All File Changes

v482_base to v483_preview (2025-05-19 to 2025-05-26) v483

• confs/hgwbeta.hg.conf
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    dc60a185cdaa9ee994f2eead63fe2e48f0804e27 Sun May 25 01:11:13 2025 -0700
    Installing updated hg.conf files from UCSC servers
• confs/hgwdev.hg.conf
  • lines changed 14, context: html, text, full: html, text
    dc60a185cdaa9ee994f2eead63fe2e48f0804e27 Sun May 25 01:11:13 2025 -0700
    Installing updated hg.conf files from UCSC servers
• docs/gatewayTutorial.md
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    2b56d112f1b132d7f52f4efada5e3026180f38b4 Mon May 26 07:55:52 2025 -0700
    Small tweaks for the initial release of the first 2 doc pages, and more importantly, fixing the makefile so that it rsyncs to hgwbeta while preserving time which is required for the RR push script, refs #30335
• docs/index.md
  • lines changed 5, context: html, text, full: html, text
    2b56d112f1b132d7f52f4efada5e3026180f38b4 Mon May 26 07:55:52 2025 -0700
    Small tweaks for the initial release of the first 2 doc pages, and more importantly, fixing the makefile so that it rsyncs to hgwbeta while preserving time which is required for the RR push script, refs #30335
• docs/makefile
  • lines changed 4, context: html, text, full: html, text
    2b56d112f1b132d7f52f4efada5e3026180f38b4 Mon May 26 07:55:52 2025 -0700
    Small tweaks for the initial release of the first 2 doc pages, and more importantly, fixing the makefile so that it rsyncs to hgwbeta while preserving time which is required for the RR push script, refs #30335
• src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html
  • lines changed 21, context: html, text, full: html, text
    65e4ffda81e8925e2f5a45629769fc95472e3b95 Wed May 21 15:46:28 2025 -0700
    SSPsyGene Broad ADGC4 timeline update per NIMH Milestone responses 2025
  • lines changed 2, context: html, text, full: html, text
    fba6fb06141cf261a967e1b7e9742f98cd492e06 Wed May 21 16:17:16 2025 -0700
    Fix to mermaid code specific to Safari, Firefox/Chrome add the 01, Safari needs 2025-07-01 date 01 format
• src/hg/hgBlat/hgBlat.c
  • lines changed 244, context: html, text, full: html, text
    0bae2d58f02a994a23de767dfb2ac8e414253a88 Mon May 19 22:05:32 2025 -0700
    Merging in simplifyBlatAlwaysCreateCT. Uses ajax and hg.conf setting. fixes #32751.
  • lines changed 26, context: html, text, full: html, text
    ded9f614498cabf4aab269835e5f6d3452d43bb5 Tue May 20 11:31:11 2025 -0700
    Removed debugging hgBlat. refs #32751
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 1, context: html, text, full: html, text
    3d0552a0dd234253147737e975229095ad93489e Mon May 26 08:34:21 2025 -0700
    Tweaking the wording to remove filler word, refs #29899
• src/hg/hgTracks/hgTracks.c
  • lines changed 7, context: html, text, full: html, text
    a7cdd40a9c37d4d90c7aa9766c5248c0cb3f259a Wed May 21 17:22:17 2025 -0700
    add bedMethyl type for custom and native tracks
• src/hg/hgTracks/hgTracks.h
  • lines changed 3, context: html, text, full: html, text
    a7cdd40a9c37d4d90c7aa9766c5248c0cb3f259a Wed May 21 17:22:17 2025 -0700
    add bedMethyl type for custom and native tracks
• src/hg/hgTracks/simpleTracks.c
  • lines changed 18, context: html, text, full: html, text
    03eac611bbafeb3463e1efcea835f85b4198092a Wed May 21 08:02:11 2025 -0700
    adapting intron tooltip text for genePred, refs #33749
  • lines changed 43, context: html, text, full: html, text
    a7cdd40a9c37d4d90c7aa9766c5248c0cb3f259a Wed May 21 17:22:17 2025 -0700
    add bedMethyl type for custom and native tracks
• src/hg/hgc/hgc.c
  • lines changed 11, context: html, text, full: html, text
    a7cdd40a9c37d4d90c7aa9766c5248c0cb3f259a Wed May 21 17:22:17 2025 -0700
    add bedMethyl type for custom and native tracks
  • lines changed 15, context: html, text, full: html, text
    581f61540ef366b8d02449f558f4f7ab26dc4ffc Thu May 22 17:03:35 2025 -0700
    add hgc click handler for bedMethyl custom tracks
• src/hg/htdocs/accessibility.html
  • lines changed 67, context: html, text, full: html, text
    e0acf54776ecc8d4f488a1ca6a2263dea409ba60 Mon May 26 07:52:47 2025 -0700
    First draft of the new accessibility page, refs #35572
• src/hg/htdocs/goldenPath/history.html
  • lines changed 1, context: html, text, full: html, text
    9c90c5586d5abf1a3f5676b4c6bbd90564205f27 Mon May 19 11:32:29 2025 -0700
    linking to GI history page, email from Rose
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 61, context: html, text, full: html, text
    bc0c95fdd2e663fdb969eed6b781f6dff967d553 Mon May 19 14:34:19 2025 -0700
    Announcing the GENOCODE Genes track for human and mouse, refs #35186 #35187 #35189
  • lines changed 31, context: html, text, full: html, text
    b48890099442a18e42a8fcb24c0ab66f9278762a Wed May 21 16:32:09 2025 -0700
    Announcing the Varaico track for hg38 and hg19, refs #34595
  • lines changed 1, context: html, text, full: html, text
    2fe5f8a63e1b5ee3d4bda7a555443ba962f7a33c Wed May 21 16:42:33 2025 -0700
    Fixing a typo in the announcement, refs #34595
  • lines changed 2, context: html, text, full: html, text
    028f8f08e2ce12dfee11e4e49464fbfb17929318 Wed May 21 16:45:04 2025 -0700
    Adding a link to the Varaico website, refs #34595
  • lines changed 6, context: html, text, full: html, text
    e511fcb8774bb67ecbcd97cd6986e7b721d52a4d Wed May 21 16:51:43 2025 -0700
    Making minor changes to the Varaico announcement, refs #34595
  • lines changed 1, context: html, text, full: html, text
    dc0850229a44224143a4e677b10c1563c3b543e5 Wed May 21 16:53:23 2025 -0700
    Changing mouse-over since it is the action, refs #34595
• src/hg/htdocs/images/browserInvertedColors.png
  • lines changed 0, context: html, text, full: html, text
    e0acf54776ecc8d4f488a1ca6a2263dea409ba60 Mon May 26 07:52:47 2025 -0700
    First draft of the new accessibility page, refs #35572
• src/hg/htdocs/images/howToChangeFont.gif
  • lines changed 0, context: html, text, full: html, text
    e0acf54776ecc8d4f488a1ca6a2263dea409ba60 Mon May 26 07:52:47 2025 -0700
    First draft of the new accessibility page, refs #35572
• src/hg/htdocs/images/increasedTooltipSize.png
  • lines changed 0, context: html, text, full: html, text
    e0acf54776ecc8d4f488a1ca6a2263dea409ba60 Mon May 26 07:52:47 2025 -0700
    First draft of the new accessibility page, refs #35572
• src/hg/htdocs/images/newsArchImages/Varaico.png
  • lines changed 0, context: html, text, full: html, text
    6ce6df9c40490432e381855a700c0cc63eb88b48 Wed May 21 16:16:12 2025 -0700
    Adding an image for the Varaico track announcement, refs #34595
• src/hg/htdocs/indexMeetings.html
  • lines changed 1, context: html, text, full: html, text
    d765356d78581ff43441a6a71d63c5c6128ba91b Sat May 24 08:01:36 2025 -0700
    Updating booth number, No RM
• src/hg/htdocs/indexNews.html
  • lines changed 13, context: html, text, full: html, text
    14c7bc5418758f5046028bb98cf589d646a9c2c5 Mon May 19 15:04:49 2025 -0700
    Adding the GENCODE Genes announcement to the indexNews page. Fixing a typo for a previous announcement, refs #35186 #35187 #35189
  • lines changed 12, context: html, text, full: html, text
    b48890099442a18e42a8fcb24c0ab66f9278762a Wed May 21 16:32:09 2025 -0700
    Announcing the Varaico track for hg38 and hg19, refs #34595
• src/hg/inc/bedMethyl.h
  • lines changed 97, context: html, text, full: html, text
    a7cdd40a9c37d4d90c7aa9766c5248c0cb3f259a Wed May 21 17:22:17 2025 -0700
    add bedMethyl type for custom and native tracks
• src/hg/js/utils.js
  • lines changed 1, context: html, text, full: html, text
    cedc077ce8279ee92431c6a56243496c1d0fa4fc Wed May 21 07:32:53 2025 -0700
    addressing a bug that Bob found in right-click - hide others, no redmine yet
• src/hg/lib/bedMethyl.as
  • lines changed 23, context: html, text, full: html, text
    a7cdd40a9c37d4d90c7aa9766c5248c0cb3f259a Wed May 21 17:22:17 2025 -0700
    add bedMethyl type for custom and native tracks
• src/hg/lib/bedMethyl.c
  • lines changed 305, context: html, text, full: html, text
    a7cdd40a9c37d4d90c7aa9766c5248c0cb3f259a Wed May 21 17:22:17 2025 -0700
    add bedMethyl type for custom and native tracks
• src/hg/lib/bedMethyl.sql
  • lines changed 26, context: html, text, full: html, text
    a7cdd40a9c37d4d90c7aa9766c5248c0cb3f259a Wed May 21 17:22:17 2025 -0700
    add bedMethyl type for custom and native tracks
• src/hg/lib/botDelay.c
  • lines changed 24, context: html, text, full: html, text
    0bad11bffc60ba7d250b33495d2f392d1964826b Tue May 20 08:39:04 2025 -0700
    Initial bottleneck change to validate hgsids without database access, refs #35763
• src/hg/lib/cart.c
  • lines changed 20, context: html, text, full: html, text
    8ada9901deb92361b234d654e108bdaa9399eb45 Wed May 21 13:37:30 2025 -0700
    trying to lock out bots that make hgsids, no redmine
  • lines changed 3, context: html, text, full: html, text
    2f8bf52537b9b144e7866b0325f8fd3f03441594 Wed May 21 13:55:38 2025 -0700
    tying down the bots a little more, no redmine
  • lines changed 8, context: html, text, full: html, text
    04e020b9f6e9910f06508451888b07bbcd01eadd Wed May 21 14:08:37 2025 -0700
    special penalty for bots with invalid hgsids
  • lines changed 8, context: html, text, full: html, text
    e1d45caaa77d9ba916ff37e09ece4df6d54c4797 Fri May 23 09:44:16 2025 -0700
    do not run bot wait code if run from cli, no redmine
• src/hg/lib/encode/bedMethyl.as
  • lines changed 15, context: html, text, full: html, text
    20b0ce9f1372455ea1baadff8cb52484192b986e Thu May 22 13:38:04 2025 -0700
    remove old ENCODE bedMethyl.as file
• src/hg/lib/hui.c
  • lines changed 2, context: html, text, full: html, text
    fdf4ab468565f1a46bfcda511737c1d6a4e79802 Tue May 20 12:08:33 2025 -0700
    add a line break after place where filters go if there are no filters
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    a7cdd40a9c37d4d90c7aa9766c5248c0cb3f259a Wed May 21 17:22:17 2025 -0700
    add bedMethyl type for custom and native tracks
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    a7cdd40a9c37d4d90c7aa9766c5248c0cb3f259a Wed May 21 17:22:17 2025 -0700
    add bedMethyl type for custom and native tracks
• src/hg/makeDb/doc/archaeaAsmHub/archaea.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    c7bad6715f205dc408321934c1a81826fb62c6f3 Wed May 21 12:26:14 2025 -0700
    adding one per user request refs #29545
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 1, context: html, text, full: html, text
    c7bad6715f205dc408321934c1a81826fb62c6f3 Wed May 21 12:26:14 2025 -0700
    adding one per user request refs #29545
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    76cfe27c9284feea7aa0c597b68ae7235fe24205 Wed May 21 12:54:05 2025 -0700
    adding one for the BRC project refs #34337
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    1015a6b47a62f5dd44c8b57730103237c6808366 Sat May 24 07:32:19 2025 -0700
    adding one per user request refs #29545
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    a391c724e8ae7c5b72ef6248a7ce6a8c57f7a8ed Sun May 25 23:00:29 2025 -0700
    adding one per user request refs #29545
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    958df42e01d6a9392368bd24fe483b152c0c5ac7 Mon May 26 13:37:11 2025 -0700
    adding two per user request refs #29545
• src/hg/makeDb/doc/bacteriaAsmHub/bacteria.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    a391c724e8ae7c5b72ef6248a7ce6a8c57f7a8ed Sun May 25 23:00:29 2025 -0700
    adding one per user request refs #29545
  • lines changed 2, context: html, text, full: html, text
    958df42e01d6a9392368bd24fe483b152c0c5ac7 Mon May 26 13:37:11 2025 -0700
    adding two per user request refs #29545
• src/hg/makeDb/doc/hg19.txt
  • lines changed 4, context: html, text, full: html, text
    c54a0adcdae338ac8e9ae230eb2da1f8d7e65207 Wed May 21 02:49:12 2025 -0700
    Adding varaico make docs
• src/hg/makeDb/doc/hg38/unusualcons.txt
  • lines changed 12, context: html, text, full: html, text
    a442752cfb1738add6158966133902bdc47e69d0 Sun May 25 14:11:39 2025 -0700
    adding ucnebase to unusual conservation track, refs #35703
• src/hg/makeDb/doc/hg38/varaico.txt
  • lines changed 10, context: html, text, full: html, text
    c54a0adcdae338ac8e9ae230eb2da1f8d7e65207 Wed May 21 02:49:12 2025 -0700
    Adding varaico make docs
• src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    1015a6b47a62f5dd44c8b57730103237c6808366 Sat May 24 07:32:19 2025 -0700
    adding one per user request refs #29545
• src/hg/makeDb/doc/tiberius.txt
  • lines changed 220, context: html, text, full: html, text
    6619816b39594b4cafca3215c7d8ac4dfd185652 Tue May 20 14:50:43 2025 -0700
    document procedure for Tiberius gene predictions addition to GenArk hubs refs #34917
  • lines changed 24, context: html, text, full: html, text
    74e53377949096d1ea6f3d78ec59b1914f1373d8 Tue May 20 14:58:35 2025 -0700
    note about trackDb files and beta and public release control refs #34917
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    02f4db8b8cb4a5fce01f05c91f2dd48bb4e4b1ac Tue May 20 15:05:30 2025 -0700
    indicate how the alpha version can be seen on genome-test refs #34917
• src/hg/makeDb/doc/viralAsmHub/viral.orderList.tsv
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    76cfe27c9284feea7aa0c597b68ae7235fe24205 Wed May 21 12:54:05 2025 -0700
    adding one for the BRC project refs #34337
• src/hg/makeDb/hgLoadBed/makefile
  • lines changed 1, context: html, text, full: html, text
    a7cdd40a9c37d4d90c7aa9766c5248c0cb3f259a Wed May 21 17:22:17 2025 -0700
    add bedMethyl type for custom and native tracks
• src/hg/makeDb/trackDb/contrib/tiberius/Tiberius.html
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    0800aafe419bb4a252a0656a75b83e89ef27ec20 Thu May 22 14:20:58 2025 -0700
    use standard UCSC format for reference refs #34917
• src/hg/makeDb/trackDb/contrib/tiberius/tiberius.trackDb.txt
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    4188ce8621f2ed8565863a04cf1743cad5a971a8 Thu May 22 15:25:52 2025 -0700
    turn off score filter for the trackUi page since all scores are zero refs #34917
• src/hg/makeDb/trackDb/human/clinvar.alpha.ra
  • lines changed 1, context: html, text, full: html, text
    697b862c4a5e14cc41f03dfa5757209898c3d5b8 Wed May 21 07:14:40 2025 -0700
    triangle decorators for the clinvar track, #35750
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    e68cc6315fa92edde16a3e27015a15cb94290440 Thu May 22 14:34:00 2025 -0700
    Adding files that were staged as the otto user, no Redmine.
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    58525d08a408e02abf1ae54baec17eab134806b9 Fri May 23 11:44:05 2025 -0700
    undoing Jairos edit that removed the clinvar alpha decorators, refs #35750
• src/hg/makeDb/trackDb/human/clinvar.ra
  • lines changed 1, context: html, text, full: html, text
    e68cc6315fa92edde16a3e27015a15cb94290440 Thu May 22 14:34:00 2025 -0700
    Adding files that were staged as the otto user, no Redmine.
• src/hg/makeDb/trackDb/human/clinvarAlpha.html
  • lines changed 206, context: html, text, full: html, text
    697b862c4a5e14cc41f03dfa5757209898c3d5b8 Wed May 21 07:14:40 2025 -0700
    triangle decorators for the clinvar track, #35750
• src/hg/makeDb/trackDb/human/hg19/knownGene.ra
  • lines changed 1, context: html, text, full: html, text
    86e7ae6ee58250f38e017cd73cffe8253d3a92bf Mon May 19 15:05:30 2025 -0700
    Adding pennantIcons for the knownGene release, refs #35186 #35187 #35189
• src/hg/makeDb/trackDb/human/hg38/knownGene.ra
  • lines changed 1, context: html, text, full: html, text
    86e7ae6ee58250f38e017cd73cffe8253d3a92bf Mon May 19 15:05:30 2025 -0700
    Adding pennantIcons for the knownGene release, refs #35186 #35187 #35189
• src/hg/makeDb/trackDb/human/hg38/unusualcons.html
  • lines changed 30, context: html, text, full: html, text
    a442752cfb1738add6158966133902bdc47e69d0 Sun May 25 14:11:39 2025 -0700
    adding ucnebase to unusual conservation track, refs #35703
• src/hg/makeDb/trackDb/human/hg38/unusualcons.ra
  • lines changed 24, context: html, text, full: html, text
    a442752cfb1738add6158966133902bdc47e69d0 Sun May 25 14:11:39 2025 -0700
    adding ucnebase to unusual conservation track, refs #35703
• src/hg/makeDb/trackDb/human/panelApp.alpha.ra
  • lines changed 104, context: html, text, full: html, text
    38f919b35b31baa4e985fa0980bc92d531eafd8d Tue May 20 14:54:20 2025 -0700
    First pass of panelApp australia track, refs #35758
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    5d72bddf0393f961e00b2b354457fdcc8e62bc8d Thu May 22 16:36:33 2025 -0700
    Updating the panelApp otto job to simplify the overall script from 3 seprate ones to a single call, and also adding support for the similar (but not identical) panelApp australia resource, refs #35758
• src/hg/makeDb/trackDb/human/panelApp.html
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    cab14fa3bf11dc42ebf6250ee322c9c5e86bcc14 Thu May 22 03:45:22 2025 -0700
    docing panelApp AU, refs #35758
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    3ff14cf26bd148e6bcf80df13e6b8c0b4c5da165 Mon May 26 01:05:46 2025 -0700
    Clarifying desc page, we no longer have missing genes except for those with version numbers <.99. Refs #35757
• src/hg/makeDb/trackDb/human/trackDb.ra
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    38f919b35b31baa4e985fa0980bc92d531eafd8d Tue May 20 14:54:20 2025 -0700
    First pass of panelApp australia track, refs #35758
  • lines changed 6, context: html, text, full: html, text
    8e903dc32b2ee82114c67f6f43c89311b3f6db2d Tue May 20 15:10:04 2025 -0700
    Adding the HTML 'varsInPubs.html' to the subtracks in the supertrack that were missing. Adding the number of publications and variant effect to the Varaico mouseover. Bolding items in the mouseover, refs #34595
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    42d1e9539243d571eeb740e71eda7e31ce5f599a Wed May 21 14:30:21 2025 -0700
    Staging the Varaico track on hgwbeta, refs # 34595
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    356669aaa62e51676e91f81dc268fcd1af1c2dda Wed May 21 15:21:28 2025 -0700
    Releasing the Varaico tracks for hg38 and hg19, refs #34595
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    b48890099442a18e42a8fcb24c0ab66f9278762a Wed May 21 16:32:09 2025 -0700
    Announcing the Varaico track for hg38 and hg19, refs #34595
• src/hg/makeDb/trackDb/human/varaico.html
  • lines changed 97, context: html, text, full: html, text
    7c6d98294ac965c787499157e31178d353caed96 Fri May 23 14:48:41 2025 -0700
    Commenting out the PubTator track since it isn't released yet, refs #34595
• src/hg/makeDb/trackDb/human/varsInPubs.html
  • lines changed 3, context: html, text, full: html, text
    07baf83163390663f5df285ebf4c620ce527fba0 Thu May 22 09:27:56 2025 -0700
    Adding a note about the coloring in the Varaico track, refs #34595
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    a2469956ad4608f62f39a0564eaba781a71f2f79 Thu May 22 14:59:35 2025 -0700
    Changing the description of the colors for the Varaico track, refs #34595
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    7c6d98294ac965c787499157e31178d353caed96 Fri May 23 14:48:41 2025 -0700
    Commenting out the PubTator track since it isn't released yet, refs #34595
• src/hg/makeDb/trackDb/mouse/mm39/knownGene.ra
  • lines changed 1, context: html, text, full: html, text
    86e7ae6ee58250f38e017cd73cffe8253d3a92bf Mon May 19 15:05:30 2025 -0700
    Adding pennantIcons for the knownGene release, refs #35186 #35187 #35189
• src/hg/utils/automation/asmHubTrackDb.sh
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    083fc14e534ca67e2355bab5b3e8f399bb0dc1f4 Wed May 21 12:22:52 2025 -0700
    beware some viral genomes will not have ix ixx files for ncbiGene track refs #34337
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    07a637e0db9080685f99bc24e161858cb3094b41 Thu May 22 13:55:53 2025 -0700
    correct URL outlink on name2 field for NCBI RefSeq gene tracks refs #34704
• src/hg/utils/automation/doAssemblyHub.pl
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    083fc14e534ca67e2355bab5b3e8f399bb0dc1f4 Wed May 21 12:22:52 2025 -0700
    beware some viral genomes will not have ix ixx files for ncbiGene track refs #34337
• src/hg/utils/automation/doRecipBest.pl
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    5c59ddc77713387809ce52e0e553eeb3e7b7ee64 Mon May 19 12:57:47 2025 -0700
    better explicit recognition of hs1 oddities refs #35712
• src/hg/utils/otto/clinvar/clinVarToBed
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    697b862c4a5e14cc41f03dfa5757209898c3d5b8 Wed May 21 07:14:40 2025 -0700
    triangle decorators for the clinvar track, #35750
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    e68cc6315fa92edde16a3e27015a15cb94290440 Thu May 22 14:34:00 2025 -0700
    Adding files that were staged as the otto user, no Redmine.
• src/hg/utils/otto/clinvar/clinvar.as
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    697b862c4a5e14cc41f03dfa5757209898c3d5b8 Wed May 21 07:14:40 2025 -0700
    triangle decorators for the clinvar track, #35750
• src/hg/utils/otto/clinvar/clinvarDecoration.as
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    e68cc6315fa92edde16a3e27015a15cb94290440 Thu May 22 14:34:00 2025 -0700
    Adding files that were staged as the otto user, no Redmine.
• src/hg/utils/otto/panelApp/doPanelApp.py
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    5d72bddf0393f961e00b2b354457fdcc8e62bc8d Thu May 22 16:36:33 2025 -0700
    Updating the panelApp otto job to simplify the overall script from 3 seprate ones to a single call, and also adding support for the similar (but not identical) panelApp australia resource, refs #35758
• src/utils/qa/weeklybld/buildEnv.csh
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    4c2504be1e5a40507ca332ef865805a176d6a154 Mon May 26 23:35:25 2025 -0700
    v483 preview1, refs #35666

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