All File Changes

v492_base to v493_preview (2025-12-15 to 2026-01-12) v493

• confs/asia.hg.conf
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    b08d682ae70813b2e919850d267d8f85946278f3 Sun Dec 21 01:11:21 2025 -0800
    Installing updated hg.conf files from UCSC servers
• confs/euro.hg.conf
  • lines changed 1, context: html, text, full: html, text
    b08d682ae70813b2e919850d267d8f85946278f3 Sun Dec 21 01:11:21 2025 -0800
    Installing updated hg.conf files from UCSC servers
• confs/hgwbeta.hg.conf
  • lines changed 2, context: html, text, full: html, text
    b08d682ae70813b2e919850d267d8f85946278f3 Sun Dec 21 01:11:21 2025 -0800
    Installing updated hg.conf files from UCSC servers
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    4c014b45c54d2754938d2f8a2f3a1e5c070ca673 Sun Jan 11 01:11:15 2026 -0800
    Installing updated hg.conf files from UCSC servers
• confs/hgwdev.hg.conf
  • lines changed 4, context: html, text, full: html, text
    4c014b45c54d2754938d2f8a2f3a1e5c070ca673 Sun Jan 11 01:11:15 2026 -0800
    Installing updated hg.conf files from UCSC servers
• confs/rr.hg.conf
  • lines changed 1, context: html, text, full: html, text
    b08d682ae70813b2e919850d267d8f85946278f3 Sun Dec 21 01:11:21 2025 -0800
    Installing updated hg.conf files from UCSC servers
• src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html
  • lines changed 23, context: html, text, full: html, text
    dcb3ea8c14f463b10d2e609ea919f8fb281a88c7 Mon Dec 15 13:21:07 2025 -0800
    Adding WUSTL ADGC7_Y2_ colE and colF, comment out %% F -adding pushes timeline beyond start of Year5
  • lines changed 39, context: html, text, full: html, text
    8d712b6c3c3fa0c5e46bc620f6e5900de699fe23 Mon Dec 15 19:29:36 2025 -0800
    Rearranging WUSTL milestones to cluster related data submissions (i.e., all mouse lines 17-22 data pushes bundled together, to display across sequential Q2,Q3,Q4).
  • lines changed 1, context: html, text, full: html, text
    8dab7e56600ef637c73c23cbd03bc1994f810539 Tue Dec 16 09:50:25 2025 -0800
    Adding name tag for ADGC7 section
  • lines changed 18, context: html, text, full: html, text
    f59128bd844a8b30a85c7e242cd68cd2773ae9f2 Tue Dec 16 14:08:34 2025 -0800
    SING Year2 milestones added.
  • lines changed 17, context: html, text, full: html, text
    84383e12e816626f6f19f56aeb9c59ae430bddc7 Thu Dec 18 13:47:51 2025 -0800
    Shortening SINGs milestone verbiage [ADGC6_Y2_E_22, refers to Y2 spreadsheet, colE,row22 to see original wording]
  • lines changed 3, context: html, text, full: html, text
    d341738a94af1c3bd941e6b068333fa1694f8839 Tue Dec 30 13:42:38 2025 -0800
    Aligning 2025Q4 milestones to Dec 31st 2025 (vs Jan 1st 2026)
  • lines changed 4, context: html, text, full: html, text
    9f531cbcbc784c0b4e5b294b97c5dc94eab0c9cc Tue Dec 30 13:45:25 2025 -0800
    Aligning 2026Q4 to Dec 31st (vs 2027 Jan 1st)
  • lines changed 67, context: html, text, full: html, text
    ab409f6a8ecc9fbcf43f914f6b74eed858f4097b Tue Dec 30 13:51:13 2025 -0800
    Aligning end Q1 to 03-31 rather than 04-01 (April 1st) for milestones
• src/hg/hgCustom/hgCustom.c
  • lines changed 15, context: html, text, full: html, text
    848d9a9fb008157a87bf7e4d69a4e50f66b69798 Mon Jan 12 06:22:38 2026 -0800
    allowing changes to custom tracks even when uploaded by URL,, refs #35492
• src/hg/hgTracks/bigBedTrack.c
  • lines changed 9, context: html, text, full: html, text
    14b9ad8df1f99ac5300f52cda10ce8066c9289c6 Wed Dec 17 12:40:40 2025 -0800
    use the bigBed header for the number of bed fields if it is NOT specified in trackDb, otherwise use the number in the trackDb type.
• src/hg/hgTracks/config.c
  • lines changed 1, context: html, text, full: html, text
    3162d1fec3dffece6f608f15eb6d46f6c46f7436 Fri Dec 5 16:13:05 2025 -0800
    Working version of custom track group 'visible' that is at the top of the group list and has all the currently visible tracks, refs #36609
• src/hg/hgTracks/hgTracks.c
  • lines changed 109, context: html, text, full: html, text
    3162d1fec3dffece6f608f15eb6d46f6c46f7436 Fri Dec 5 16:13:05 2025 -0800
    Working version of custom track group 'visible' that is at the top of the group list and has all the currently visible tracks, refs #36609
  • lines changed 1, context: html, text, full: html, text
    54b5b867f2722552874fded91f2dc25cf92f2823 Mon Dec 15 15:53:04 2025 -0800
    Fix typo leftover after merge
  • lines changed 1, context: html, text, full: html, text
    487b4ab002819d30ffe4831a2137653f6094cbbf Tue Dec 16 08:24:43 2025 -0800
    make disconnect button appear on hub error, refs #36791
  • lines changed 14, context: html, text, full: html, text
    7f7a44a19ff9a54dbaf894365d30e394e802024b Wed Dec 17 12:15:31 2025 -0800
    Do not show 'visible tracks' group unless there are more than 32 top level tracks, refs Hiram complaint
  • lines changed 5, context: html, text, full: html, text
    fae41a099c878e826bbb0b8e4f26d3381262dc9b Mon Jan 12 05:00:25 2026 -0800
    making hub error message prettier, refs #36916
  • lines changed 1, context: html, text, full: html, text
    64f0134fda55184221ebae340f9cf9c4ecc7a5a1 Mon Jan 12 05:16:58 2026 -0800
    small note to hub errors, refs #36916
• src/hg/hgTracks/hgTracks.h
  • lines changed 6, context: html, text, full: html, text
    3162d1fec3dffece6f608f15eb6d46f6c46f7436 Fri Dec 5 16:13:05 2025 -0800
    Working version of custom track group 'visible' that is at the top of the group list and has all the currently visible tracks, refs #36609
• src/hg/hgTracks/hicTrack.c
  • lines changed 22, context: html, text, full: html, text
    34f380bfb0b4003a23fe2e00be6bdac6af326cda Mon Dec 15 15:20:13 2025 -0800
    Adding hicArcLimit and hicArcLimitEnabled settings to let people prevent excessive arc counts from overwhelming a Hi-C display with data, refs #36774
  • lines changed 33, context: html, text, full: html, text
    57aba7b8fb23d9bdbeceb665a001452e6d7a6b99 Thu Jan 8 00:37:48 2026 -0800
    An attempt at better auto-scaling for Hi-C colors in arc mode, refs #36774
• src/hg/hgTracks/searchTracks.c
  • lines changed 1, context: html, text, full: html, text
    3162d1fec3dffece6f608f15eb6d46f6c46f7436 Fri Dec 5 16:13:05 2025 -0800
    Working version of custom track group 'visible' that is at the top of the group list and has all the currently visible tracks, refs #36609
• src/hg/hgVai/hgVai.c
  • lines changed 24, context: html, text, full: html, text
    63890999edbfdac428544f159a33e503618ca7f8 Wed Jan 7 13:56:43 2026 -0800
    Add support for vai.pl to accept a GenArk assembly accession as db, and for hgVai to accept a geneTrack without the hub_number_ prefix when db is a hub.
• src/hg/hgc/bigBedClick.c
  • lines changed 1, context: html, text, full: html, text
    14b9ad8df1f99ac5300f52cda10ce8066c9289c6 Wed Dec 17 12:40:40 2025 -0800
    use the bigBed header for the number of bed fields if it is NOT specified in trackDb, otherwise use the number in the trackDb type.
  • lines changed 8, context: html, text, full: html, text
    1b08e1ab8215cbd95cc76f7bdf1feff353815daa Sun Jan 11 09:19:06 2026 -0800
    remove warning when definedFieldCount in bigBed headers is not the same as the value in the trackDb statement.
• src/hg/hgc/hgc.c
  • lines changed 27, context: html, text, full: html, text
    f7f5b164d6bacfd8da9b8f7772497ef971f2b0f8 Fri Dec 19 11:37:31 2025 -0800
    Add options -chrom -start -end -range -bed -positions -udcDir to bigMafToMaf. Adds -positions to bigBedToBed. Moved parsePosition and parseRange routines into common.c so they could be shared with these and other utilities. -range has one 0-based start on commandline. -positions is a file with a list of 1-based starts. fixes #28109
• src/hg/htdocs/cite.html
  • lines changed 2, context: html, text, full: html, text
    9aca47b7143b576d084806a387fae54a16cf76f6 Fri Jan 9 14:11:54 2026 -0800
    Updating our latest publication, refs #36899
  • lines changed 6, context: html, text, full: html, text
    1c01e2809ff01dfe507a9977be2b5f3682133a4a Fri Jan 9 15:26:16 2026 -0800
    Forgot one spot to add the new publication, apparently it goes in 3 different places.
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 44, context: html, text, full: html, text
    4a87b1269ea7ed40e2904c15bafda61f62d4f567 Wed Jan 7 11:33:28 2026 -0800
    Adding information about include statements to hub docs, refs #20909
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    3c1e958a16b6d79f859d0f51368d767acce0457c Wed Jan 7 19:49:26 2026 -0800
    Added some text and chromAlias/chromAuthority link to help pages, refs #33014
  • lines changed 10, context: html, text, full: html, text
    dd05936cd30e6438d5085146d9d843047739f63e Fri Jan 9 16:00:19 2026 -0800
    Updating and adding extraIndex and searchIndex documentation to the track hubs help page, refs #19337
• src/hg/htdocs/goldenPath/help/hubQuickStart.html
  • lines changed 7, context: html, text, full: html, text
    3c1e958a16b6d79f859d0f51368d767acce0457c Wed Jan 7 19:49:26 2026 -0800
    Added some text and chromAlias/chromAuthority link to help pages, refs #33014
• src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html
  • lines changed 6, context: html, text, full: html, text
    3c1e958a16b6d79f859d0f51368d767acce0457c Wed Jan 7 19:49:26 2026 -0800
    Added some text and chromAlias/chromAuthority link to help pages, refs #33014
• src/hg/htdocs/goldenPath/help/mirrorManual.html
  • lines changed 17, context: html, text, full: html, text
    14712b4b8359f75ff22425058919a5983443dc59 Mon Dec 15 13:07:53 2025 -0800
    documenting captcha exceptions, no redmine, email from Hiram
• src/hg/htdocs/goldenPath/help/trackDb/changes.html
  • lines changed 6, context: html, text, full: html, text
    1c07e6e9103123809e420560f2ebf370dde996ea Sun Jan 11 21:24:24 2026 -0800
    Docs for the hicArcLimit and hicArcLimitEnabled setings, which control how many arcs are actually drawn in arc mode, refs #36774
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
  • lines changed 8, context: html, text, full: html, text
    1c07e6e9103123809e420560f2ebf370dde996ea Sun Jan 11 21:24:24 2026 -0800
    Docs for the hicArcLimit and hicArcLimitEnabled setings, which control how many arcs are actually drawn in arc mode, refs #36774
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html
  • lines changed 20, context: html, text, full: html, text
    c7c977ef035c3ea2a45e3394f5d0fe9c1ed0739b Wed Dec 24 10:56:26 2025 -0800
    adding bulleted list of ra stanza specification, refs #35619
  • lines changed 7, context: html, text, full: html, text
    4a87b1269ea7ed40e2904c15bafda61f62d4f567 Wed Jan 7 11:33:28 2026 -0800
    Adding information about include statements to hub docs, refs #20909
  • lines changed 6, context: html, text, full: html, text
    1c07e6e9103123809e420560f2ebf370dde996ea Sun Jan 11 21:24:24 2026 -0800
    Docs for the hicArcLimit and hicArcLimitEnabled setings, which control how many arcs are actually drawn in arc mode, refs #36774
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 6, context: html, text, full: html, text
    f06a9447a309d1f7084c87f0d65290a0fba435d9 Sat Jan 10 17:34:05 2026 -0800
    Updating the doc to say that mean+whiskers is the default for windowingFunction, refs #27966
  • lines changed 21, context: html, text, full: html, text
    1c07e6e9103123809e420560f2ebf370dde996ea Sun Jan 11 21:24:24 2026 -0800
    Docs for the hicArcLimit and hicArcLimitEnabled setings, which control how many arcs are actually drawn in arc mode, refs #36774
  • lines changed 12, context: html, text, full: html, text
    f85252e8231a8fef12bfcc37a3a6c20a7e1f9e19 Mon Jan 12 10:03:34 2026 -0800
    Adjustments to the default hicArcLimit value, refs #36774
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 22, context: html, text, full: html, text
    fb0974b26c4adb2ed270215ee30899f13a5fced4 Thu Dec 18 16:41:37 2025 -0800
    adding announcement for ancient hominids tracks, refs #36586
  • lines changed 150, context: html, text, full: html, text
    73c100526aa0bad1111e65bc746734dc3b859796 Mon Dec 22 14:45:20 2025 -0800
    Releasing and announcing the EVA Release 8 tracks, refs #36512
  • lines changed 3, context: html, text, full: html, text
    7151483319835fd736f3fbe0966c8f1476298d04 Tue Dec 23 12:36:27 2025 -0800
    correcting title for ancient hominids announcement, adding link to announcement from home page, refs #36586
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 9, context: html, text, full: html, text
    9aca47b7143b576d084806a387fae54a16cf76f6 Fri Jan 9 14:11:54 2026 -0800
    Updating our latest publication, refs #36899
• src/hg/htdocs/images/newsArchImages/ancientHominids.png
  • lines changed 0, context: html, text, full: html, text
    fb0974b26c4adb2ed270215ee30899f13a5fced4 Thu Dec 18 16:41:37 2025 -0800
    adding announcement for ancient hominids tracks, refs #36586
• src/hg/htdocs/images/tutorialImages/gif/hgCustomStep1.gif
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    90314789a66b74d3daab9c15c7b76e7ce52ac9c3 Tue Dec 16 14:30:40 2025 -0800
    Adding the first gif for the markdown tutorial, refs #34354
• src/hg/htdocs/images/tutorialImages/gif/hgCustomStep2.gif
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    26499ff398107a6638cd998562b04789d18828c4 Tue Dec 16 15:15:32 2025 -0800
    Adding the rest of the GIFs for the hgCustom markdown tutorial, refs #34354
• src/hg/htdocs/images/tutorialImages/gif/hgCustomStep3.gif
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    26499ff398107a6638cd998562b04789d18828c4 Tue Dec 16 15:15:32 2025 -0800
    Adding the rest of the GIFs for the hgCustom markdown tutorial, refs #34354
• src/hg/htdocs/images/tutorialImages/gif/hgCustomStep4.gif
  • lines changed 0, context: html, text, full: html, text
    26499ff398107a6638cd998562b04789d18828c4 Tue Dec 16 15:15:32 2025 -0800
    Adding the rest of the GIFs for the hgCustom markdown tutorial, refs #34354
• src/hg/htdocs/images/tutorialImages/gif/hgCustomStep5.gif
  • lines changed 0, context: html, text, full: html, text
    26499ff398107a6638cd998562b04789d18828c4 Tue Dec 16 15:15:32 2025 -0800
    Adding the rest of the GIFs for the hgCustom markdown tutorial, refs #34354
• src/hg/htdocs/images/tutorialImages/hgCustomAnnotated_pt1.png
  • lines changed 0, context: html, text, full: html, text
    2c3d558fb966d23257d3760a8e76080de47063c0 Tue Dec 16 13:57:59 2025 -0800
    Adding the annotated hgCustom images for the markdown tutorial, refs #34354
• src/hg/htdocs/images/tutorialImages/hgCustomAnnotated_pt2.png
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    2c3d558fb966d23257d3760a8e76080de47063c0 Tue Dec 16 13:57:59 2025 -0800
    Adding the annotated hgCustom images for the markdown tutorial, refs #34354
• src/hg/htdocs/inc/hgMyData.html
  • lines changed 1, context: html, text, full: html, text
    6247a8f89bd752edbb1777cebc5c7c5372a9d738 Tue Dec 16 09:34:16 2025 -0800
    Fixing a typo from code review. refs #36851
  • lines changed 1, context: html, text, full: html, text
    2ab535c78777f5b40d7436c9cd573ef8dfae9052 Wed Dec 31 14:50:40 2025 -0800
    replacing quick start link with link to hub basics page, refs #28347
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    73c100526aa0bad1111e65bc746734dc3b859796 Mon Dec 22 14:45:20 2025 -0800
    Releasing and announcing the EVA Release 8 tracks, refs #36512
  • lines changed 12, context: html, text, full: html, text
    7151483319835fd736f3fbe0966c8f1476298d04 Tue Dec 23 12:36:27 2025 -0800
    correcting title for ancient hominids announcement, adding link to announcement from home page, refs #36586
• src/hg/htdocs/store.html
  • lines changed 81, context: html, text, full: html, text
    16ee6f78ca9975afc0dea807de321331929799ab Wed Dec 17 09:46:15 2025 -0800
    Adding CRISPRware to the store.
  • lines changed 10, context: html, text, full: html, text
    647d13011cbe8def7b6dbbc5c849fc4c93008df4 Wed Dec 17 09:48:43 2025 -0800
    A quick update.
  • lines changed 4, context: html, text, full: html, text
    fc01cb610a90c3ee353e9372b0d756ae8b0a2880 Fri Dec 19 09:16:17 2025 -0800
    Updating contact for external software
• src/hg/htdocs/style/HGStyle.css
  • lines changed 2, context: html, text, full: html, text
    3162d1fec3dffece6f608f15eb6d46f6c46f7436 Fri Dec 5 16:13:05 2025 -0800
    Working version of custom track group 'visible' that is at the top of the group list and has all the currently visible tracks, refs #36609
• src/hg/hubApi/tests/makefile
  • lines changed 5, context: html, text, full: html, text
    747ceb988787624f37b1243a09bf6905e3ae981e Wed Jan 7 10:31:14 2026 -0800
    removing list22 test since it changes frequently, refs #36463
• src/hg/inc/hicUi.h
  • lines changed 5, context: html, text, full: html, text
    34f380bfb0b4003a23fe2e00be6bdac6af326cda Mon Dec 15 15:20:13 2025 -0800
    Adding hicArcLimit and hicArcLimitEnabled settings to let people prevent excessive arc counts from overwhelming a Hi-C display with data, refs #36774
• src/hg/js/hgTracks.js
  • lines changed 5, context: html, text, full: html, text
    3162d1fec3dffece6f608f15eb6d46f6c46f7436 Fri Dec 5 16:13:05 2025 -0800
    Working version of custom track group 'visible' that is at the top of the group list and has all the currently visible tracks, refs #36609
• src/hg/js/hui.js
  • lines changed 4, context: html, text, full: html, text
    5a1d1a25ff3a7a7001e5dd98e1e4879b6f3ebe9d Tue Dec 16 16:15:02 2025 -0800
    Fix up jsOnEventById calls to javascript literal encode the id's, so the ids can have parens, single quotes, double quotes, etc in them and still be selected. Fix up the matrix checkbox code to htmlEncode the subgroups so subgroups can have parens, single quotes, etc in them and still work as class names and selectors, refs #36841
• src/hg/lib/customFactory.c
  • lines changed 7, context: html, text, full: html, text
    a9389f2c0af99f64b1f32353499fb48b4aca0872 Thu Jan 8 13:15:09 2026 -0800
    whitelist genark in localUrl paths in isValidBigDataUrl() in customFactory.c
• src/hg/lib/genbank.c
  • lines changed 3, context: html, text, full: html, text
    f7f5b164d6bacfd8da9b8f7772497ef971f2b0f8 Fri Dec 19 11:37:31 2025 -0800
    Add options -chrom -start -end -range -bed -positions -udcDir to bigMafToMaf. Adds -positions to bigBedToBed. Moved parsePosition and parseRange routines into common.c so they could be shared with these and other utilities. -range has one 0-based start on commandline. -positions is a file with a list of 1-based starts. fixes #28109
• src/hg/lib/hdb.c
  • lines changed 26, context: html, text, full: html, text
    f7f5b164d6bacfd8da9b8f7772497ef971f2b0f8 Fri Dec 19 11:37:31 2025 -0800
    Add options -chrom -start -end -range -bed -positions -udcDir to bigMafToMaf. Adds -positions to bigBedToBed. Moved parsePosition and parseRange routines into common.c so they could be shared with these and other utilities. -range has one 0-based start on commandline. -positions is a file with a list of 1-based starts. fixes #28109
• src/hg/lib/hicUi.c
  • lines changed 56, context: html, text, full: html, text
    34f380bfb0b4003a23fe2e00be6bdac6af326cda Mon Dec 15 15:20:13 2025 -0800
    Adding hicArcLimit and hicArcLimitEnabled settings to let people prevent excessive arc counts from overwhelming a Hi-C display with data, refs #36774
  • lines changed 2, context: html, text, full: html, text
    57aba7b8fb23d9bdbeceb665a001452e6d7a6b99 Thu Jan 8 00:37:48 2026 -0800
    An attempt at better auto-scaling for Hi-C colors in arc mode, refs #36774
• src/hg/lib/hui.c
  • lines changed 16, context: html, text, full: html, text
    5a1d1a25ff3a7a7001e5dd98e1e4879b6f3ebe9d Tue Dec 16 16:15:02 2025 -0800
    Fix up jsOnEventById calls to javascript literal encode the id's, so the ids can have parens, single quotes, double quotes, etc in them and still be selected. Fix up the matrix checkbox code to htmlEncode the subgroups so subgroups can have parens, single quotes, etc in them and still work as class names and selectors, refs #36841
  • lines changed 1, context: html, text, full: html, text
    0b24a835ce4160b634eea9c8f8e0fb29c910feb3 Tue Jan 6 13:05:08 2026 -0800
    do not show table browser link for super tracks, email from Mark, no redmine
• src/hg/lib/trackDbCustom.c
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    faae11b2f6fe529451664e1d979ca8426a9b4a73 Sun Jan 11 09:05:10 2026 -0800
    Revert "bigBeds with less than five fields with filters should show them on the" This reverts commit 5602c6f4da7d31d02fcf849c6dce1ef329cca3ef.
• src/hg/lib/trackHub.c
  • lines changed 7, context: html, text, full: html, text
    4cf72ff67368e864c7e80b8918245689d22264f6 Mon Dec 15 17:06:21 2025 -0800
    Reapply "Little patch for udc.localDir and trackHub security for local bigDataUrl disallowed for non-local hubUrl. We have to double check the cached trackDb data. fixes #34544" This reverts commit b1d12cdd8bea10895a0ff1b787f5c0549cb76d7a. Revert the reversion!
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    e028ddcac656a6b6e3e923b00d3e6233059d79e7 Mon Dec 15 17:07:09 2025 -0800
    Reapply "freeMem was crashing for settings values, cannot do that for settings returned from trackDbCache. refs #34544, #36835, #36834" This reverts commit 648f90bb5f2bbbf365a7005a69fdfa82c37057e0. Revert the reversion!
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    168f1d98aebcb04463c0a90e2249aa4414530e8a Fri Dec 19 13:34:48 2025 -0800
    Revert "Reapply "freeMem was crashing for settings values, cannot do that for settings returned from trackDbCache. refs #34544, #36835, #36834"" This reverts commit e028ddcac656a6b6e3e923b00d3e6233059d79e7. We can use touch single file hub.txt or rm -rf $cacheTrackDbDir to force updating the trackDb cache and still allow udc.localDir to be used.
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    e95fa927a040a8d89ac8e63e0cf0622c4efd1374 Fri Dec 19 13:36:23 2025 -0800
    Revert "Reapply "Little patch for udc.localDir and trackHub security for local bigDataUrl disallowed for non-local hubUrl. We have to double check the cached trackDb data. fixes #34544"" This reverts commit 4cf72ff67368e864c7e80b8918245689d22264f6. We can use touch single file hub.txt or rm -rf $cacheTrackDbDir to force updating the trackDb cache and still allow udc.localDir to be used.
• src/hg/makeDb/doc/archaeaAsmHub/archaea.orderList.tsv
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    bd4e8fdfa8af70460de2f21bb3555a93331d4e88 Fri Dec 26 12:51:22 2025 -0800
    RefSeq update refs #29545
• src/hg/makeDb/doc/asmHubs/mkGenomes.pl
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    419c9b44aca638612f184d11f406c6d01269e01f Tue Jan 6 09:42:11 2026 -0800
    do not update groups.txt if it remains identical to template source refs #29545
• src/hg/makeDb/doc/bacteriaAsmHub/bacteria.orderList.tsv
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    334039f0943574d0c1d988b016b6052ff0a09228 Tue Dec 23 21:13:03 2025 -0800
    adding a couple per user requests refs #29545
  • lines changed 487, context: html, text, full: html, text
    bd4e8fdfa8af70460de2f21bb3555a93331d4e88 Fri Dec 26 12:51:22 2025 -0800
    RefSeq update refs #29545
• src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv
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    bd4e8fdfa8af70460de2f21bb3555a93331d4e88 Fri Dec 26 12:51:22 2025 -0800
    RefSeq update refs #29545
• src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv
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    334039f0943574d0c1d988b016b6052ff0a09228 Tue Dec 23 21:13:03 2025 -0800
    adding a couple per user requests refs #29545
  • lines changed 6, context: html, text, full: html, text
    bd4e8fdfa8af70460de2f21bb3555a93331d4e88 Fri Dec 26 12:51:22 2025 -0800
    RefSeq update refs #29545
• src/hg/makeDb/doc/hg38/clsLongReadRna.txt
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    66604eefdbb0971ed43ee81bd6f18cc3a409e304 Sat Jan 10 13:18:44 2026 -0800
    color-code clsLongReadRna modles (#36908)
• src/hg/makeDb/doc/hg38/gnomad.txt
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    fd5b9c605c39c5b83b630926419897d9dbd69c37 Fri Jan 9 14:22:19 2026 -0800
    Adding to the makedoc, the gnomAD v4.1 CNV track update with the gnomad.v4.1.cnv.all.bed data. Also, updated the hgdownload URL in the track description, refs #36837
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
  • lines changed 7, context: html, text, full: html, text
    bd4e8fdfa8af70460de2f21bb3555a93331d4e88 Fri Dec 26 12:51:22 2025 -0800
    RefSeq update refs #29545
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
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    334039f0943574d0c1d988b016b6052ff0a09228 Tue Dec 23 21:13:03 2025 -0800
    adding a couple per user requests refs #29545
  • lines changed 5, context: html, text, full: html, text
    bd4e8fdfa8af70460de2f21bb3555a93331d4e88 Fri Dec 26 12:51:22 2025 -0800
    RefSeq update refs #29545
• src/hg/makeDb/doc/mm10.clsLongReadRna.txt
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    66604eefdbb0971ed43ee81bd6f18cc3a409e304 Sat Jan 10 13:18:44 2026 -0800
    color-code clsLongReadRna modles (#36908)
• src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv
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    bd4e8fdfa8af70460de2f21bb3555a93331d4e88 Fri Dec 26 12:51:22 2025 -0800
    RefSeq update refs #29545
• src/hg/makeDb/doc/viralAsmHub/viral.orderList.tsv
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    bd4e8fdfa8af70460de2f21bb3555a93331d4e88 Fri Dec 26 12:51:22 2025 -0800
    RefSeq update refs #29545
• src/hg/makeDb/outside/clsLongReadRna/clsModelBed.as
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    66604eefdbb0971ed43ee81bd6f18cc3a409e304 Sat Jan 10 13:18:44 2026 -0800
    color-code clsLongReadRna modles (#36908)
• src/hg/makeDb/outside/clsLongReadRna/clsTrackTool
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    66604eefdbb0971ed43ee81bd6f18cc3a409e304 Sat Jan 10 13:18:44 2026 -0800
    color-code clsLongReadRna modles (#36908)
• src/hg/makeDb/trackDb/TOGAv2.html
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    6120d02a6aa7faf052299967d8bace2d2d706ad3 Mon Dec 15 13:06:28 2025 -0800
    one additional color code definition for paralogous annotations refs #35776
• src/hg/makeDb/trackDb/bacteria/staAur2/cons369way.html
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    7a820a27de93e79180f99ae0e149585b5d1bb126 Tue Dec 23 16:02:10 2025 -0800
    adding better species coloring description to rest of conservation tracks, refs #27217
• src/hg/makeDb/trackDb/betaGenArk.txt
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    06dd761c2c6ddc53e7e191203da75569b1c1cb9c Mon Dec 15 13:11:12 2025 -0800
    adding TOGAv2 refs #35776
• src/hg/makeDb/trackDb/birds/geoFor1/cons7way.html
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    7a820a27de93e79180f99ae0e149585b5d1bb126 Tue Dec 23 16:02:10 2025 -0800
    adding better species coloring description to rest of conservation tracks, refs #27217
• src/hg/makeDb/trackDb/bushbaby/otoGar3/cons3way.html
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    7a820a27de93e79180f99ae0e149585b5d1bb126 Tue Dec 23 16:02:10 2025 -0800
    adding better species coloring description to rest of conservation tracks, refs #27217
• src/hg/makeDb/trackDb/cat/felCat4/cons6way.html
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    7a820a27de93e79180f99ae0e149585b5d1bb126 Tue Dec 23 16:02:10 2025 -0800
    adding better species coloring description to rest of conservation tracks, refs #27217
• src/hg/makeDb/trackDb/chicken/galGal6/cons77way.html
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    7a820a27de93e79180f99ae0e149585b5d1bb126 Tue Dec 23 16:02:10 2025 -0800
    adding better species coloring description to rest of conservation tracks, refs #27217
• src/hg/makeDb/trackDb/chimp/panTro3/cons12way.html
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    7a820a27de93e79180f99ae0e149585b5d1bb126 Tue Dec 23 16:02:10 2025 -0800
    adding better species coloring description to rest of conservation tracks, refs #27217
• src/hg/makeDb/trackDb/cow/bosTau4/multiz5way.html
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    7a820a27de93e79180f99ae0e149585b5d1bb126 Tue Dec 23 16:02:10 2025 -0800
    adding better species coloring description to rest of conservation tracks, refs #27217
• src/hg/makeDb/trackDb/criGri/regenCho1/cons7way.html
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    7a820a27de93e79180f99ae0e149585b5d1bb126 Tue Dec 23 16:02:10 2025 -0800
    adding better species coloring description to rest of conservation tracks, refs #27217
• src/hg/makeDb/trackDb/drosophila/dm6/cons124way.html
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    7a820a27de93e79180f99ae0e149585b5d1bb126 Tue Dec 23 16:02:10 2025 -0800
    adding better species coloring description to rest of conservation tracks, refs #27217
• src/hg/makeDb/trackDb/drosophila/dm6/cons27way.html
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    7a820a27de93e79180f99ae0e149585b5d1bb126 Tue Dec 23 16:02:10 2025 -0800
    adding better species coloring description to rest of conservation tracks, refs #27217
• src/hg/makeDb/trackDb/ebola/eboVir3/cons160way.html
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    7a820a27de93e79180f99ae0e149585b5d1bb126 Tue Dec 23 16:02:10 2025 -0800
    adding better species coloring description to rest of conservation tracks, refs #27217
• src/hg/makeDb/trackDb/evaSnp.alpha.ra
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    fbe00baffdd77e3280b684b54757de7090cf21e9 Tue Dec 16 16:37:41 2025 -0800
    Updating the EVA SNP track description, adding pennantIcon, and adding beta tag, refs #36512
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    482cc4cb3426acbc68d9410a92988729f0928c18 Fri Dec 19 13:55:57 2025 -0800
    Releasing the EVA Release 8 tracks, refs #36512
• src/hg/makeDb/trackDb/evaSnp.ra
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    482cc4cb3426acbc68d9410a92988729f0928c18 Fri Dec 19 13:55:57 2025 -0800
    Releasing the EVA Release 8 tracks, refs #36512
• src/hg/makeDb/trackDb/evaSnpContainer.html
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    fbe00baffdd77e3280b684b54757de7090cf21e9 Tue Dec 16 16:37:41 2025 -0800
    Updating the EVA SNP track description, adding pennantIcon, and adding beta tag, refs #36512
• src/hg/makeDb/trackDb/galVar/galVar1/cons4way.html
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    7a820a27de93e79180f99ae0e149585b5d1bb126 Tue Dec 23 16:02:10 2025 -0800
    adding better species coloring description to rest of conservation tracks, refs #27217
• src/hg/makeDb/trackDb/galVar/galVar1/cons5way.html
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    7a820a27de93e79180f99ae0e149585b5d1bb126 Tue Dec 23 16:02:10 2025 -0800
    adding better species coloring description to rest of conservation tracks, refs #27217
• src/hg/makeDb/trackDb/galVar/galVar1/cons6way.html
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    7a820a27de93e79180f99ae0e149585b5d1bb126 Tue Dec 23 16:02:10 2025 -0800
    adding better species coloring description to rest of conservation tracks, refs #27217
• src/hg/makeDb/trackDb/guineaPig/cavPor3/cons5way.html
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    7a820a27de93e79180f99ae0e149585b5d1bb126 Tue Dec 23 16:02:10 2025 -0800
    adding better species coloring description to rest of conservation tracks, refs #27217
• src/hg/makeDb/trackDb/guineaPig/cavPor3/cons6way.html
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    7a820a27de93e79180f99ae0e149585b5d1bb126 Tue Dec 23 16:02:10 2025 -0800
    adding better species coloring description to rest of conservation tracks, refs #27217
• src/hg/makeDb/trackDb/horse/equCab2/multiz6way.html
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    7a820a27de93e79180f99ae0e149585b5d1bb126 Tue Dec 23 16:02:10 2025 -0800
    adding better species coloring description to rest of conservation tracks, refs #27217
• src/hg/makeDb/trackDb/human/chm13/html/GCA_009914755.4_T2T-CHM13v2.0.sedefSegDups.html
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    c177d102b0a4e3e72f82a3dc5f5adbdc0fe3f53d Wed Dec 31 09:35:36 2025 -0800
    fixed wierd language or typo that seems to be from copying description from various places outside of the browser code
• src/hg/makeDb/trackDb/human/g2p.ra
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    d3e77d28330c5c21d88a9deaef31d80dadd966ea Mon Jan 5 11:09:33 2026 -0800
    Squashing stale pennantIcons, no RM.
• src/hg/makeDb/trackDb/human/hg18/cons44way.html
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    7a820a27de93e79180f99ae0e149585b5d1bb126 Tue Dec 23 16:02:10 2025 -0800
    adding better species coloring description to rest of conservation tracks, refs #27217
• src/hg/makeDb/trackDb/human/hg18/multiz28way.html
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    7a820a27de93e79180f99ae0e149585b5d1bb126 Tue Dec 23 16:02:10 2025 -0800
    adding better species coloring description to rest of conservation tracks, refs #27217
• src/hg/makeDb/trackDb/human/hg19/cons100way.html
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    3bcdba0cb7f7281dc131c2c59684980741a841e6 Tue Dec 23 15:34:36 2025 -0800
    Adding better description of species coloring in conservation tracks, refs #27217
• src/hg/makeDb/trackDb/human/hg19/cons46way.html
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    3bcdba0cb7f7281dc131c2c59684980741a841e6 Tue Dec 23 15:34:36 2025 -0800
    Adding better description of species coloring in conservation tracks, refs #27217
• src/hg/makeDb/trackDb/human/hg19/knownGene.ra
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    d3e77d28330c5c21d88a9deaef31d80dadd966ea Mon Jan 5 11:09:33 2026 -0800
    Squashing stale pennantIcons, no RM.
• src/hg/makeDb/trackDb/human/hg19/trackDb.gencode.ra
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    d3e77d28330c5c21d88a9deaef31d80dadd966ea Mon Jan 5 11:09:33 2026 -0800
    Squashing stale pennantIcons, no RM.
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
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    d3e77d28330c5c21d88a9deaef31d80dadd966ea Mon Jan 5 11:09:33 2026 -0800
    Squashing stale pennantIcons, no RM.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV49lift37.ra
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    d3e77d28330c5c21d88a9deaef31d80dadd966ea Mon Jan 5 11:09:33 2026 -0800
    Squashing stale pennantIcons, no RM.
• src/hg/makeDb/trackDb/human/hg38/cCREregistry.html
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    828e8fde956c566c299dd09ccde15f217de365a3 Wed Jan 7 16:54:30 2026 -0800
    Final touches to the track, feedback from Zhiping. Reordering the registry tracks to be alphbetical by longLabel, but still keep data types together and updating the refences to the nature article that has now published. Refs #34109
• src/hg/makeDb/trackDb/human/hg38/cCREsSuper.html
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    828e8fde956c566c299dd09ccde15f217de365a3 Wed Jan 7 16:54:30 2026 -0800
    Final touches to the track, feedback from Zhiping. Reordering the registry tracks to be alphbetical by longLabel, but still keep data types together and updating the refences to the nature article that has now published. Refs #34109
• src/hg/makeDb/trackDb/human/hg38/clsLongReadRna.html
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    66604eefdbb0971ed43ee81bd6f18cc3a409e304 Sat Jan 10 13:18:44 2026 -0800
    color-code clsLongReadRna modles (#36908)
• src/hg/makeDb/trackDb/human/hg38/clsLongReadRna.ra
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    66604eefdbb0971ed43ee81bd6f18cc3a409e304 Sat Jan 10 13:18:44 2026 -0800
    color-code clsLongReadRna modles (#36908)
• src/hg/makeDb/trackDb/human/hg38/cons100way.html
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    3bcdba0cb7f7281dc131c2c59684980741a841e6 Tue Dec 23 15:34:36 2025 -0800
    Adding better description of species coloring in conservation tracks, refs #27217
• src/hg/makeDb/trackDb/human/hg38/cons17way.html
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    3bcdba0cb7f7281dc131c2c59684980741a841e6 Tue Dec 23 15:34:36 2025 -0800
    Adding better description of species coloring in conservation tracks, refs #27217
• src/hg/makeDb/trackDb/human/hg38/cons20way.html
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    3bcdba0cb7f7281dc131c2c59684980741a841e6 Tue Dec 23 15:34:36 2025 -0800
    Adding better description of species coloring in conservation tracks, refs #27217
• src/hg/makeDb/trackDb/human/hg38/cons241way.html
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    3bcdba0cb7f7281dc131c2c59684980741a841e6 Tue Dec 23 15:34:36 2025 -0800
    Adding better description of species coloring in conservation tracks, refs #27217
• src/hg/makeDb/trackDb/human/hg38/cons27way.html
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    3bcdba0cb7f7281dc131c2c59684980741a841e6 Tue Dec 23 15:34:36 2025 -0800
    Adding better description of species coloring in conservation tracks, refs #27217
• src/hg/makeDb/trackDb/human/hg38/cons30way.html
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    3bcdba0cb7f7281dc131c2c59684980741a841e6 Tue Dec 23 15:34:36 2025 -0800
    Adding better description of species coloring in conservation tracks, refs #27217
• src/hg/makeDb/trackDb/human/hg38/cons470way.html
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    3bcdba0cb7f7281dc131c2c59684980741a841e6 Tue Dec 23 15:34:36 2025 -0800
    Adding better description of species coloring in conservation tracks, refs #27217
• src/hg/makeDb/trackDb/human/hg38/cons4way.html
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    3bcdba0cb7f7281dc131c2c59684980741a841e6 Tue Dec 23 15:34:36 2025 -0800
    Adding better description of species coloring in conservation tracks, refs #27217
• src/hg/makeDb/trackDb/human/hg38/cons5way.html
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    3bcdba0cb7f7281dc131c2c59684980741a841e6 Tue Dec 23 15:34:36 2025 -0800
    Adding better description of species coloring in conservation tracks, refs #27217
• src/hg/makeDb/trackDb/human/hg38/cons7way.html
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    3bcdba0cb7f7281dc131c2c59684980741a841e6 Tue Dec 23 15:34:36 2025 -0800
    Adding better description of species coloring in conservation tracks, refs #27217
• src/hg/makeDb/trackDb/human/hg38/coreCollection.html
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    828e8fde956c566c299dd09ccde15f217de365a3 Wed Jan 7 16:54:30 2026 -0800
    Final touches to the track, feedback from Zhiping. Reordering the registry tracks to be alphbetical by longLabel, but still keep data types together and updating the refences to the nature article that has now published. Refs #34109
• src/hg/makeDb/trackDb/human/hg38/encode4.ccres.ra
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    d8000af8628f18a03b5fa88b0734a7d8d57e2138 Tue Jan 6 13:25:17 2026 -0800
    Feedback from Zhiping, refs #34109
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    cffb8890582724fc07e5319b3b46e1cbb3a479f9 Wed Jan 7 10:34:48 2026 -0800
    More CfFeedback from Zhiping, adding numbers to all the data types refs #34109
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    828e8fde956c566c299dd09ccde15f217de365a3 Wed Jan 7 16:54:30 2026 -0800
    Final touches to the track, feedback from Zhiping. Reordering the registry tracks to be alphbetical by longLabel, but still keep data types together and updating the refences to the nature article that has now published. Refs #34109
• src/hg/makeDb/trackDb/human/hg38/gnomadCNV.html
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    fd5b9c605c39c5b83b630926419897d9dbd69c37 Fri Jan 9 14:22:19 2026 -0800
    Adding to the makedoc, the gnomAD v4.1 CNV track update with the gnomad.v4.1.cnv.all.bed data. Also, updated the hgdownload URL in the track description, refs #36837
• src/hg/makeDb/trackDb/human/hg38/knownGene.ra
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    d3e77d28330c5c21d88a9deaef31d80dadd966ea Mon Jan 5 11:09:33 2026 -0800
    Squashing stale pennantIcons, no RM.
• src/hg/makeDb/trackDb/human/hg38/long_read_transcripts.ra
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    d3e77d28330c5c21d88a9deaef31d80dadd966ea Mon Jan 5 11:09:33 2026 -0800
    Squashing stale pennantIcons, no RM.
• src/hg/makeDb/trackDb/human/hg38/mavedb.ra
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    d3e77d28330c5c21d88a9deaef31d80dadd966ea Mon Jan 5 11:09:33 2026 -0800
    Squashing stale pennantIcons, no RM.
• src/hg/makeDb/trackDb/human/hg38/problematic.ra
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    d3e77d28330c5c21d88a9deaef31d80dadd966ea Mon Jan 5 11:09:33 2026 -0800
    Squashing stale pennantIcons, no RM.
• src/hg/makeDb/trackDb/human/hg38/trackDb.gencode.ra
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    d3e77d28330c5c21d88a9deaef31d80dadd966ea Mon Jan 5 11:09:33 2026 -0800
    Squashing stale pennantIcons, no RM.
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
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    d3e77d28330c5c21d88a9deaef31d80dadd966ea Mon Jan 5 11:09:33 2026 -0800
    Squashing stale pennantIcons, no RM.
• src/hg/makeDb/trackDb/human/hg38/unusualcons.ra
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    d3e77d28330c5c21d88a9deaef31d80dadd966ea Mon Jan 5 11:09:33 2026 -0800
    Squashing stale pennantIcons, no RM.
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV49.ra
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    d3e77d28330c5c21d88a9deaef31d80dadd966ea Mon Jan 5 11:09:33 2026 -0800
    Squashing stale pennantIcons, no RM.
• src/hg/makeDb/trackDb/human/hs1/html/sedefSegDups.html
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    c177d102b0a4e3e72f82a3dc5f5adbdc0fe3f53d Wed Dec 31 09:35:36 2025 -0800
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• src/hg/makeDb/trackDb/human/longReadVariants.ra
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• src/hg/makeDb/trackDb/human/spliceAIWt.ra
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• src/hg/makeDb/trackDb/human/spliceImpactSuper.ra
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• src/hg/makeDb/trackDb/human/trackDb.ra
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    150d6eac0d7fa08368b11b25ad8f6b4e84143243 Tue Dec 16 15:13:55 2025 -0800
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• src/hg/makeDb/trackDb/human/varFreqs.ra
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    150d6eac0d7fa08368b11b25ad8f6b4e84143243 Tue Dec 16 15:13:55 2025 -0800
    more docs for var freqs track
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    116b634888c8642526859fb6d1134a52c078a909 Tue Dec 16 16:09:08 2025 -0800
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    031b776b108157a3c41e4643b4ae132877234789 Tue Dec 16 16:12:57 2025 -0800
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    598adc82015a64774f87a3cd2d6a97e77906544b Thu Jan 8 08:13:11 2026 -0800
    adding SFARI SPARK WES to variant frequencies track, refs #36642
• src/hg/makeDb/trackDb/lamprey/petMar1/multiz6way.html
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    7a820a27de93e79180f99ae0e149585b5d1bb126 Tue Dec 23 16:02:10 2025 -0800
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• src/hg/makeDb/trackDb/lamprey/petMar2/cons7way.html
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    7a820a27de93e79180f99ae0e149585b5d1bb126 Tue Dec 23 16:02:10 2025 -0800
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• src/hg/makeDb/trackDb/lancelet/braFlo1/multiz5way.html
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    7a820a27de93e79180f99ae0e149585b5d1bb126 Tue Dec 23 16:02:10 2025 -0800
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• src/hg/makeDb/trackDb/lizard/anoCar2/cons7way.html
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    7a820a27de93e79180f99ae0e149585b5d1bb126 Tue Dec 23 16:02:10 2025 -0800
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• src/hg/makeDb/trackDb/marmoset/calJac1/multiz9way.html
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    7a820a27de93e79180f99ae0e149585b5d1bb126 Tue Dec 23 16:02:10 2025 -0800
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• src/hg/makeDb/trackDb/marmoset/calJac3/cons13way.html
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    7a820a27de93e79180f99ae0e149585b5d1bb126 Tue Dec 23 16:02:10 2025 -0800
    adding better species coloring description to rest of conservation tracks, refs #27217
• src/hg/makeDb/trackDb/mouse/mm10/clsLongReadRna.html
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    66604eefdbb0971ed43ee81bd6f18cc3a409e304 Sat Jan 10 13:18:44 2026 -0800
    color-code clsLongReadRna modles (#36908)
• src/hg/makeDb/trackDb/mouse/mm10/clsLongReadRna.ra
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    66604eefdbb0971ed43ee81bd6f18cc3a409e304 Sat Jan 10 13:18:44 2026 -0800
    color-code clsLongReadRna modles (#36908)
• src/hg/makeDb/trackDb/mouse/mm10/cons4way.html
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    3bcdba0cb7f7281dc131c2c59684980741a841e6 Tue Dec 23 15:34:36 2025 -0800
    Adding better description of species coloring in conservation tracks, refs #27217
• src/hg/makeDb/trackDb/mouse/mm10/cons60way.html
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    3bcdba0cb7f7281dc131c2c59684980741a841e6 Tue Dec 23 15:34:36 2025 -0800
    Adding better description of species coloring in conservation tracks, refs #27217
• src/hg/makeDb/trackDb/mouse/mm10/long_read_transcripts.ra
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    d3e77d28330c5c21d88a9deaef31d80dadd966ea Mon Jan 5 11:09:33 2026 -0800
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• src/hg/makeDb/trackDb/mouse/mm39/cons35way.html
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    3bcdba0cb7f7281dc131c2c59684980741a841e6 Tue Dec 23 15:34:36 2025 -0800
    Adding better description of species coloring in conservation tracks, refs #27217
• src/hg/makeDb/trackDb/mouse/mm39/knownGene.ra
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• src/hg/makeDb/trackDb/mouse/mm39/trackDb.gencode.ra
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• src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM38.ra
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• src/hg/makeDb/trackDb/mouse/mm9/cons30way.html
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    7a820a27de93e79180f99ae0e149585b5d1bb126 Tue Dec 23 16:02:10 2025 -0800
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• src/hg/makeDb/trackDb/mouse/mm9/multiz30way.html
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    7a820a27de93e79180f99ae0e149585b5d1bb126 Tue Dec 23 16:02:10 2025 -0800
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• src/hg/makeDb/trackDb/mouseLemur/micMur3/cons3way.html
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    7a820a27de93e79180f99ae0e149585b5d1bb126 Tue Dec 23 16:02:10 2025 -0800
    adding better species coloring description to rest of conservation tracks, refs #27217
• src/hg/makeDb/trackDb/orangutan/ponAbe2/multiz8way.html
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    7a820a27de93e79180f99ae0e149585b5d1bb126 Tue Dec 23 16:02:10 2025 -0800
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• src/hg/makeDb/trackDb/publicGenArk.txt
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    1f57795eeb934d739cb4b3050a0484f29dd50fec Tue Jan 6 14:33:57 2026 -0800
    try out the VEuPathDB and TOGAv2 tracks refs #35778 #35776
• src/hg/makeDb/trackDb/rat/regenRn1/cons7way.html
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    7a820a27de93e79180f99ae0e149585b5d1bb126 Tue Dec 23 16:02:10 2025 -0800
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• src/hg/makeDb/trackDb/rat/rn5/cons13way.html
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    7a820a27de93e79180f99ae0e149585b5d1bb126 Tue Dec 23 16:02:10 2025 -0800
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• src/hg/makeDb/trackDb/rat/rn6/cons20way.html
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    7a820a27de93e79180f99ae0e149585b5d1bb126 Tue Dec 23 16:02:10 2025 -0800
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• src/hg/makeDb/trackDb/rhesus/rheMac10/trackDb.ra
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    d3e77d28330c5c21d88a9deaef31d80dadd966ea Mon Jan 5 11:09:33 2026 -0800
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• src/hg/makeDb/trackDb/sacCer/sacCer2/multiz7way.html
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    7a820a27de93e79180f99ae0e149585b5d1bb126 Tue Dec 23 16:02:10 2025 -0800
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• src/hg/makeDb/trackDb/sacCer/sacCer3/multiz7way.html
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    7a820a27de93e79180f99ae0e149585b5d1bb126 Tue Dec 23 16:02:10 2025 -0800
    adding better species coloring description to rest of conservation tracks, refs #27217
• src/hg/makeDb/trackDb/tagTypes.tab
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    34f380bfb0b4003a23fe2e00be6bdac6af326cda Mon Dec 15 15:20:13 2025 -0800
    Adding hicArcLimit and hicArcLimitEnabled settings to let people prevent excessive arc counts from overwhelming a Hi-C display with data, refs #36774
• src/hg/makeDb/trackDb/tarsier/tarSyr2/cons17way.html
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    7a820a27de93e79180f99ae0e149585b5d1bb126 Tue Dec 23 16:02:10 2025 -0800
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• src/hg/makeDb/trackDb/tarsier/tarSyr2/cons20way.html
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    7a820a27de93e79180f99ae0e149585b5d1bb126 Tue Dec 23 16:02:10 2025 -0800
    adding better species coloring description to rest of conservation tracks, refs #27217
• src/hg/makeDb/trackDb/trackDb.ra
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    fbe00baffdd77e3280b684b54757de7090cf21e9 Tue Dec 16 16:37:41 2025 -0800
    Updating the EVA SNP track description, adding pennantIcon, and adding beta tag, refs #36512
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    482cc4cb3426acbc68d9410a92988729f0928c18 Fri Dec 19 13:55:57 2025 -0800
    Releasing the EVA Release 8 tracks, refs #36512
• src/hg/makeDb/trackDb/treeShrew/tupChi1/cons4way.html
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    7a820a27de93e79180f99ae0e149585b5d1bb126 Tue Dec 23 16:02:10 2025 -0800
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• src/hg/makeDb/trackDb/treeShrew/tupChi1/cons5way.html
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    7a820a27de93e79180f99ae0e149585b5d1bb126 Tue Dec 23 16:02:10 2025 -0800
    adding better species coloring description to rest of conservation tracks, refs #27217
• src/hg/makeDb/trackDb/virus/wuhCor1/cons119way.html
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    7a820a27de93e79180f99ae0e149585b5d1bb126 Tue Dec 23 16:02:10 2025 -0800
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• src/hg/makeDb/trackDb/virus/wuhCor1/cons44way.html
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• src/hg/makeDb/trackDb/virus/wuhCor1/cons7way.html
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    7a820a27de93e79180f99ae0e149585b5d1bb126 Tue Dec 23 16:02:10 2025 -0800
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• src/hg/makeDb/trackDb/worm/ce10/cons7way.html
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    7a820a27de93e79180f99ae0e149585b5d1bb126 Tue Dec 23 16:02:10 2025 -0800
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• src/hg/makeDb/trackDb/worm/ce10/cons9way.html
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    7a820a27de93e79180f99ae0e149585b5d1bb126 Tue Dec 23 16:02:10 2025 -0800
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• src/hg/makeDb/trackDb/worm/ce11/cons135way.html
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    7a820a27de93e79180f99ae0e149585b5d1bb126 Tue Dec 23 16:02:10 2025 -0800
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    7a820a27de93e79180f99ae0e149585b5d1bb126 Tue Dec 23 16:02:10 2025 -0800
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• src/hg/makeDb/trackDb/worm/ce9/cons10way.html
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    7a820a27de93e79180f99ae0e149585b5d1bb126 Tue Dec 23 16:02:10 2025 -0800
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• src/hg/makeDb/trackDb/xenTro/xenTro9/cons11way.html
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    7a820a27de93e79180f99ae0e149585b5d1bb126 Tue Dec 23 16:02:10 2025 -0800
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• src/hg/makeDb/trackDb/zebrafish/danRer10/cons12way.html
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    7a820a27de93e79180f99ae0e149585b5d1bb126 Tue Dec 23 16:02:10 2025 -0800
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• src/hg/makeDb/trackDb/zebrafish/danRer6/multiz6way.html
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    7a820a27de93e79180f99ae0e149585b5d1bb126 Tue Dec 23 16:02:10 2025 -0800
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• src/hg/makeDb/trackDb/zebrafish/danRer7/cons8way.html
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    7a820a27de93e79180f99ae0e149585b5d1bb126 Tue Dec 23 16:02:10 2025 -0800
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• src/hg/utils/automation/blastz-run-ucsc
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    a5855ded640de30881d63cf3255399cc3c8e4238 Sat Dec 20 12:44:18 2025 -0800
    fixup empty lav result for axt output per Michael Hiller
• src/hg/utils/automation/doBlastzChainNet.pl
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    6b4d4242132b637c7ae9a2da8d63efea608d41af Mon Dec 22 18:51:50 2025 -0800
    get the liftOver and quickLift links properly in place for both database and GenArk browsers and the entries into the liftOverChain and quickLiftChain tables
• src/hg/utils/automation/doFasTAN.pl
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    74421edfd8c8e930e3bc90e86f87c7dab8031e95 Wed Jan 7 09:23:34 2026 -0800
    correct name on buildDir
• src/hg/utils/bigMafToMaf/bigMafToMaf.c
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    f7f5b164d6bacfd8da9b8f7772497ef971f2b0f8 Fri Dec 19 11:37:31 2025 -0800
    Add options -chrom -start -end -range -bed -positions -udcDir to bigMafToMaf. Adds -positions to bigBedToBed. Moved parsePosition and parseRange routines into common.c so they could be shared with these and other utilities. -range has one 0-based start on commandline. -positions is a file with a list of 1-based starts. fixes #28109
• src/hg/utils/otto/genArk/README
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    d425930659b77acd38c14eaefda720d52da1ddc1 Mon Dec 15 16:28:32 2025 -0800
    more detail on these push procedures
• src/hg/utils/otto/genArk/quickPush.pl
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    e17a685b61034584686ffa679916f6b3373a9c05 Wed Dec 17 10:07:07 2025 -0800
    adding --mkpath to the rsync for the contrib directory since it can be multiple levels deep refs #35776
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    3ffb2a7935a31d3dc7d1c43de0386cd4e3369863 Mon Jan 5 15:59:21 2026 -0800
    fix error in path name for beta push refs #35776
• src/hg/utils/otto/genCC/doGenCC.py
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    742602cf67e7fa9cb6584bbefe1512774b8277bc Wed Dec 17 15:25:41 2025 -0800
    Sorting the input file for the bedToBigBed command, no Redmine.
• src/hg/utils/otto/sarscov2phylo/annotatedNotDesignated
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    6847a63f394675d928eaec7dc14f8186b543b921 Thu Dec 4 15:31:22 2025 -0800
    Added BA.3.2 (back on Sep 5)
• src/hg/utils/otto/sarscov2phylo/branchSpecificMask.py
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    89f51d3b8c35a428f22c245aabc29f2461e66b62 Thu Dec 4 15:32:17 2025 -0800
    Added support for exclusions keyword (back on Oct 29)
• src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml
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    28c91a2f0848971d9f707c0a034c48f57757a4b5 Tue Dec 2 15:32:59 2025 -0800
    Use new exclusions keyword to prevent real G23599T reversion from being masked under XFJ.3.1. Change has been in place since Oct 29, just committing it now.
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    366028b554770e59a35f881811dd006c047ce9c6 Thu Dec 4 15:32:59 2025 -0800
    Added RE.1.1 reversions and site requested by @ryhisner
• src/hg/utils/otto/sarscov2phylo/includeRecombinants.tsv
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    b4e69d4d3191c71792bef68e94152c893a9065cf Thu Dec 4 15:45:12 2025 -0800
    Added a few more IDs that were being filtered out
• src/hg/utils/otto/sarscov2phylo/nextstrain.clade-mutations.tsv
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    c8dcfe3047cce1f843f987307c989a32d38cbd32 Thu Dec 4 15:34:34 2025 -0800
    Added XFG (back on Sep 5)
• src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv
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    70c31dff04e7892e0318c3380479e61cfe2d68ab Wed Jan 7 14:00:07 2026 -0800
    Major overhaul of file format now that matUtils annotate supports including mutations from parent lineage, with the addition of thousands of new lineages since the old file format made the file too large for kent repo limits.
• src/hg/utils/otto/sarscov2phylo/updateLineageTreePb.sh
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    8cab21c8b8a5e84a3491b796bd6590c5d6905325 Thu Dec 4 15:45:54 2025 -0800
    Added a couple samples to spare for reversion-riddled LF.7.6.5
• src/hg/utils/vai.pl
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    63890999edbfdac428544f159a33e503618ca7f8 Wed Jan 7 13:56:43 2026 -0800
    Add support for vai.pl to accept a GenArk assembly accession as db, and for hgVai to accept a geneTrack without the hub_number_ prefix when db is a hub.
• src/inc/common.h
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    f7f5b164d6bacfd8da9b8f7772497ef971f2b0f8 Fri Dec 19 11:37:31 2025 -0800
    Add options -chrom -start -end -range -bed -positions -udcDir to bigMafToMaf. Adds -positions to bigBedToBed. Moved parsePosition and parseRange routines into common.c so they could be shared with these and other utilities. -range has one 0-based start on commandline. -positions is a file with a list of 1-based starts. fixes #28109
• src/lib/cheapcgi.c
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    5a1d1a25ff3a7a7001e5dd98e1e4879b6f3ebe9d Tue Dec 16 16:15:02 2025 -0800
    Fix up jsOnEventById calls to javascript literal encode the id's, so the ids can have parens, single quotes, double quotes, etc in them and still be selected. Fix up the matrix checkbox code to htmlEncode the subgroups so subgroups can have parens, single quotes, etc in them and still work as class names and selectors, refs #36841
• src/lib/common.c
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    f7f5b164d6bacfd8da9b8f7772497ef971f2b0f8 Fri Dec 19 11:37:31 2025 -0800
    Add options -chrom -start -end -range -bed -positions -udcDir to bigMafToMaf. Adds -positions to bigBedToBed. Moved parsePosition and parseRange routines into common.c so they could be shared with these and other utilities. -range has one 0-based start on commandline. -positions is a file with a list of 1-based starts. fixes #28109
• src/lib/vcf.c
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    bac2b49a9cf03181c21ba22ab9ce4696f5735160 Fri Jan 9 05:42:08 2026 -0800
    in the SHANK2 locus, the Japan ToMMV VCF files has more than 1024 infos in a repeat, so making the buffer bigger, variant frequencies track
• src/product/mirrorManual.txt
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    14712b4b8359f75ff22425058919a5983443dc59 Mon Dec 15 13:07:53 2025 -0800
    documenting captcha exceptions, no redmine, email from Hiram
• src/utils/bigBedToBed/bigBedToBed.c
  • lines changed 58, context: html, text, full: html, text
    f7f5b164d6bacfd8da9b8f7772497ef971f2b0f8 Fri Dec 19 11:37:31 2025 -0800
    Add options -chrom -start -end -range -bed -positions -udcDir to bigMafToMaf. Adds -positions to bigBedToBed. Moved parsePosition and parseRange routines into common.c so they could be shared with these and other utilities. -range has one 0-based start on commandline. -positions is a file with a list of 1-based starts. fixes #28109
• src/utils/pslMap/pslMap.c
  • lines changed 16, context: html, text, full: html, text
    c56be670aa15932c81d5a1b751af166e0e26b2be Tue Dec 30 12:49:16 2025 -0800
    allow pslMap to remotely access chain psl input file
• src/utils/pslMap/tests/makefile
  • lines changed 21, context: html, text, full: html, text
    c56be670aa15932c81d5a1b751af166e0e26b2be Tue Dec 30 12:49:16 2025 -0800
    allow pslMap to remotely access chain psl input file
• src/utils/pslMapPostChain/pslMapPostChain.c
  • lines changed 3, context: html, text, full: html, text
    42238ba03380b2bc19818cabb5576b0cfb6d8644 Mon Jan 12 07:10:04 2026 -0800
    removed warning comment that is no long true
• src/utils/qa/checkErrorLogsAreUpToDate.py
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    d02300cbe391cf7cbea38da034b4826c305076d5 Fri Jan 2 09:25:34 2026 -0800
    Extending the check to 45 days as sometimes the asia logs are about 35 days before updating. No RM.
• src/utils/qa/qaTestScript.py
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    81789ef504369535518ea38e0cfd122ea339767b Mon Dec 15 22:07:17 2025 -0800
    Updating test due to a change in a HGVS search, refs #36201

• lines changed: 9883
• files changed: 245