All File Changes

v491_preview to v491_preview2 (2025-11-10 to 2025-11-17) v491

• confs/asia.hg.conf
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    6e27a55f81bd2868c8f8869b6e852678cb956da4 Sun Nov 16 01:11:21 2025 -0800
    Installing updated hg.conf files from UCSC servers
• confs/euro.hg.conf
  • lines changed 13, context: html, text, full: html, text
    6e27a55f81bd2868c8f8869b6e852678cb956da4 Sun Nov 16 01:11:21 2025 -0800
    Installing updated hg.conf files from UCSC servers
• confs/hgwbeta.hg.conf
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    6e27a55f81bd2868c8f8869b6e852678cb956da4 Sun Nov 16 01:11:21 2025 -0800
    Installing updated hg.conf files from UCSC servers
• confs/hgwdev.hg.conf
  • lines changed 4, context: html, text, full: html, text
    6e27a55f81bd2868c8f8869b6e852678cb956da4 Sun Nov 16 01:11:21 2025 -0800
    Installing updated hg.conf files from UCSC servers
• confs/rr.hg.conf
  • lines changed 13, context: html, text, full: html, text
    6e27a55f81bd2868c8f8869b6e852678cb956da4 Sun Nov 16 01:11:21 2025 -0800
    Installing updated hg.conf files from UCSC servers
• src/hg/hgBlat/hgBlat.c
  • lines changed 12, context: html, text, full: html, text
    df22e780c9e8a304b59e6d26bc34e0f729e33e45 Thu Nov 13 17:07:54 2025 -0800
    Adds a checkbox that turns on rearrangement mode automatically for all CTs generated by hgBlat. This is one of the main features of the ticket, but not all desired features. fixes #32857
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    6670ef9fcc219c28fed26eb4a4b327c32ed434fe Fri Nov 14 11:50:42 2025 -0800
    Improves the GUI on hgBlat page with popup icon suggestion from Max. refs #32857
• src/hg/hgTracks/pubsTracks.c
  • lines changed 6, context: html, text, full: html, text
    8ccd7f957e100e1a7e719fcc1a75584b534ea744 Fri Nov 14 14:52:32 2025 -0800
    fix problem with quickLift refs #36702
• src/hg/hgTracks/simpleTracks.c
  • lines changed 2, context: html, text, full: html, text
    a18667f760788b11c048f407bbeb7aaf7b4306e4 Fri Nov 14 08:45:08 2025 -0800
    fix a problem with highlight item when displaying a bigBed 3 refs #36673
• src/hg/hgc/hgc.c
  • lines changed 8, context: html, text, full: html, text
    df22e780c9e8a304b59e6d26bc34e0f729e33e45 Thu Nov 13 17:07:54 2025 -0800
    Adds a checkbox that turns on rearrangement mode automatically for all CTs generated by hgBlat. This is one of the main features of the ticket, but not all desired features. fixes #32857
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 27, context: html, text, full: html, text
    846b16c08f03187d48734d7a860a8d1ff8528570 Fri Nov 14 18:53:15 2025 -0800
    Releasing and announcing the Varaico tracks, refs #36612
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    75643f700f21c6f707600cda76f84106f33a6e53 Mon Nov 17 15:45:46 2025 -0800
    Making some edits for the release 2 Varaico track announcement, refs #36612
• src/hg/htdocs/images/encode4cCREs.png
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    f218966d365c540769dea62fd1dc20266e61f412 Fri Nov 14 15:49:58 2025 -0800
    Updating ENCODE cCREs track based on collaborator feedback, refs #34109
• src/hg/htdocs/images/newsArchImages/varaicoRelease2.png
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    846b16c08f03187d48734d7a860a8d1ff8528570 Fri Nov 14 18:53:15 2025 -0800
    Releasing and announcing the Varaico tracks, refs #36612
• src/hg/htdocs/inc/download.topbar.html
  • lines changed 18, context: html, text, full: html, text
    36bb74ca50afcf9f7c1764043ed6d099769c8d3a Thu Nov 13 12:12:11 2025 -0800
    This file came up in the static doc cron, and we decided to drop it, No RM
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    846b16c08f03187d48734d7a860a8d1ff8528570 Fri Nov 14 18:53:15 2025 -0800
    Releasing and announcing the Varaico tracks, refs #36612
• src/hg/htdocs/robots.rr.txt
  • lines changed 2, context: html, text, full: html, text
    40ce56ee9a7c7f56b40aea9edcf9f2ca1935d478 Thu Nov 13 14:50:41 2025 -0800
    Removing hgsids from the block since google should auto recognize session IDs, and disallowing the trash directory from everyone.
• src/hg/htdocs/store.html
  • lines changed 376, context: html, text, full: html, text
    999f5e62c138b09e9713aa3bea25ca32684aa74a Fri Oct 31 15:45:54 2025 -0700
    Quick first draft of new store static page
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    5b7348689a625afac34b501ce1d15491d8008bec Fri Nov 14 09:34:12 2025 -0800
    EULA update
• src/hg/htdocs/store/UCSC_GB_EULA.pdf
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    4efde720dcef3d4be6fe58ca6baff9f0ef46a51b Fri Nov 14 09:27:06 2025 -0800
    Adding EULA to the new store static page
• src/hg/hubApi/liftOver.c
  • lines changed 19, context: html, text, full: html, text
    054cf0f3a8507c04aecde986ecee4f2979b8d4f3 Mon Nov 10 15:00:32 2025 -0800
    Make listExisting endpoint to hubApi/liftOver respect fromGenome and toGenome arguments, taking precedence over the filter argument. If both fromGenome and toGenome arguments are present they are ANDed together
• src/hg/hubApi/tests/expected/bigDbSnp.gz
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    8c01fb3679ac642e37aaaea705a5365e41f6f013 Thu Nov 13 15:52:59 2025 -0800
    updates to hubApi makefile and expected outputs, refs #36463
• src/hg/hubApi/tests/expected/err53.gz
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    8c01fb3679ac642e37aaaea705a5365e41f6f013 Thu Nov 13 15:52:59 2025 -0800
    updates to hubApi makefile and expected outputs, refs #36463
• src/hg/hubApi/tests/expected/list02.gz
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    8c01fb3679ac642e37aaaea705a5365e41f6f013 Thu Nov 13 15:52:59 2025 -0800
    updates to hubApi makefile and expected outputs, refs #36463
• src/hg/hubApi/tests/expected/list03.gz
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    8c01fb3679ac642e37aaaea705a5365e41f6f013 Thu Nov 13 15:52:59 2025 -0800
    updates to hubApi makefile and expected outputs, refs #36463
• src/hg/hubApi/tests/expected/list08.gz
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    8c01fb3679ac642e37aaaea705a5365e41f6f013 Thu Nov 13 15:52:59 2025 -0800
    updates to hubApi makefile and expected outputs, refs #36463
• src/hg/hubApi/tests/expected/list09.gz
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    8c01fb3679ac642e37aaaea705a5365e41f6f013 Thu Nov 13 15:52:59 2025 -0800
    updates to hubApi makefile and expected outputs, refs #36463
• src/hg/hubApi/tests/expected/list20.gz
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    8c01fb3679ac642e37aaaea705a5365e41f6f013 Thu Nov 13 15:52:59 2025 -0800
    updates to hubApi makefile and expected outputs, refs #36463
• src/hg/hubApi/tests/expected/list22.gz
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    8c01fb3679ac642e37aaaea705a5365e41f6f013 Thu Nov 13 15:52:59 2025 -0800
    updates to hubApi makefile and expected outputs, refs #36463
• src/hg/hubApi/tests/expected/list23.gz
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    8c01fb3679ac642e37aaaea705a5365e41f6f013 Thu Nov 13 15:52:59 2025 -0800
    updates to hubApi makefile and expected outputs, refs #36463
• src/hg/hubApi/tests/expected/list25.gz
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    8c01fb3679ac642e37aaaea705a5365e41f6f013 Thu Nov 13 15:52:59 2025 -0800
    updates to hubApi makefile and expected outputs, refs #36463
• src/hg/hubApi/tests/expected/list27.gz
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    8c01fb3679ac642e37aaaea705a5365e41f6f013 Thu Nov 13 15:52:59 2025 -0800
    updates to hubApi makefile and expected outputs, refs #36463
• src/hg/hubApi/tests/expected/list28.gz
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    8c01fb3679ac642e37aaaea705a5365e41f6f013 Thu Nov 13 15:52:59 2025 -0800
    updates to hubApi makefile and expected outputs, refs #36463
• src/hg/hubApi/tests/expected/list29.gz
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    8c01fb3679ac642e37aaaea705a5365e41f6f013 Thu Nov 13 15:52:59 2025 -0800
    updates to hubApi makefile and expected outputs, refs #36463
• src/hg/hubApi/tests/expected/list32.gz
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    8c01fb3679ac642e37aaaea705a5365e41f6f013 Thu Nov 13 15:52:59 2025 -0800
    updates to hubApi makefile and expected outputs, refs #36463
• src/hg/hubApi/tests/expected/schema04.gz
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    8c01fb3679ac642e37aaaea705a5365e41f6f013 Thu Nov 13 15:52:59 2025 -0800
    updates to hubApi makefile and expected outputs, refs #36463
• src/hg/hubApi/tests/expected/schema08.gz
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    8c01fb3679ac642e37aaaea705a5365e41f6f013 Thu Nov 13 15:52:59 2025 -0800
    updates to hubApi makefile and expected outputs, refs #36463
• src/hg/hubApi/tests/expected/schema09.gz
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    8c01fb3679ac642e37aaaea705a5365e41f6f013 Thu Nov 13 15:52:59 2025 -0800
    updates to hubApi makefile and expected outputs, refs #36463
• src/hg/hubApi/tests/expected/test14.gz
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    8c01fb3679ac642e37aaaea705a5365e41f6f013 Thu Nov 13 15:52:59 2025 -0800
    updates to hubApi makefile and expected outputs, refs #36463
• src/hg/hubApi/tests/expected/test15.gz
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    8c01fb3679ac642e37aaaea705a5365e41f6f013 Thu Nov 13 15:52:59 2025 -0800
    updates to hubApi makefile and expected outputs, refs #36463
• src/hg/hubApi/tests/expected/test16.gz
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    8c01fb3679ac642e37aaaea705a5365e41f6f013 Thu Nov 13 15:52:59 2025 -0800
    updates to hubApi makefile and expected outputs, refs #36463
• src/hg/hubApi/tests/makefile
  • lines changed 17, context: html, text, full: html, text
    8c01fb3679ac642e37aaaea705a5365e41f6f013 Thu Nov 13 15:52:59 2025 -0800
    updates to hubApi makefile and expected outputs, refs #36463
• src/hg/js/igvFileHelper.js
  • lines changed 5, context: html, text, full: html, text
    5d6dbfb0879ab769c41f832feb2a1a83415ea0f5 Fri Nov 14 07:12:22 2025 -0800
    avoid error message when igv button is not found, refs #36673
• src/hg/lib/cartTrackDb.c
  • lines changed 2, context: html, text, full: html, text
    56e0ec54f202496d46891c2760b01c556b4f75c9 Mon Nov 10 12:07:24 2025 -0800
    We added super tracks to the trackDb list when hashing up all the tracks and groups, so don't call hubCollectTracks again when finding searchable tracks because the track db list got all rearranged and it now points to a stale copy, refs #36640
• src/hg/lib/hgFind.c
  • lines changed 2, context: html, text, full: html, text
    56e0ec54f202496d46891c2760b01c556b4f75c9 Mon Nov 10 12:07:24 2025 -0800
    We added super tracks to the trackDb list when hashing up all the tracks and groups, so don't call hubCollectTracks again when finding searchable tracks because the track db list got all rearranged and it now points to a stale copy, refs #36640
• src/hg/lib/trackHub.c
  • lines changed 1, context: html, text, full: html, text
    8ccd7f957e100e1a7e719fcc1a75584b534ea744 Fri Nov 14 14:52:32 2025 -0800
    fix problem with quickLift refs #36702
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
  • lines changed 3, context: html, text, full: html, text
    1f7d97621a6e5fd65c1d5330ad3034e342fe0af4 Fri Nov 14 13:11:08 2025 -0800
    adding a couple per user requests refs #29545
• src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv
  • lines changed 6, context: html, text, full: html, text
    1f7d97621a6e5fd65c1d5330ad3034e342fe0af4 Fri Nov 14 13:11:08 2025 -0800
    adding a couple per user requests refs #29545
• src/hg/makeDb/trackDb/human/decipher.ra
  • lines changed 11, context: html, text, full: html, text
    1ba5b0add20a55b2d31bd504f6aa88a339431e5b Wed Nov 12 15:27:10 2025 -0800
    Removing the DDG2P track from the decipher container. Updating the decipher track description page since it doesn't have DDG2P. Making the G2P track public, refs #36529 #36469
• src/hg/makeDb/trackDb/human/decipherContainer.html
  • lines changed 53, context: html, text, full: html, text
    1ba5b0add20a55b2d31bd504f6aa88a339431e5b Wed Nov 12 15:27:10 2025 -0800
    Removing the DDG2P track from the decipher container. Updating the decipher track description page since it doesn't have DDG2P. Making the G2P track public, refs #36529 #36469
• src/hg/makeDb/trackDb/human/g2p.html
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    3c1a5b0ba4e9a44e2d62b7dfbd521b813e2e9305 Mon Nov 10 16:38:58 2025 -0800
    Updating the colors on the track description page to reflect the colors that are now used in the track, refs #36469
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    991d6b875ab1bb832434ca3f939ff77de3d6d786 Thu Nov 13 14:59:51 2025 -0800
    Updating the track descripiton page since the g2p track isn't just about DDG2P, refs #36469
• src/hg/makeDb/trackDb/human/hg38/cCREsSuper.html
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    f218966d365c540769dea62fd1dc20266e61f412 Fri Nov 14 15:49:58 2025 -0800
    Updating ENCODE cCREs track based on collaborator feedback, refs #34109
• src/hg/makeDb/trackDb/human/hg38/coreCollection.html
  • lines changed 3, context: html, text, full: html, text
    f218966d365c540769dea62fd1dc20266e61f412 Fri Nov 14 15:49:58 2025 -0800
    Updating ENCODE cCREs track based on collaborator feedback, refs #34109
• src/hg/makeDb/trackDb/human/hg38/encode.cCREs.override.ra
  • lines changed 2, context: html, text, full: html, text
    f218966d365c540769dea62fd1dc20266e61f412 Fri Nov 14 15:49:58 2025 -0800
    Updating ENCODE cCREs track based on collaborator feedback, refs #34109
• src/hg/makeDb/trackDb/human/hg38/encode4.ccres.ra
  • lines changed 194, context: html, text, full: html, text
    f218966d365c540769dea62fd1dc20266e61f412 Fri Nov 14 15:49:58 2025 -0800
    Updating ENCODE cCREs track based on collaborator feedback, refs #34109
• src/hg/makeDb/trackDb/human/phasedVars.ra
  • lines changed 50, context: html, text, full: html, text
    172029e2893855d715acbfb8c69f30380a5c45ac Fri Nov 14 08:34:01 2025 -0800
    creating phased variants track,refs #36642
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    1ba5b0add20a55b2d31bd504f6aa88a339431e5b Wed Nov 12 15:27:10 2025 -0800
    Removing the DDG2P track from the decipher container. Updating the decipher track description page since it doesn't have DDG2P. Making the G2P track public, refs #36529 #36469
  • lines changed 1, context: html, text, full: html, text
    172029e2893855d715acbfb8c69f30380a5c45ac Fri Nov 14 08:34:01 2025 -0800
    creating phased variants track,refs #36642
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    846b16c08f03187d48734d7a860a8d1ff8528570 Fri Nov 14 18:53:15 2025 -0800
    Releasing and announcing the Varaico tracks, refs #36612
• src/hg/makeDb/trackDb/human/varFreqs.html
  • lines changed 36, context: html, text, full: html, text
    5ea5925226bd7ccbfcdda2fe987f7fff6122dabf Mon Nov 10 16:42:14 2025 -0800
    Moving the Simons Genome Diversity track next to the Mexico Biobank track since those are the only two available for hg19. refs #36642
  • lines changed 99, context: html, text, full: html, text
    f7758c83e2610580346c95832cb4624aa9fae0fd Mon Nov 10 17:18:01 2025 -0800
    Making each list item less than 100 character. Fixing special characters using HTML entiites. Adding a missing URL. Removing duplicate entires, refs #36642
  • lines changed 26, context: html, text, full: html, text
    616cfce6b21924d958892448c83b7701f715416b Tue Nov 11 14:17:47 2025 -0800
    Fixing other special characters. refs #36642
  • lines changed 31, context: html, text, full: html, text
    c3fee0a7bfcd442f7e2b148b594c8829a3ac0094 Tue Nov 11 15:34:37 2025 -0800
    Bolding the names of the tracks on the track description page. Mentioning which tracks are only available for which assemblies. refs #36642
  • lines changed 1, context: html, text, full: html, text
    8382ac50957fae1cb423ee002b1e07fdfd0be957 Wed Nov 12 12:10:51 2025 -0800
    Fixing a link to the HGDP website/paper, refs #36642
• src/hg/makeDb/trackDb/human/varFreqs.ra
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    cca998bda09944c623133471d226e46f83bb0eb3 Wed Nov 12 12:11:32 2025 -0800
    Updating the shortLabel for teh Variant Frequencies supertrack, refs #36642
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    caa794e0cc58eb9996fd610aefffbefdb2df4996 Fri Nov 14 05:37:02 2025 -0800
    adding aou test to varFreqs track, refs #36642
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    172029e2893855d715acbfb8c69f30380a5c45ac Fri Nov 14 08:34:01 2025 -0800
    creating phased variants track,refs #36642
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    e78d4f46d0c2a3d1e3b65e768dcd160dbd8cd894 Mon Nov 17 09:57:38 2025 -0800
    fixing dupe
• src/hg/utils/otto/genArk/devList.sh
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    fe64f9f342b7d4dd802dcedcf140072d7c90c5df Fri Nov 14 13:18:28 2025 -0800
    adding the gbdb/*/liftOver files to the otto push list refs #35575
• src/hg/utils/otto/genArk/gbDbGenArkList.sh
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    fe64f9f342b7d4dd802dcedcf140072d7c90c5df Fri Nov 14 13:18:28 2025 -0800
    adding the gbdb/*/liftOver files to the otto push list refs #35575
• src/product/installer/browserSetup.sh
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    0779bf44084776ce790a66ca1ceca29deec9ce82 Fri Nov 14 11:55:52 2025 -0800
    fixing gbic script error, email from David Hoover

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• files changed: 72