accd47fa53d Tue Oct 28 14:32:23 2025 -0700
    accidentally committed a value in the previous commit, taking that back
• src/hg/inc/hgConfig.h
  • lines changed 3, context: html, text, full: html, text
    ae63ce55185746c5fabb2ead8cc20215faada36d Mon Nov 3 08:03:14 2025 -0800
    adding ancient dna track, refs #36592
• src/hg/inc/hui.h
  • lines changed 3, context: html, text, full: html, text
    e19ee3ea7321255582381b70affa42a281441665 Tue Oct 28 10:06:09 2025 -0700
    fix broken build for Max
  • lines changed 4, context: html, text, full: html, text
    850b9b7d97d7a0fc1ea8f5357132b95aba4dda37 Tue Oct 28 14:30:19 2025 -0700
    forgot to commit a file in last commit
• src/hg/inc/mafGene.h
  • lines changed 13, context: html, text, full: html, text
    4d80894351b62c4daa432279691a9ef73717d86b Wed Oct 29 08:57:35 2025 -0700
    allow mafGene to use bigMaf and twoBit instead of database
• src/hg/js/hgGateway.js
  • lines changed 3, context: html, text, full: html, text
    e275bb31c96733585d0a1d511fa992f10fa56b69 Fri Oct 31 16:13:13 2025 -0700
    Support gnomAD variation and range specifiers like 4-1234-2234 and 5-12345-A-C, refs #36388
• src/hg/js/hgMyData.js
  • lines changed 3, context: html, text, full: html, text
    c6205c84da7c9f650587fca703ff83fddf8db693 Fri Oct 31 16:25:53 2025 -0700
    Do not send the async request to get hubSpace ui state on page load if the user is not logged in, refs Max discussion
• src/hg/js/hgSearch.js
  • lines changed 3, context: html, text, full: html, text
    e275bb31c96733585d0a1d511fa992f10fa56b69 Fri Oct 31 16:13:13 2025 -0700
    Support gnomAD variation and range specifiers like 4-1234-2234 and 5-12345-A-C, refs #36388
• src/hg/js/hgTracks.js
  • lines changed 2, context: html, text, full: html, text
    807acfef611a3ec3b523d1b409c8fa799a034d7e Tue Oct 28 08:49:59 2025 -0700
    refresh page right away when hide group is clicked, refs #36354
  • lines changed 3, context: html, text, full: html, text
    e275bb31c96733585d0a1d511fa992f10fa56b69 Fri Oct 31 16:13:13 2025 -0700
    Support gnomAD variation and range specifiers like 4-1234-2234 and 5-12345-A-C, refs #36388
  • lines changed 13, context: html, text, full: html, text
    ae63ce55185746c5fabb2ead8cc20215faada36d Mon Nov 3 08:03:14 2025 -0800
    adding ancient dna track, refs #36592
• src/hg/js/subCfg.js
  • lines changed 18, context: html, text, full: html, text
    ae63ce55185746c5fabb2ead8cc20215faada36d Mon Nov 3 08:03:14 2025 -0800
    adding ancient dna track, refs #36592
• src/hg/js/utils.js
  • lines changed 8, context: html, text, full: html, text
    7b392cbce42b3629202ba2934040c53cc52ce244 Wed Oct 29 14:57:30 2025 -0700
    Prevent multiple click events from happening for each gear/x button, refs #36620
  • lines changed 5, context: html, text, full: html, text
    e275bb31c96733585d0a1d511fa992f10fa56b69 Fri Oct 31 16:13:13 2025 -0700
    Support gnomAD variation and range specifiers like 4-1234-2234 and 5-12345-A-C, refs #36388
  • lines changed 1, context: html, text, full: html, text
    ae63ce55185746c5fabb2ead8cc20215faada36d Mon Nov 3 08:03:14 2025 -0800
    adding ancient dna track, refs #36592
• src/hg/lib/cart.c
  • lines changed 5, context: html, text, full: html, text
    ae63ce55185746c5fabb2ead8cc20215faada36d Mon Nov 3 08:03:14 2025 -0800
    adding ancient dna track, refs #36592
• src/hg/lib/fasTAN.as
  • lines changed 9, context: html, text, full: html, text
    0987ef2a57422e1b7a0227b9abd7fadac942e2e8 Fri Oct 31 15:36:18 2025 -0700
    bed file definition of the output from FasTAN
  • lines changed 1, context: html, text, full: html, text
    8c9fa3d2aef3a6cd7681748602fc303842196f5e Fri Oct 31 15:46:47 2025 -0700
    correct possessive
• src/hg/lib/hdb.c
  • lines changed 4, context: html, text, full: html, text
    39795df20ecc6043b12a9a8aa9c08660a1571bd0 Thu Oct 30 03:49:31 2025 -0700
    fixing hgBlat error when using apiKey, refs #36428
• src/hg/lib/hgConfig.c
  • lines changed 14, context: html, text, full: html, text
    ae63ce55185746c5fabb2ead8cc20215faada36d Mon Nov 3 08:03:14 2025 -0800
    adding ancient dna track, refs #36592
• src/hg/lib/hgFind.c
  • lines changed 37, context: html, text, full: html, text
    e275bb31c96733585d0a1d511fa992f10fa56b69 Fri Oct 31 16:13:13 2025 -0700
    Support gnomAD variation and range specifiers like 4-1234-2234 and 5-12345-A-C, refs #36388
• src/hg/lib/hui.c
  • lines changed 19, context: html, text, full: html, text
    ee8b9b26531c6606398b89ef86aa72469ab92bd5 Tue Oct 28 09:29:27 2025 -0700
    adding new info icon to group and making the hide group button do a refresh, refs #36610
• src/hg/lib/mafGene.c
  • lines changed 68, context: html, text, full: html, text
    4d80894351b62c4daa432279691a9ef73717d86b Wed Oct 29 08:57:35 2025 -0700
    allow mafGene to use bigMaf and twoBit instead of database
• src/hg/lib/straw/makefile
  • lines changed 2, context: html, text, full: html, text
    9ec8ecc35be16510fa842e1c47f9e821d0e90f0f Fri Oct 31 02:30:41 2025 -0700
    adding a few suggested changes from Galaxy, see https://github.com/bioconda/bioconda-recipes/blob/master/recipes/ucsc-mafgene/0001-include.patch, no redmine
• src/hg/makeDb/doc/hg38/ancient.txt
  • lines changed 15, context: html, text, full: html, text
    80165cbc77565f3c2bdfc9acce4fe66d0f02ad55 Mon Nov 3 13:58:56 2025 -0800
    adding make doc for ancient track, refs #36592
• src/hg/makeDb/doc/hg38/encode4.cCREs.txt
  • lines changed 603, context: html, text, full: html, text
    2197cb4ee08a947521c3d4204d2fc37ee4ab18fe Mon Nov 3 14:57:41 2025 -0800
    ENCODE4 cCREs makedoc, refs #34923
• src/hg/makeDb/hgLoadMaf/hgLoadMafSummary.c
  • lines changed 29, context: html, text, full: html, text
    ae63ce55185746c5fabb2ead8cc20215faada36d Mon Nov 3 08:03:14 2025 -0800
    adding ancient dna track, refs #36592
• src/hg/makeDb/trackDb/human/bayesDel.ra
  • lines changed 1, context: html, text, full: html, text
    ae63ce55185746c5fabb2ead8cc20215faada36d Mon Nov 3 08:03:14 2025 -0800
    adding ancient dna track, refs #36592
• src/hg/makeDb/trackDb/human/g2p.ra
  • lines changed 12, context: html, text, full: html, text
    0746a44f97862ebea8f04b4acde9b928e65ed854 Thu Oct 30 11:21:21 2025 -0700
    Updating the g2p track since there will only be one track for the g2p project with each of the panels, refs #36529
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    85de37a5b85f0c548370ae425e48259fd0bbf26f Thu Oct 30 11:25:12 2025 -0700
    Updating the visibility since the g2p track will not be on by default, refs #36469
• src/hg/makeDb/trackDb/human/hg19/knownGene.alpha.ra
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    c15a59c6ddc7428025519ec671af0a7d4649d7be Thu Oct 30 16:50:26 2025 -0700
    Releasing the new GENCODE Known Gene tracks V49, v49lift37, and VM38, refs #36169 #36167 #36165
• src/hg/makeDb/trackDb/human/hg19/knownGene.ra
  • lines changed 7, context: html, text, full: html, text
    c15a59c6ddc7428025519ec671af0a7d4649d7be Thu Oct 30 16:50:26 2025 -0700
    Releasing the new GENCODE Known Gene tracks V49, v49lift37, and VM38, refs #36169 #36167 #36165
• src/hg/makeDb/trackDb/human/hg19/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    410bc23ea2ad4369745b5f80f2f805bd81e201e4 Wed Oct 29 17:41:51 2025 -0700
    Staging 3 All GENCODE tracks, refs #36170 #36168 #36166
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
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    755b77137deee2a6ca9375f3f483bd38b2d4aa08 Wed Oct 29 22:08:13 2025 -0700
    Staging the GENCODE v49/v49lift37/vM38 KnownGene tracks on hgwbeta, refs #36169 #36167 #36165
  • lines changed 2, context: html, text, full: html, text
    c15a59c6ddc7428025519ec671af0a7d4649d7be Thu Oct 30 16:50:26 2025 -0700
    Releasing the new GENCODE Known Gene tracks V49, v49lift37, and VM38, refs #36169 #36167 #36165
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV48lift37.ra
  • lines changed 1, context: html, text, full: html, text
    410bc23ea2ad4369745b5f80f2f805bd81e201e4 Wed Oct 29 17:41:51 2025 -0700
    Staging 3 All GENCODE tracks, refs #36170 #36168 #36166
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV49lift37.ra
  • lines changed 1, context: html, text, full: html, text
    410bc23ea2ad4369745b5f80f2f805bd81e201e4 Wed Oct 29 17:41:51 2025 -0700
    Staging 3 All GENCODE tracks, refs #36170 #36168 #36166
• src/hg/makeDb/trackDb/human/hg38/ancient.html
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    b36aef93464d21c304c09a9a301c56f7d051be96 Mon Nov 3 13:41:45 2025 -0800
    filtering ancient VCF files, refs #36592
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    da8d0706020df39b6c2cc5b5dacb22a5e7242462 Mon Nov 3 13:59:26 2025 -0800
    track doc for ancient track, refs #36592
• src/hg/makeDb/trackDb/human/hg38/ancient.ra
  • lines changed 25, context: html, text, full: html, text
    ae63ce55185746c5fabb2ead8cc20215faada36d Mon Nov 3 08:03:14 2025 -0800
    adding ancient dna track, refs #36592
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    b36aef93464d21c304c09a9a301c56f7d051be96 Mon Nov 3 13:41:45 2025 -0800
    filtering ancient VCF files, refs #36592
• src/hg/makeDb/trackDb/human/hg38/cCREregistry.html
  • lines changed 121, context: html, text, full: html, text
    8a3f24f0e70e94dc4812283bbd60c715651d6c46 Mon Nov 3 14:50:27 2025 -0800
    Staging the ENCODE4 cCREs track. Next step is asking for feedback from the authors, refs #34923
• src/hg/makeDb/trackDb/human/hg38/cCREsSuper.html
  • lines changed 20, context: html, text, full: html, text
    8a3f24f0e70e94dc4812283bbd60c715651d6c46 Mon Nov 3 14:50:27 2025 -0800
    Staging the ENCODE4 cCREs track. Next step is asking for feedback from the authors, refs #34923
• src/hg/makeDb/trackDb/human/hg38/coreCollection.html
  • lines changed 147, context: html, text, full: html, text
    8a3f24f0e70e94dc4812283bbd60c715651d6c46 Mon Nov 3 14:50:27 2025 -0800
    Staging the ENCODE4 cCREs track. Next step is asking for feedback from the authors, refs #34923
• src/hg/makeDb/trackDb/human/hg38/encode.cCREs.override.ra
  • lines changed 18, context: html, text, full: html, text
    8a3f24f0e70e94dc4812283bbd60c715651d6c46 Mon Nov 3 14:50:27 2025 -0800
    Staging the ENCODE4 cCREs track. Next step is asking for feedback from the authors, refs #34923
• src/hg/makeDb/trackDb/human/hg38/encode3.ra
  • lines changed 1, context: html, text, full: html, text
    ae63ce55185746c5fabb2ead8cc20215faada36d Mon Nov 3 08:03:14 2025 -0800
    adding ancient dna track, refs #36592
• src/hg/makeDb/trackDb/human/hg38/encode4.ccres.ra
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    8a3f24f0e70e94dc4812283bbd60c715651d6c46 Mon Nov 3 14:50:27 2025 -0800
    Staging the ENCODE4 cCREs track. Next step is asking for feedback from the authors, refs #34923
• src/hg/makeDb/trackDb/human/hg38/knownGene.alpha.ra
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    c15a59c6ddc7428025519ec671af0a7d4649d7be Thu Oct 30 16:50:26 2025 -0700
    Releasing the new GENCODE Known Gene tracks V49, v49lift37, and VM38, refs #36169 #36167 #36165
• src/hg/makeDb/trackDb/human/hg38/knownGene.ra
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    c15a59c6ddc7428025519ec671af0a7d4649d7be Thu Oct 30 16:50:26 2025 -0700
    Releasing the new GENCODE Known Gene tracks V49, v49lift37, and VM38, refs #36169 #36167 #36165
• src/hg/makeDb/trackDb/human/hg38/rnaMod.html
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    6a7655f06c1581853f1a028eb29e17caecfba6a0 Wed Oct 29 07:26:54 2025 -0700
    adding RNA modifications superTrack, refs #36613
• src/hg/makeDb/trackDb/human/hg38/rnaMod.ra
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    6a7655f06c1581853f1a028eb29e17caecfba6a0 Wed Oct 29 07:26:54 2025 -0700
    adding RNA modifications superTrack, refs #36613
• src/hg/makeDb/trackDb/human/hg38/topmed.ra
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    030cc7d4165ee6b37bd4c9ecfb443fb39ac2468d Mon Nov 3 07:59:26 2025 -0800
    updating mexico biobank track, and related tracks, refs #36259
• src/hg/makeDb/trackDb/human/hg38/trackDb.gencode.ra
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    410bc23ea2ad4369745b5f80f2f805bd81e201e4 Wed Oct 29 17:41:51 2025 -0700
    Staging 3 All GENCODE tracks, refs #36170 #36168 #36166
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
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    6a7655f06c1581853f1a028eb29e17caecfba6a0 Wed Oct 29 07:26:54 2025 -0700
    adding RNA modifications superTrack, refs #36613
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    755b77137deee2a6ca9375f3f483bd38b2d4aa08 Wed Oct 29 22:08:13 2025 -0700
    Staging the GENCODE v49/v49lift37/vM38 KnownGene tracks on hgwbeta, refs #36169 #36167 #36165
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    c15a59c6ddc7428025519ec671af0a7d4649d7be Thu Oct 30 16:50:26 2025 -0700
    Releasing the new GENCODE Known Gene tracks V49, v49lift37, and VM38, refs #36169 #36167 #36165
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    030cc7d4165ee6b37bd4c9ecfb443fb39ac2468d Mon Nov 3 07:59:26 2025 -0800
    updating mexico biobank track, and related tracks, refs #36259
• src/hg/makeDb/trackDb/human/hg38/varFreqs.html
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    2eb76dc0d29bb19615c354880a3a58830664b05d Thu Oct 30 07:16:23 2025 -0700
    adding MCPS Mexico city variants, refs #36628
• src/hg/makeDb/trackDb/human/hg38/varFreqs.ra
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    2eb76dc0d29bb19615c354880a3a58830664b05d Thu Oct 30 07:16:23 2025 -0700
    adding MCPS Mexico city variants, refs #36628
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    708f8ae536c8b06b97d7f60ae5fb816c806a0caa Thu Oct 30 07:17:03 2025 -0700
    typo in previous commit
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    030cc7d4165ee6b37bd4c9ecfb443fb39ac2468d Mon Nov 3 07:59:26 2025 -0800
    updating mexico biobank track, and related tracks, refs #36259
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV48.ra
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    410bc23ea2ad4369745b5f80f2f805bd81e201e4 Wed Oct 29 17:41:51 2025 -0700
    Staging 3 All GENCODE tracks, refs #36170 #36168 #36166
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV49.ra
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    410bc23ea2ad4369745b5f80f2f805bd81e201e4 Wed Oct 29 17:41:51 2025 -0700
    Staging 3 All GENCODE tracks, refs #36170 #36168 #36166
• src/hg/makeDb/trackDb/human/spliceAI.ra
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    ae63ce55185746c5fabb2ead8cc20215faada36d Mon Nov 3 08:03:14 2025 -0800
    adding ancient dna track, refs #36592
• src/hg/makeDb/trackDb/human/trackDb.ra
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    f64ee094d4f3ebf0399403c71094c012482e89fb Wed Oct 29 03:05:04 2025 -0700
    Added Varaico suppl track
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    300b9e062efb576d651f590652f3440e24a06caf Wed Oct 29 03:08:15 2025 -0700
    Small fix for varaico test tracks
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    6f10041ba5ff3c54884a1416e5ca72277fcdea77 Wed Oct 29 03:09:01 2025 -0700
    varaico track naming fix
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    030cc7d4165ee6b37bd4c9ecfb443fb39ac2468d Mon Nov 3 07:59:26 2025 -0800
    updating mexico biobank track, and related tracks, refs #36259
• src/hg/makeDb/trackDb/human/varFreqs.html
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    030cc7d4165ee6b37bd4c9ecfb443fb39ac2468d Mon Nov 3 07:59:26 2025 -0800
    updating mexico biobank track, and related tracks, refs #36259
• src/hg/makeDb/trackDb/human/varFreqs.ra
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    030cc7d4165ee6b37bd4c9ecfb443fb39ac2468d Mon Nov 3 07:59:26 2025 -0800
    updating mexico biobank track, and related tracks, refs #36259
• src/hg/makeDb/trackDb/mouse/mm39/knownGene.alpha.ra
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    c15a59c6ddc7428025519ec671af0a7d4649d7be Thu Oct 30 16:50:26 2025 -0700
    Releasing the new GENCODE Known Gene tracks V49, v49lift37, and VM38, refs #36169 #36167 #36165
• src/hg/makeDb/trackDb/mouse/mm39/knownGene.ra
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    c15a59c6ddc7428025519ec671af0a7d4649d7be Thu Oct 30 16:50:26 2025 -0700
    Releasing the new GENCODE Known Gene tracks V49, v49lift37, and VM38, refs #36169 #36167 #36165
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.gencode.ra
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    410bc23ea2ad4369745b5f80f2f805bd81e201e4 Wed Oct 29 17:41:51 2025 -0700
    Staging 3 All GENCODE tracks, refs #36170 #36168 #36166
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.ra
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    755b77137deee2a6ca9375f3f483bd38b2d4aa08 Wed Oct 29 22:08:13 2025 -0700
    Staging the GENCODE v49/v49lift37/vM38 KnownGene tracks on hgwbeta, refs #36169 #36167 #36165
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    c15a59c6ddc7428025519ec671af0a7d4649d7be Thu Oct 30 16:50:26 2025 -0700
    Releasing the new GENCODE Known Gene tracks V49, v49lift37, and VM38, refs #36169 #36167 #36165
• src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM37.ra
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    410bc23ea2ad4369745b5f80f2f805bd81e201e4 Wed Oct 29 17:41:51 2025 -0700
    Staging 3 All GENCODE tracks, refs #36170 #36168 #36166
• src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM38.ra
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    410bc23ea2ad4369745b5f80f2f805bd81e201e4 Wed Oct 29 17:41:51 2025 -0700
    Staging 3 All GENCODE tracks, refs #36170 #36168 #36166
• src/hg/ratStuff/mafGene/mafGene.c
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    4d80894351b62c4daa432279691a9ef73717d86b Wed Oct 29 08:57:35 2025 -0700
    allow mafGene to use bigMaf and twoBit instead of database
• src/hg/utils/automation/doBlastzChainNet.pl
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    207b18d3428f769b443fb13c35fdfc3af2444936 Wed Oct 29 09:56:14 2025 -0700
    raise CPU limit to 12 for the chain step refs #36546
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    e24709a4ec08445450979b1ba907671aafacc13c Wed Oct 29 09:56:14 2025 -0700
    raise memory limit to 12G for the chain step refs #36546
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    b9326c31b78f235181798c5df993f610db395049 Wed Oct 29 10:59:37 2025 -0700
    raise memory limit to 12G for the chain step refs #36546
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    163e38242d3cd8d004882cfef7a557c9944f59e3 Wed Oct 29 11:24:47 2025 -0700
    default cluster should be hgwdev not obsolete ku refs #36546
• src/hg/utils/automation/doFasTAN.pl
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    64f5aaf6b778b991cadb76a605325760cef3fd71 Fri Oct 31 15:25:00 2025 -0700
    Adding Gene Meyers' FasTAN tandem repeat finder procedure
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    582e3e62507cc29716f2d19896a4ba90d927ce53 Fri Oct 31 15:32:13 2025 -0700
    Correct Myers name spelling
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    39c14307224404251ce37952391cc6b7babea0f7 Fri Oct 31 15:47:31 2025 -0700
    with specific fasTAN.as schema definition
• src/hg/utils/automation/doLongdust.pl
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    f7b43908c094bc252185289d72755b4f55b0f623 Wed Oct 29 16:45:30 2025 -0700
    beginning of an auto script to run the longdust procedure on an assembly
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    6e7e7ed56bc4de54088e81e32068fb14c4dfaac3 Thu Oct 30 11:44:32 2025 -0700
    may be complete at this time
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    a02fe4b3289da1d30d52ba60b769644e9a3d8454 Thu Oct 30 12:51:55 2025 -0700
    correct start up for the bedResult step
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    afb5dbee2256da1db93064340dcf4508aee3955f Fri Oct 31 14:26:41 2025 -0700
    needs to have a db argument and write out a version.txt file
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    b6999503af29255b9956d018763bdc6b46965d36 Fri Oct 31 14:42:29 2025 -0700
    more cleanup
• src/hg/utils/hubCheck/example2.bb
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    06d473692425fe85d92aac2b87a114e04f3158b1 Tue Oct 28 09:40:08 2025 -0700
    It would of course be better to actually check these than skip them, however that could take a long time to do, so just tweaking hubCheck to skip the complex settings like was already done tdbQuery. Users at least will not be nagged about new settings being reported as invalid. fixes #28113
• src/hg/utils/hubCheck/fooy
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    06d473692425fe85d92aac2b87a114e04f3158b1 Tue Oct 28 09:40:08 2025 -0700
    It would of course be better to actually check these than skip them, however that could take a long time to do, so just tweaking hubCheck to skip the complex settings like was already done tdbQuery. Users at least will not be nagged about new settings being reported as invalid. fixes #28113
• src/hg/utils/hubCheck/fuck
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    06d473692425fe85d92aac2b87a114e04f3158b1 Tue Oct 28 09:40:08 2025 -0700
    It would of course be better to actually check these than skip them, however that could take a long time to do, so just tweaking hubCheck to skip the complex settings like was already done tdbQuery. Users at least will not be nagged about new settings being reported as invalid. fixes #28113
• src/hg/utils/hubCheck/hubCheck.c
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    06d473692425fe85d92aac2b87a114e04f3158b1 Tue Oct 28 09:40:08 2025 -0700
    It would of course be better to actually check these than skip them, however that could take a long time to do, so just tweaking hubCheck to skip the complex settings like was already done tdbQuery. Users at least will not be nagged about new settings being reported as invalid. fixes #28113
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    5b70110640deb5caa53d235351efd24f16da013b Tue Oct 28 11:11:53 2025 -0700
    Missing single quote in the warning message, from Maxs helpful code review feedback
• src/hg/utils/hubCheck/hubCheck.c.debugBadFEFFCharsInHubtxtDropBox
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    06d473692425fe85d92aac2b87a114e04f3158b1 Tue Oct 28 09:40:08 2025 -0700
    It would of course be better to actually check these than skip them, however that could take a long time to do, so just tweaking hubCheck to skip the complex settings like was already done tdbQuery. Users at least will not be nagged about new settings being reported as invalid. fixes #28113
• src/hg/utils/hubCheck/hubCheck.c.debugWhyAreSomeSitesSlow
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    06d473692425fe85d92aac2b87a114e04f3158b1 Tue Oct 28 09:40:08 2025 -0700
    It would of course be better to actually check these than skip them, however that could take a long time to do, so just tweaking hubCheck to skip the complex settings like was already done tdbQuery. Users at least will not be nagged about new settings being reported as invalid. fixes #28113
• src/hg/utils/hubCheck/hubCheck.c.rejectedLogLevelAsNotUseful
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    06d473692425fe85d92aac2b87a114e04f3158b1 Tue Oct 28 09:40:08 2025 -0700
    It would of course be better to actually check these than skip them, however that could take a long time to do, so just tweaking hubCheck to skip the complex settings like was already done tdbQuery. Users at least will not be nagged about new settings being reported as invalid. fixes #28113
• src/hg/utils/hubCheck/tracks.tmp
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    06d473692425fe85d92aac2b87a114e04f3158b1 Tue Oct 28 09:40:08 2025 -0700
    It would of course be better to actually check these than skip them, however that could take a long time to do, so just tweaking hubCheck to skip the complex settings like was already done tdbQuery. Users at least will not be nagged about new settings being reported as invalid. fixes #28113
• src/hg/utils/otto/genArk/pushFromBetaToRR.sh
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    773fabd8bcd1acc5bdcc5dc27ef7fba3c8050c76 Tue Oct 28 11:13:34 2025 -0700
    script to use by cluster admin to push out from hgwbeta to the RR refs #35575
• src/hg/utils/otto/genArk/pushNewOnes.sh
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    1be49dce000ce111f3d1a81b4aef086e6d579f4c Mon Oct 27 16:43:09 2025 -0700
    reset the scripts to only push from hgwdev to hgwbeta refs #35575
• src/hg/utils/otto/genArk/quickLiftNew.sh
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    1be49dce000ce111f3d1a81b4aef086e6d579f4c Mon Oct 27 16:43:09 2025 -0700
    reset the scripts to only push from hgwdev to hgwbeta refs #35575
• src/hg/utils/otto/genArk/whatIsNew.sh
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    1be49dce000ce111f3d1a81b4aef086e6d579f4c Mon Oct 27 16:43:09 2025 -0700
    reset the scripts to only push from hgwdev to hgwbeta refs #35575
• src/hg/utils/otto/genCC/doGenCC.py
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    06cdca9abaf78e2d0d4c0b3b1f781be687cbc31b Tue Oct 28 09:43:24 2025 -0700
    Swapping the colors of Definitive and Strong as Sarah Hunt mentioned they are wrong in an email, refs #36469
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    7896c8bb187a552b4eb7ea3781d3f02ffba32104 Tue Oct 28 09:53:46 2025 -0700
    Used the wrong shebang, refs #36469
• src/hg/utils/otto/panelApp/updatePanelApp
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    ae63ce55185746c5fabb2ead8cc20215faada36d Mon Nov 3 08:03:14 2025 -0800
    adding ancient dna track, refs #36592
• src/hg/utils/otto/pubtatorDbSnp/doUpdate.sh
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    c457ec09c7a040b0fd9e0bd2b52587593f07fa64 Thu Sep 11 08:40:28 2025 -0700
    Better pubtator update
• src/hg/utils/tdbQuery/tdbQuery.c
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    06d473692425fe85d92aac2b87a114e04f3158b1 Tue Oct 28 09:40:08 2025 -0700
    It would of course be better to actually check these than skip them, however that could take a long time to do, so just tweaking hubCheck to skip the complex settings like was already done tdbQuery. Users at least will not be nagged about new settings being reported as invalid. fixes #28113
• src/inc/common.mk
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    030cc7d4165ee6b37bd4c9ecfb443fb39ac2468d Mon Nov 3 07:59:26 2025 -0800
    updating mexico biobank track, and related tracks, refs #36259
• src/lib/common.c
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    ae63ce55185746c5fabb2ead8cc20215faada36d Mon Nov 3 08:03:14 2025 -0800
    adding ancient dna track, refs #36592
• src/product/ex.hg.conf
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    c1656450f6173c484473f04c6f176f8d64ff9b9c Wed Oct 29 16:54:27 2025 -0700
    Documenting new hg.conf settings, refs #36533
• src/product/installer/browserSetup.sh
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    848a8115f69b649893ca9af7b6a689d99c4dd0a8 Fri Oct 31 01:52:08 2025 -0700
    trying to install special rhel repos, no ticket yet, ML from Susanne Kandolf
• src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed
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    9ec8ecc35be16510fa842e1c47f9e821d0e90f0f Fri Oct 31 02:30:41 2025 -0700
    adding a few suggested changes from Galaxy, see https://github.com/bioconda/bioconda-recipes/blob/master/recipes/ucsc-mafgene/0001-include.patch, no redmine

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