All File Changes

v488_preview to v488_preview2 (2025-09-08 to 2025-09-15) v488

• confs/rr.hg.conf
  • lines changed 6, context: html, text, full: html, text
    b2cc7d95d4215f6ca8640be579e9a535c20074b6 Sun Sep 14 01:11:14 2025 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html
  • lines changed 7, context: html, text, full: html, text
    0bc87919de5b41d084130480ec851ab93f718925 Wed Sep 10 12:06:40 2025 -0700
    Aligning ADGC3 & ADGC4 to Start Year2 by dropping Q1 2024 past items
  • lines changed 3, context: html, text, full: html, text
    8d0f447512945c3836ddd109eabeae0ffb7b6add Thu Sep 11 11:43:15 2025 -0700
    Aligning ADGC1 & ADGC2 to Start Grant Year2, displaying all timelines at same base graph
• src/hg/hgGene/rnaStructure.c
  • lines changed 8, context: html, text, full: html, text
    f658d6278f6d4c686f79dd8fbf8c5895380a91ed Mon Sep 8 16:48:39 2025 -0700
    ongoing fixes to quickLift
• src/hg/hgTables/userRegions.c
  • lines changed 2, context: html, text, full: html, text
    4db0b922300631fc32d34c5b5ac010018723905e Mon Sep 8 13:57:08 2025 -0700
    Fix misplaced htmlClose call in table browser set user regions, refs #36284
• src/hg/hgTracks/bedTrack.c
  • lines changed 1, context: html, text, full: html, text
    51b12665a66876e1bbf7b022682a2050d4eb227d Fri Sep 12 13:03:18 2025 -0700
    some fixes for quickLifted custom tracks
• src/hg/hgTracks/bigBedTrack.c
  • lines changed 93, context: html, text, full: html, text
    5c07c3be13c9f363e02a8ed1f090172bc807e393 Mon Sep 8 14:30:29 2025 -0700
    Revert "Deals with multi-region and bigBeds so limitWiggle optimization works properly with all windows or regions. Fixes error test cases in rm35580 as well as full chromosome and recount3 and lrg and unusual tracks etc. fixes 35580" This reverts commit 4833b6c8e4583d27b99b06a6bdf0357fe786215d.
  • lines changed 92, context: html, text, full: html, text
    a137caa4731599f89daf08875f24bcb19b11e597 Thu Sep 11 14:32:31 2025 -0700
    Deals with multi-region and bigBeds so limitWiggle optimization works properly with all windows or regions. Fixes error test cases in rm35580 as well as full chromosome and recount3 and lrg and unusual tracks etc. Also works with quickLift and bigLollly now. Tested all tracks on hg38 and some public trackhubs. fixes #35580
• src/hg/hgTracks/hgTracks.c
  • lines changed 39, context: html, text, full: html, text
    5c07c3be13c9f363e02a8ed1f090172bc807e393 Mon Sep 8 14:30:29 2025 -0700
    Revert "Deals with multi-region and bigBeds so limitWiggle optimization works properly with all windows or regions. Fixes error test cases in rm35580 as well as full chromosome and recount3 and lrg and unusual tracks etc. fixes 35580" This reverts commit 4833b6c8e4583d27b99b06a6bdf0357fe786215d.
  • lines changed 89, context: html, text, full: html, text
    a137caa4731599f89daf08875f24bcb19b11e597 Thu Sep 11 14:32:31 2025 -0700
    Deals with multi-region and bigBeds so limitWiggle optimization works properly with all windows or regions. Fixes error test cases in rm35580 as well as full chromosome and recount3 and lrg and unusual tracks etc. Also works with quickLift and bigLollly now. Tested all tracks on hg38 and some public trackhubs. fixes #35580
  • lines changed 1, context: html, text, full: html, text
    4c6d2bf78e0ad85c283310b6a00c26fd0a82fb2e Mon Sep 15 03:46:21 2025 -0700
    adding a hub quick connect dialog box. qa still can decide if this should go into the menu somewhere, refs #35667
  • lines changed 9, context: html, text, full: html, text
    9d2d19a718d8c3d99f5d73ab1a16283d2fa39c9b Mon Sep 15 03:57:22 2025 -0700
    adding a hide all button to hub group blue bars, refs #36354
  • lines changed 16, context: html, text, full: html, text
    2f73d7595b0e37b159e9c9355f8e99512bf37e81 Wed Sep 10 08:33:03 2025 -0700
    Merging Jim Robinsons code into the kent tree. Due to whitespace changes in his IDE, I'm merging this manually. The original code is at https://github.com/igvteam/ucsc_dev/. changes up to 48816bc are included. Also adding an API call to get the 2bit file and code to use it.
• src/hg/hgTracks/hgTracks.h
  • lines changed 1, context: html, text, full: html, text
    5c07c3be13c9f363e02a8ed1f090172bc807e393 Mon Sep 8 14:30:29 2025 -0700
    Revert "Deals with multi-region and bigBeds so limitWiggle optimization works properly with all windows or regions. Fixes error test cases in rm35580 as well as full chromosome and recount3 and lrg and unusual tracks etc. fixes 35580" This reverts commit 4833b6c8e4583d27b99b06a6bdf0357fe786215d.
  • lines changed 1, context: html, text, full: html, text
    a137caa4731599f89daf08875f24bcb19b11e597 Thu Sep 11 14:32:31 2025 -0700
    Deals with multi-region and bigBeds so limitWiggle optimization works properly with all windows or regions. Fixes error test cases in rm35580 as well as full chromosome and recount3 and lrg and unusual tracks etc. Also works with quickLift and bigLollly now. Tested all tracks on hg38 and some public trackhubs. fixes #35580
• src/hg/hgTracks/quickLift.c
  • lines changed 43, context: html, text, full: html, text
    254686140b97de7d7f85906dcf70f78a9601d7d0 Mon Sep 8 15:10:10 2025 -0700
    ongoing work on quickLift
• src/hg/hgc/hgc.c
  • lines changed 2, context: html, text, full: html, text
    254686140b97de7d7f85906dcf70f78a9601d7d0 Mon Sep 8 15:10:10 2025 -0700
    ongoing work on quickLift
  • lines changed 10, context: html, text, full: html, text
    f658d6278f6d4c686f79dd8fbf8c5895380a91ed Mon Sep 8 16:48:39 2025 -0700
    ongoing fixes to quickLift
  • lines changed 2, context: html, text, full: html, text
    51b12665a66876e1bbf7b022682a2050d4eb227d Fri Sep 12 13:03:18 2025 -0700
    some fixes for quickLifted custom tracks
• src/hg/hgc/wiggleClick.c
  • lines changed 1, context: html, text, full: html, text
    254686140b97de7d7f85906dcf70f78a9601d7d0 Mon Sep 8 15:10:10 2025 -0700
    ongoing work on quickLift
• src/hg/htdocs/admin/filePicker.html
  • lines changed 188, context: html, text, full: html, text
    2f73d7595b0e37b159e9c9355f8e99512bf37e81 Wed Sep 10 08:33:03 2025 -0700
    Merging Jim Robinsons code into the kent tree. Due to whitespace changes in his IDE, I'm merging this manually. The original code is at https://github.com/igvteam/ucsc_dev/. changes up to 48816bc are included. Also adding an API call to get the 2bit file and code to use it.
• src/hg/htdocs/goldenPath/help/assemblyHubHelp.html
  • lines changed 102, context: html, text, full: html, text
    add669d23a4b18c14371a461ac9ab766e18db54f Sun Sep 14 16:10:11 2025 -0700
    Adding chromAlias and chromAuthority settings to the Assembly Hub User Guide, refs #33014
• src/hg/htdocs/goldenPath/help/posters.html
  • lines changed 1, context: html, text, full: html, text
    f6ca5fc6ba8154ce7b2a87e5641260eb2d777865 Fri Sep 12 10:03:31 2025 -0700
    Code review edits, refs #36325
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html
  • lines changed 1, context: html, text, full: html, text
    90f0feb00613517f42d046bc13ac406561fd03f0 Wed Sep 10 09:17:02 2025 -0700
    Changing syntax to be in line with the rest of the site, such as hgHubConnect, refs #35618
• src/hg/htdocs/indexMeetings.html
  • lines changed 1, context: html, text, full: html, text
    5e51194ea6a91df57ef522f299d0b259e0ad8792 Sun Sep 14 16:44:29 2025 -0700
    Adding poster gallery link to the home page and training page, refs #36182
• src/hg/htdocs/training/index.html
  • lines changed 4, context: html, text, full: html, text
    5e51194ea6a91df57ef522f299d0b259e0ad8792 Sun Sep 14 16:44:29 2025 -0700
    Adding poster gallery link to the home page and training page, refs #36182
• src/hg/hubApi/apiUtils.c
  • lines changed 7, context: html, text, full: html, text
    2f73d7595b0e37b159e9c9355f8e99512bf37e81 Wed Sep 10 08:33:03 2025 -0700
    Merging Jim Robinsons code into the kent tree. Due to whitespace changes in his IDE, I'm merging this manually. The original code is at https://github.com/igvteam/ucsc_dev/. changes up to 48816bc are included. Also adding an API call to get the 2bit file and code to use it.
• src/hg/hubApi/dataApi.h
  • lines changed 3, context: html, text, full: html, text
    2f73d7595b0e37b159e9c9355f8e99512bf37e81 Wed Sep 10 08:33:03 2025 -0700
    Merging Jim Robinsons code into the kent tree. Due to whitespace changes in his IDE, I'm merging this manually. The original code is at https://github.com/igvteam/ucsc_dev/. changes up to 48816bc are included. Also adding an API call to get the 2bit file and code to use it.
• src/hg/hubApi/hubApi.c
  • lines changed 1, context: html, text, full: html, text
    2f73d7595b0e37b159e9c9355f8e99512bf37e81 Wed Sep 10 08:33:03 2025 -0700
    Merging Jim Robinsons code into the kent tree. Due to whitespace changes in his IDE, I'm merging this manually. The original code is at https://github.com/igvteam/ucsc_dev/. changes up to 48816bc are included. Also adding an API call to get the 2bit file and code to use it.
• src/hg/hubApi/liftOver.c
  • lines changed 3, context: html, text, full: html, text
    b1ece0f85392e86c466550496925f7f1cffa61be Mon Sep 8 16:06:09 2025 -0700
    hgParseChromRange does not require a database or genome name refs #35976
  • lines changed 1, context: html, text, full: html, text
    e8c22713a73f66943a295ed2b4912e6d8069e782 Wed Sep 10 16:54:43 2025 -0700
    allow quickLiftChain and liftOverChain tables to have different names specified in hg.conf
• src/hg/hubApi/list.c
  • lines changed 34, context: html, text, full: html, text
    2f73d7595b0e37b159e9c9355f8e99512bf37e81 Wed Sep 10 08:33:03 2025 -0700
    Merging Jim Robinsons code into the kent tree. Due to whitespace changes in his IDE, I'm merging this manually. The original code is at https://github.com/igvteam/ucsc_dev/. changes up to 48816bc are included. Also adding an API call to get the 2bit file and code to use it.
• src/hg/inc/liftOver.h
  • lines changed 5, context: html, text, full: html, text
    e8c22713a73f66943a295ed2b4912e6d8069e782 Wed Sep 10 16:54:43 2025 -0700
    allow quickLiftChain and liftOverChain tables to have different names specified in hg.conf
• src/hg/inc/quickLift.h
  • lines changed 5, context: html, text, full: html, text
    e8c22713a73f66943a295ed2b4912e6d8069e782 Wed Sep 10 16:54:43 2025 -0700
    allow quickLiftChain and liftOverChain tables to have different names specified in hg.conf
• src/hg/js/autocomplete.js
  • lines changed 2, context: html, text, full: html, text
    3d8b0303c81cfaa92123682a67e37c104b0bcf55 Wed Sep 10 07:53:46 2025 -0700
    shortening the help text under the position box, not sure why this never made it out, foudn in sandbox, refs #35939
• src/hg/js/hgTracks.js
  • lines changed 4, context: html, text, full: html, text
    8d2c44d8112018dbb115baa707dbffc4778a7006 Wed Sep 10 08:01:40 2025 -0700
    upgrading code for post-2013 nodejs/jshint, refs #36336
  • lines changed 28, context: html, text, full: html, text
    4c6d2bf78e0ad85c283310b6a00c26fd0a82fb2e Mon Sep 15 03:46:21 2025 -0700
    adding a hub quick connect dialog box. qa still can decide if this should go into the menu somewhere, refs #35667
  • lines changed 8, context: html, text, full: html, text
    9d2d19a718d8c3d99f5d73ab1a16283d2fa39c9b Mon Sep 15 03:57:22 2025 -0700
    adding a hide all button to hub group blue bars, refs #36354
  • lines changed 5, context: html, text, full: html, text
    a32a98bb08bff855c70e1bdb82b31088f5d0e7b8 Mon Sep 15 04:21:57 2025 -0700
    forgot to set cart variables, refs #36354
  • lines changed 53, context: html, text, full: html, text
    2f73d7595b0e37b159e9c9355f8e99512bf37e81 Wed Sep 10 08:33:03 2025 -0700
    Merging Jim Robinsons code into the kent tree. Due to whitespace changes in his IDE, I'm merging this manually. The original code is at https://github.com/igvteam/ucsc_dev/. changes up to 48816bc are included. Also adding an API call to get the 2bit file and code to use it.
• src/hg/js/hgc.js
  • lines changed 1, context: html, text, full: html, text
    8d2c44d8112018dbb115baa707dbffc4778a7006 Wed Sep 10 08:01:40 2025 -0700
    upgrading code for post-2013 nodejs/jshint, refs #36336
• src/hg/js/igv.min.js
  • lines changed 36, context: html, text, full: html, text
    2f73d7595b0e37b159e9c9355f8e99512bf37e81 Wed Sep 10 08:33:03 2025 -0700
    Merging Jim Robinsons code into the kent tree. Due to whitespace changes in his IDE, I'm merging this manually. The original code is at https://github.com/igvteam/ucsc_dev/. changes up to 48816bc are included. Also adding an API call to get the 2bit file and code to use it.
• src/hg/js/igvFileHelper.js
  • lines changed 667, context: html, text, full: html, text
    2f73d7595b0e37b159e9c9355f8e99512bf37e81 Wed Sep 10 08:33:03 2025 -0700
    Merging Jim Robinsons code into the kent tree. Due to whitespace changes in his IDE, I'm merging this manually. The original code is at https://github.com/igvteam/ucsc_dev/. changes up to 48816bc are included. Also adding an API call to get the 2bit file and code to use it.
• src/hg/js/makefile
  • lines changed 2, context: html, text, full: html, text
    2f73d7595b0e37b159e9c9355f8e99512bf37e81 Wed Sep 10 08:33:03 2025 -0700
    Merging Jim Robinsons code into the kent tree. Due to whitespace changes in his IDE, I'm merging this manually. The original code is at https://github.com/igvteam/ucsc_dev/. changes up to 48816bc are included. Also adding an API call to get the 2bit file and code to use it.
• src/hg/js/utils.js
  • lines changed 16, context: html, text, full: html, text
    8d2c44d8112018dbb115baa707dbffc4778a7006 Wed Sep 10 08:01:40 2025 -0700
    upgrading code for post-2013 nodejs/jshint, refs #36336
• src/hg/lib/cart.c
  • lines changed 3, context: html, text, full: html, text
    f658d6278f6d4c686f79dd8fbf8c5895380a91ed Mon Sep 8 16:48:39 2025 -0700
    ongoing fixes to quickLift
• src/hg/lib/hubConnect.c
  • lines changed 17, context: html, text, full: html, text
    254686140b97de7d7f85906dcf70f78a9601d7d0 Mon Sep 8 15:10:10 2025 -0700
    ongoing work on quickLift
  • lines changed 2, context: html, text, full: html, text
    e8c22713a73f66943a295ed2b4912e6d8069e782 Wed Sep 10 16:54:43 2025 -0700
    allow quickLiftChain and liftOverChain tables to have different names specified in hg.conf
• src/hg/lib/hui.c
  • lines changed 11, context: html, text, full: html, text
    254686140b97de7d7f85906dcf70f78a9601d7d0 Mon Sep 8 15:10:10 2025 -0700
    ongoing work on quickLift
• src/hg/lib/liftOver.c
  • lines changed 17, context: html, text, full: html, text
    e8c22713a73f66943a295ed2b4912e6d8069e782 Wed Sep 10 16:54:43 2025 -0700
    allow quickLiftChain and liftOverChain tables to have different names specified in hg.conf
• src/hg/lib/quickLift.c
  • lines changed 14, context: html, text, full: html, text
    e8c22713a73f66943a295ed2b4912e6d8069e782 Wed Sep 10 16:54:43 2025 -0700
    allow quickLiftChain and liftOverChain tables to have different names specified in hg.conf
  • lines changed 10, context: html, text, full: html, text
    51b12665a66876e1bbf7b022682a2050d4eb227d Fri Sep 12 13:03:18 2025 -0700
    some fixes for quickLifted custom tracks
• src/hg/lib/trackHub.c
  • lines changed 1, context: html, text, full: html, text
    2f215ce23581e32e517c7d617744d12989a96fb8 Tue Sep 9 13:53:03 2025 -0700
    when writing out quickLift hubs, strip hub name off of the parent statment of children of supertracks
• src/hg/makeDb/doc/asmHubs/findTaxon.pl
  • lines changed 82, context: html, text, full: html, text
    fe164c83850e2adba662df57142d37321d581236 Tue Sep 9 22:16:59 2025 -0700
    helper script for runBuild to find a reasonable RepeatMasker species to work with
• src/hg/makeDb/doc/asmHubs/quickLiftCatchUp.sh
  • lines changed 178, context: html, text, full: html, text
    ff30bada6966beec40c9341d94268dfe0f14b9b8 Thu Sep 11 13:15:16 2025 -0700
    helper script to catch up a quick lift set of files, symLinks and table entry refs #35575
• src/hg/makeDb/doc/bacteriaAsmHub/bacteria.orderList.tsv
  • lines changed 3, context: html, text, full: html, text
    45dbcb20cdbe097028c25110bff00cad6040ef3a Sat Sep 13 21:46:41 2025 -0700
    BRC update with over 3000 fungi refs #34337
• src/hg/makeDb/doc/brcAsmHub/brc.orderList.tsv
  • lines changed 3105, context: html, text, full: html, text
    7e6daa6f46ec1bc05211edb7d6241970f5afffea Sat Sep 13 22:15:32 2025 -0700
    BRC update bringing in about 3000 fungi refs #34337
• src/hg/makeDb/doc/fungiAsmHub/fungi.orderList.tsv
  • lines changed 3004, context: html, text, full: html, text
    45dbcb20cdbe097028c25110bff00cad6040ef3a Sat Sep 13 21:46:41 2025 -0700
    BRC update with over 3000 fungi refs #34337
• src/hg/makeDb/doc/hg19.gencode.txt
  • lines changed 3, context: html, text, full: html, text
    7d44b7fe975dd2c2772e0c64d30de9116bea66b8 Mon Sep 8 20:56:48 2025 -0700
    GENCODE V49lift38 release
• src/hg/makeDb/doc/hg38/gencode.txt
  • lines changed 2, context: html, text, full: html, text
    c18913f32735ca8e22e6a930ba00be3e7bafebee Mon Sep 8 19:11:01 2025 -0700
    GENCODE V49 release
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
  • lines changed 84, context: html, text, full: html, text
    aceeb7010c33195c4544bb76d1e56bfcc6d47239 Thu Sep 11 10:47:17 2025 -0700
    BRC update refs #34337
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    ff9e2fd834147f20ca56c3fcf674932d65fef3e3 Thu Sep 11 14:24:09 2025 -0700
    adding GCA_018389105.1 chambered nautilus per user request refs #29545
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    1a6e991e410cd9c58c1887c6d1b1cb9536ebcc0a Sat Sep 13 21:47:18 2025 -0700
    adding one per user request refs #29545
• src/hg/makeDb/doc/mm39/gencode.txt
  • lines changed 2, context: html, text, full: html, text
    3cc90c0cb01fa157d588f0dd60a019567b5a8955 Mon Sep 8 19:43:38 2025 -0700
    GENCODE VM38 release
• src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv
  • lines changed 8, context: html, text, full: html, text
    45dbcb20cdbe097028c25110bff00cad6040ef3a Sat Sep 13 21:46:41 2025 -0700
    BRC update with over 3000 fungi refs #34337
• src/hg/makeDb/hgAddLiftOverChain/hgAddLiftOverChain.c
  • lines changed 12, context: html, text, full: html, text
    e8c22713a73f66943a295ed2b4912e6d8069e782 Wed Sep 10 16:54:43 2025 -0700
    allow quickLiftChain and liftOverChain tables to have different names specified in hg.conf
• src/hg/makeDb/outside/gencode/gencodeLoad.mk
  • lines changed 4, context: html, text, full: html, text
    c18913f32735ca8e22e6a930ba00be3e7bafebee Mon Sep 8 19:11:01 2025 -0700
    GENCODE V49 release
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    3cc90c0cb01fa157d588f0dd60a019567b5a8955 Mon Sep 8 19:43:38 2025 -0700
    GENCODE VM38 release
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    7d44b7fe975dd2c2772e0c64d30de9116bea66b8 Mon Sep 8 20:56:48 2025 -0700
    GENCODE V49lift38 release
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeSuper.html
  • lines changed 4, context: html, text, full: html, text
    7d44b7fe975dd2c2772e0c64d30de9116bea66b8 Mon Sep 8 20:56:48 2025 -0700
    GENCODE V49lift38 release
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV49lift37.html
  • lines changed 1, context: html, text, full: html, text
    7d44b7fe975dd2c2772e0c64d30de9116bea66b8 Mon Sep 8 20:56:48 2025 -0700
    GENCODE V49lift38 release
• src/hg/makeDb/trackDb/human/hg38/problematic.html
  • lines changed 50, context: html, text, full: html, text
    6385e3fd28c67715eecf32186c47d5a7831059b3 Fri Sep 12 14:53:13 2025 -0700
    Updates to the Panmask Easy 151b track, refs #36293
• src/hg/makeDb/trackDb/human/hg38/problematic.ra
  • lines changed 3, context: html, text, full: html, text
    6385e3fd28c67715eecf32186c47d5a7831059b3 Fri Sep 12 14:53:13 2025 -0700
    Updates to the Panmask Easy 151b track, refs #36293
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeSuper.html
  • lines changed 4, context: html, text, full: html, text
    c18913f32735ca8e22e6a930ba00be3e7bafebee Mon Sep 8 19:11:01 2025 -0700
    GENCODE V49 release
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV49.html
  • lines changed 2, context: html, text, full: html, text
    c18913f32735ca8e22e6a930ba00be3e7bafebee Mon Sep 8 19:11:01 2025 -0700
    GENCODE V49 release
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV49.ra
  • lines changed 5, context: html, text, full: html, text
    c18913f32735ca8e22e6a930ba00be3e7bafebee Mon Sep 8 19:11:01 2025 -0700
    GENCODE V49 release
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    f6ca5fc6ba8154ce7b2a87e5641260eb2d777865 Fri Sep 12 10:03:31 2025 -0700
    Code review edits, refs #36325
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    a32a98bb08bff855c70e1bdb82b31088f5d0e7b8 Mon Sep 15 04:21:57 2025 -0700
    forgot to set cart variables, refs #36354
• src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeSuper.html
  • lines changed 4, context: html, text, full: html, text
    3cc90c0cb01fa157d588f0dd60a019567b5a8955 Mon Sep 8 19:43:38 2025 -0700
    GENCODE VM38 release
• src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM38.html
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    3cc90c0cb01fa157d588f0dd60a019567b5a8955 Mon Sep 8 19:43:38 2025 -0700
    GENCODE VM38 release
• src/hg/utils/automation/addQuickLift.py
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    ca0c31de09f0b88ca2a5c9b5c6d897768470740e Thu Sep 11 13:19:22 2025 -0700
    quickLiftChain table entry script refs #35575
• src/hg/utils/automation/asmHubRepeatMasker.sh
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    3cc8e060d62a38f811bfe8b66f3a33c1ca5049fd Sat Sep 13 09:00:04 2025 -0700
    temporary work around bugs in RepeatMasker code
• src/hg/utils/automation/asmHubTrackDb.sh
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    6eff6b0c070a6bcbaf607c38239f51616d83bc96 Wed Sep 10 19:45:33 2025 -0700
    eliminate the rnaSeqData include statement no longer exists refs #13553
• src/hg/utils/automation/doRepeatMasker.pl
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    7c88fd330d657bfc6007f75c75545ba63e94d87d Thu Sep 11 15:17:40 2025 -0700
    adding -uncurated to the version 4.2.1 operation
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    0cef6a4b1d730f0ecb4a5c8a0c0de6ce7a2fb13a Fri Sep 12 18:53:51 2025 -0700
    temporary work-around to fix the align.tsv issue for RM 4.2.1
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    3cc8e060d62a38f811bfe8b66f3a33c1ca5049fd Sat Sep 13 09:00:04 2025 -0700
    temporary work around bugs in RepeatMasker code
• src/inc/cheapcgi.h
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    9d2d19a718d8c3d99f5d73ab1a16283d2fa39c9b Mon Sep 15 03:57:22 2025 -0700
    adding a hide all button to hub group blue bars, refs #36354
• src/inc/common.mk
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    8d2c44d8112018dbb115baa707dbffc4778a7006 Wed Sep 10 08:01:40 2025 -0700
    upgrading code for post-2013 nodejs/jshint, refs #36336
• src/lib/cheapcgi.c
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    9d2d19a718d8c3d99f5d73ab1a16283d2fa39c9b Mon Sep 15 03:57:22 2025 -0700
    adding a hide all button to hub group blue bars, refs #36354
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    39594035d23df2f5465f6661eac3fe9a6384622c Mon Sep 15 10:46:59 2025 -0700
    fixing bug in previous commit, refs #36254
• src/utils/qa/qaTestScript.py
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    157dc0bbb3f55a968bbd13cb8ec466a43a144f17 Mon Sep 8 23:10:52 2025 -0700
    Updating link for GenArk Rabbit Hub test, No RM

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