All File Changes

v472_preview to v472_preview2 (2024-09-23 to 2024-09-30) v472

• src/hg/hgGateway/hgGateway.c
  • lines changed 11, context: html, text, full: html, text
    2776159fd4f68c3c5a1a114f238dc2f568a5bd64 Fri Sep 27 11:07:16 2024 -0700
    allow use of new genark table with more columns refs #32596
  • lines changed 71, context: html, text, full: html, text
    621822a450d38d641f59df03aa461fa7dba64da6 Fri Sep 27 15:24:08 2024 -0700
    now with one word searches on the assemblyList table refs #32596
  • lines changed 2, context: html, text, full: html, text
    5442a9baf9e3667418b1dbda2225d9c9389b7249 Fri Sep 27 15:35:26 2024 -0700
    order by priority for the assemblyList result refs #32596
  • lines changed 8, context: html, text, full: html, text
    e5297f22c5d7c1cb0b041b0ea4c66206a244c90b Mon Sep 30 10:36:52 2024 -0700
    add multiple word search to the hgGateway assembly search box function refs #32596
  • lines changed 8, context: html, text, full: html, text
    ccda596950ffdad4d7560c1bb660b31c1bd3b55a Mon Sep 30 11:07:54 2024 -0700
    put a limit on genark returned list refs #32596
• src/hg/hgTables/identifiers.c
  • lines changed 2, context: html, text, full: html, text
    a6770479059c1d3ed0a77f69ceac2ae19981e89f Thu Sep 26 18:29:31 2024 -0700
    Since hubs like Tair10 call these functions with a NULL conn, just needed to add a check for that in hgTables identifiers getXrefInfo function. fixes #34495
• src/hg/hgTracks/config.c
  • lines changed 9, context: html, text, full: html, text
    1d351c15d3e2f6c7e3cb5e9773d2d38327bc9a36 Tue Sep 24 17:24:02 2024 -0700
    It turns out that parallelFetch.timeout already implements this Revert "add ability to set a timeout on remote loads" This reverts commit 6afa9dd4343c3b66ff09f39735170ec8be5f282e.
  • lines changed 5, context: html, text, full: html, text
    80094ad7168ce2e636ae8a28c742c32b174dfb92 Thu Sep 26 13:26:12 2024 -0700
    allow users to change parallelFetch.timeout from the configure screen
• src/hg/hgTracks/hgTracks.c
  • lines changed 85, context: html, text, full: html, text
    3351b7938091d8bccaea76ef006d729f5e169a4f Tue Sep 24 17:23:10 2024 -0700
    if we go over the 32k PNG size limit, put all the tracks that can wiggle into wiggle mode and try again
  • lines changed 48, context: html, text, full: html, text
    1d351c15d3e2f6c7e3cb5e9773d2d38327bc9a36 Tue Sep 24 17:24:02 2024 -0700
    It turns out that parallelFetch.timeout already implements this Revert "add ability to set a timeout on remote loads" This reverts commit 6afa9dd4343c3b66ff09f39735170ec8be5f282e.
  • lines changed 85, context: html, text, full: html, text
    d7861537f514c72ecd89dd51389794cd8f07baef Wed Sep 25 09:15:28 2024 -0700
    Revert "if we go over the 32k PNG size limit, put all the tracks that can wiggle" This reverts commit 3351b7938091d8bccaea76ef006d729f5e169a4f.
  • lines changed 13, context: html, text, full: html, text
    80094ad7168ce2e636ae8a28c742c32b174dfb92 Thu Sep 26 13:26:12 2024 -0700
    allow users to change parallelFetch.timeout from the configure screen
  • lines changed 85, context: html, text, full: html, text
    25d11f512ac8d8b6605b81a770e0a6d9b121ec12 Thu Sep 26 13:31:58 2024 -0700
    Revert "Revert "if we go over the 32k PNG size limit, put all the tracks that can wiggle"" This reverts commit d7861537f514c72ecd89dd51389794cd8f07baef.
  • lines changed 2, context: html, text, full: html, text
    f1d2ee5e0e45a31e08d56f8cc104f3c57a6d32f2 Thu Sep 26 14:29:52 2024 -0700
    fix a couple of bugs in the 32K redraw code.
  • lines changed 3, context: html, text, full: html, text
    706e531073a5d75568667727f0f995c28d964612 Fri Sep 27 11:48:47 2024 -0700
    add a warning message if exceed 32k and went into density coverage for all bed tracks
• src/hg/hgTracks/hgTracks.h
  • lines changed 1, context: html, text, full: html, text
    3351b7938091d8bccaea76ef006d729f5e169a4f Tue Sep 24 17:23:10 2024 -0700
    if we go over the 32k PNG size limit, put all the tracks that can wiggle into wiggle mode and try again
  • lines changed 3, context: html, text, full: html, text
    1d351c15d3e2f6c7e3cb5e9773d2d38327bc9a36 Tue Sep 24 17:24:02 2024 -0700
    It turns out that parallelFetch.timeout already implements this Revert "add ability to set a timeout on remote loads" This reverts commit 6afa9dd4343c3b66ff09f39735170ec8be5f282e.
  • lines changed 1, context: html, text, full: html, text
    d7861537f514c72ecd89dd51389794cd8f07baef Wed Sep 25 09:15:28 2024 -0700
    Revert "if we go over the 32k PNG size limit, put all the tracks that can wiggle" This reverts commit 3351b7938091d8bccaea76ef006d729f5e169a4f.
  • lines changed 3, context: html, text, full: html, text
    80094ad7168ce2e636ae8a28c742c32b174dfb92 Thu Sep 26 13:26:12 2024 -0700
    allow users to change parallelFetch.timeout from the configure screen
  • lines changed 1, context: html, text, full: html, text
    25d11f512ac8d8b6605b81a770e0a6d9b121ec12 Thu Sep 26 13:31:58 2024 -0700
    Revert "Revert "if we go over the 32k PNG size limit, put all the tracks that can wiggle"" This reverts commit d7861537f514c72ecd89dd51389794cd8f07baef.
• src/hg/hgTracks/simpleTracks.c
  • lines changed 5, context: html, text, full: html, text
    3351b7938091d8bccaea76ef006d729f5e169a4f Tue Sep 24 17:23:10 2024 -0700
    if we go over the 32k PNG size limit, put all the tracks that can wiggle into wiggle mode and try again
  • lines changed 5, context: html, text, full: html, text
    d7861537f514c72ecd89dd51389794cd8f07baef Wed Sep 25 09:15:28 2024 -0700
    Revert "if we go over the 32k PNG size limit, put all the tracks that can wiggle" This reverts commit 3351b7938091d8bccaea76ef006d729f5e169a4f.
  • lines changed 5, context: html, text, full: html, text
    25d11f512ac8d8b6605b81a770e0a6d9b121ec12 Thu Sep 26 13:31:58 2024 -0700
    Revert "Revert "if we go over the 32k PNG size limit, put all the tracks that can wiggle"" This reverts commit d7861537f514c72ecd89dd51389794cd8f07baef.
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 21, context: html, text, full: html, text
    ab7e6d991f9378a256768008d3f98458c748af21 Tue Sep 24 13:04:06 2024 -0700
    Announcing the NuMTs track for hg38, refs #34302
  • lines changed 1, context: html, text, full: html, text
    e4eac4b68e48f4b7989d7471d0147c325cce4c6c Tue Sep 24 15:13:49 2024 -0700
    Fixing a typo (grey --> gray), refs #34303
  • lines changed 47, context: html, text, full: html, text
    7e865ba003ca775541643d5eeeb56c597f3417e7 Fri Sep 27 15:36:02 2024 -0700
    Releasing the six new gnomAD v4.1 tracks, #34511
  • lines changed 47, context: html, text, full: html, text
    42a90b406e18f8eb88ecf4ee3ee96f54a5814f75 Fri Sep 27 17:07:16 2024 -0700
    Revert "Releasing the six new gnomAD v4.1 tracks, #34511" This reverts commit 7e865ba003ca775541643d5eeeb56c597f3417e7.
  • lines changed 50, context: html, text, full: html, text
    5d9669325edefa6193f94910b74dc48f9655ffc7 Sun Sep 29 17:50:32 2024 -0700
    Releasing the six new gnomAD v4.1 tracks, #34511
• src/hg/htdocs/images/clinicalTutorialIcon.png
  • lines changed 0, context: html, text, full: html, text
    3fb4a7e834dedd4424da92fd024e0a7aabd2f639 Thu Sep 26 18:02:19 2024 -0700
    Adding the icon for the temporary tutorial ad on the home page, refs #33485
• src/hg/htdocs/images/gnomADv4_GATK_gCNV.png
  • lines changed 0, context: html, text, full: html, text
    70a4785a3f116a48ccf18c302a68de4d47ea2f0c Wed Sep 25 10:58:36 2024 -0700
    Making edits to the gnomAD v4.1 CNV track from Lou's feedback, refs #34253
• src/hg/htdocs/index.html
  • lines changed 15, context: html, text, full: html, text
    2148a49f49c7a74ec76d7ea2a8ffadee504a7175 Thu Sep 26 18:05:25 2024 -0700
    Adding a little padding I hadn't noticed we needed on dev because of our development environment warning, refs #33485
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    ab7e6d991f9378a256768008d3f98458c748af21 Tue Sep 24 13:04:06 2024 -0700
    Announcing the NuMTs track for hg38, refs #34302
  • lines changed 12, context: html, text, full: html, text
    7e865ba003ca775541643d5eeeb56c597f3417e7 Fri Sep 27 15:36:02 2024 -0700
    Releasing the six new gnomAD v4.1 tracks, #34511
  • lines changed 12, context: html, text, full: html, text
    42a90b406e18f8eb88ecf4ee3ee96f54a5814f75 Fri Sep 27 17:07:16 2024 -0700
    Revert "Releasing the six new gnomAD v4.1 tracks, #34511" This reverts commit 7e865ba003ca775541643d5eeeb56c597f3417e7.
  • lines changed 12, context: html, text, full: html, text
    5d9669325edefa6193f94910b74dc48f9655ffc7 Sun Sep 29 17:50:32 2024 -0700
    Releasing the six new gnomAD v4.1 tracks, #34511
• src/hg/hubApi/findGenome.c
  • lines changed 20, context: html, text, full: html, text
    9d9f00e7ae0c4007130239f651fbc587f25f244f Tue Sep 24 23:02:55 2024 -0700
    eliminate specific references to hgcentraltest refs #32596
• src/hg/inc/assemblyList.h
  • lines changed 6, context: html, text, full: html, text
    e5297f22c5d7c1cb0b041b0ea4c66206a244c90b Mon Sep 30 10:36:52 2024 -0700
    add multiple word search to the hgGateway assembly search box function refs #32596
• src/hg/inc/fakeCurl.h
  • lines changed 2, context: html, text, full: html, text
    8ea9060d3944ce427e6485c356edc26d7dafb8d3 Wed Sep 25 15:57:16 2024 -0700
    fakeCurl needn't open the same file repeatedly for requests to the same URL, refs #34493
• src/hg/js/hgTracks.js
  • lines changed 2, context: html, text, full: html, text
    0f6dbe96fa46d69d5f198bdd5b5ed242b069fab9 Mon Sep 23 15:17:40 2024 -0700
    Make sure there is only one highlight color picker for the track highlightBy settings, since they all share the same highlight color. Add an info icon to note that all highlights use the same color and are additive.
  • lines changed 4, context: html, text, full: html, text
    2f8c4b4c077c8704674e72050fada6f5a7da63ab Thu Sep 26 12:12:45 2024 -0700
    Remove recommended track sets title hack and make the dialog non-resizable, refs Max meeting
  • lines changed 10, context: html, text, full: html, text
    b0b2f92c21f27f0bd4a365f92e5ffeac448b4639 Fri Sep 27 10:07:09 2024 -0700
    Make all dialogs not resizable, refs #13253
  • lines changed 102, context: html, text, full: html, text
    9a6f8e36d8af2950b88c9613c0003f1dc298507e Mon Sep 30 03:07:22 2024 -0700
    adding right click options: hide all others, move to top/bottom, refs #23793
• src/hg/js/hui.js
  • lines changed 5, context: html, text, full: html, text
    0f6dbe96fa46d69d5f198bdd5b5ed242b069fab9 Mon Sep 23 15:17:40 2024 -0700
    Make sure there is only one highlight color picker for the track highlightBy settings, since they all share the same highlight color. Add an info icon to note that all highlights use the same color and are additive.
  • lines changed 7, context: html, text, full: html, text
    7de2982a8966b32914d5d20b76b5f2cf97f7cd7d Wed Sep 25 15:34:46 2024 -0700
    Fix checkbox selection not graying out options as a result of jquery upgrade, refs #13253
• src/hg/js/spectrum.min.js
  • lines changed 1, context: html, text, full: html, text
    0c4fb9ff22eb8f8379f00dea9fba9680f965d57e Tue Sep 24 12:49:50 2024 -0700
    Make span elements for spectrum palette not self closing because jquery 3.5 does not allow those types of tags anymore in the .html method, whic h spectrum.min.js relies on, refs #13253
• src/hg/js/tutorials/clinicalTutorial.js
  • lines changed 2, context: html, text, full: html, text
    12c96f9dbae79c62ed691034dc9bc2d1a1f0f3a6 Tue Sep 24 16:14:57 2024 -0700
    Addding a note that you can convert between hg19 and hg38, refs #33732
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    6c72914d7ab77f5f3debc1fda9c8ee6de3957842 Tue Sep 24 16:44:13 2024 -0700
    Fixing some issues that came up after Chris upgraded the jQuery version. refs #33732
  • lines changed 2, context: html, text, full: html, text
    7d2c19927eb35296e4b37b8516fcb8c4d6a65529 Tue Sep 24 16:51:11 2024 -0700
    Editing the conversion tooltip. Making the text more specific to hg38/hg19 since those are what the clinicians will be using, refs #33732
• src/hg/js/ui.dropdownchecklist.js
  • lines changed 2, context: html, text, full: html, text
    9532bd0c7e1a42a9f035550a5b46a181564f23ca Tue Sep 24 12:00:13 2024 -0700
    Change dropdownchecklist parent height calculation to use offset() instead of position() because the position() function now uses the parents offset instead of the document offset, refs #13253
• src/hg/lib/assemblyList.c
  • lines changed 40, context: html, text, full: html, text
    e5297f22c5d7c1cb0b041b0ea4c66206a244c90b Mon Sep 30 10:36:52 2024 -0700
    add multiple word search to the hgGateway assembly search box function refs #32596
• src/hg/lib/customFactory.c
  • lines changed 3, context: html, text, full: html, text
    0cafd2babfa1a47969f1a138da19600bbcfdd1e6 Mon Sep 30 09:17:46 2024 -0700
    Expanding error for local udc load when udc.localDir hasn't been set, no ticket
• src/hg/lib/fakeCurl.c
  • lines changed 26, context: html, text, full: html, text
    8ea9060d3944ce427e6485c356edc26d7dafb8d3 Wed Sep 25 15:57:16 2024 -0700
    fakeCurl needn't open the same file repeatedly for requests to the same URL, refs #34493
• src/hg/lib/genark.sql
  • lines changed 1, context: html, text, full: html, text
    e7b66711387ac5b785cd52148ca4ce1180609167 Fri Sep 27 11:13:00 2024 -0700
    add the FULLTEXT index refs #32596
• src/hg/lib/hui.c
  • lines changed 13, context: html, text, full: html, text
    0f6dbe96fa46d69d5f198bdd5b5ed242b069fab9 Mon Sep 23 15:17:40 2024 -0700
    Make sure there is only one highlight color picker for the track highlightBy settings, since they all share the same highlight color. Add an info icon to note that all highlights use the same color and are additive.
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 14, context: html, text, full: html, text
    772a45f22132de29b8ab26d4b42a2c0fe6088ae5 Tue Sep 24 10:16:18 2024 -0700
    BRC update nearing completion refs #34337
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    47ed7b59bcc5fb7777382709b4ae4e3b27ba2b5a Tue Sep 24 14:37:08 2024 -0700
    eliminate some duplicates refs $34337
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    766cc89bdfe27cfd40cd68e46eb266dccdfe6077 Wed Sep 25 23:28:03 2024 -0700
    BRC update refs #34337
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    6cb05644f9dc2dcb89eba11052f5a218116c083c Thu Sep 26 08:52:03 2024 -0700
    eliminate mistaken duplicates refs #34337
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    ea5d663f1b5af778bb8ba4d10d956d248c9566c2 Thu Sep 26 14:28:03 2024 -0700
    BRC update gets up to 769 refs #34337
• src/hg/makeDb/doc/asmHubs/sendToHgdownload.sh
  • lines changed 4, context: html, text, full: html, text
    444891eef90db1bdbff678ed49c19f3fd5c9f68d Tue Sep 24 15:31:27 2024 -0700
    do not try to send UCSC database browsers refs #34337
• src/hg/makeDb/doc/asmHubs/tsvToJson.py
  • lines changed 2, context: html, text, full: html, text
    9cf3f9dfbd2770a517953c7f43ffade95be9a9de Tue Sep 24 15:26:53 2024 -0700
    add the ucscBrowser link to the stderr outpur ref #34337
• src/hg/makeDb/doc/brcAsmHub/brc.orderList.tsv
  • lines changed 23, context: html, text, full: html, text
    772a45f22132de29b8ab26d4b42a2c0fe6088ae5 Tue Sep 24 10:16:18 2024 -0700
    BRC update nearing completion refs #34337
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    ea5d663f1b5af778bb8ba4d10d956d248c9566c2 Thu Sep 26 14:28:03 2024 -0700
    BRC update gets up to 769 refs #34337
• src/hg/makeDb/doc/fungiAsmHub/fungi.orderList.tsv
  • lines changed 6, context: html, text, full: html, text
    36a317dc1cd15748c1fe2b18eef4991141fe1464 Mon Sep 23 15:13:11 2024 -0700
    BRC update moved some to legacy refs #34337
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    772a45f22132de29b8ab26d4b42a2c0fe6088ae5 Tue Sep 24 10:16:18 2024 -0700
    BRC update nearing completion refs #34337
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    f9f8a289464407f2f6a3337760bf8270d2117517 Tue Sep 24 14:36:40 2024 -0700
    asmHubs/master.run.list
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    9a4f1d0a4e48296598ef888c93c89930518ed59b Wed Sep 25 14:36:20 2024 -0700
    eliminate some duplicates refs #34337
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    766cc89bdfe27cfd40cd68e46eb266dccdfe6077 Wed Sep 25 23:28:03 2024 -0700
    BRC update refs #34337
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
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    c4c8fc39c7091c0f19878c93f8b92897c756b95d Mon Sep 23 15:15:11 2024 -0700
    BRC moved one to legacy refs #34337
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    772a45f22132de29b8ab26d4b42a2c0fe6088ae5 Tue Sep 24 10:16:18 2024 -0700
    BRC update nearing completion refs #34337
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    f9f8a289464407f2f6a3337760bf8270d2117517 Tue Sep 24 14:36:40 2024 -0700
    asmHubs/master.run.list
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    9a4f1d0a4e48296598ef888c93c89930518ed59b Wed Sep 25 14:36:20 2024 -0700
    eliminate some duplicates refs #34337
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    766cc89bdfe27cfd40cd68e46eb266dccdfe6077 Wed Sep 25 23:28:03 2024 -0700
    BRC update refs #34337
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    6cb05644f9dc2dcb89eba11052f5a218116c083c Thu Sep 26 08:52:03 2024 -0700
    eliminate mistaken duplicates refs #34337
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    ea5d663f1b5af778bb8ba4d10d956d248c9566c2 Thu Sep 26 14:28:03 2024 -0700
    BRC update gets up to 769 refs #34337
• src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt
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    9a4f1d0a4e48296598ef888c93c89930518ed59b Wed Sep 25 14:36:20 2024 -0700
    eliminate some duplicates refs #34337
• src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv
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    9a4f1d0a4e48296598ef888c93c89930518ed59b Wed Sep 25 14:36:20 2024 -0700
    eliminate some duplicates refs #34337
• src/hg/makeDb/trackDb/human/hg38/gnomad.alpha.ra
  • lines changed 4, context: html, text, full: html, text
    70a4785a3f116a48ccf18c302a68de4d47ea2f0c Wed Sep 25 10:58:36 2024 -0700
    Making edits to the gnomAD v4.1 CNV track from Lou's feedback, refs #34253
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    97cc4f750cfcd08cd7f5a5197d56db498ad4053c Wed Sep 25 16:14:29 2024 -0700
    Making small tweaks to gnomAD CNV track, upper case the short label and more information on the desc page. Refs #34253
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    5d9669325edefa6193f94910b74dc48f9655ffc7 Sun Sep 29 17:50:32 2024 -0700
    Releasing the six new gnomAD v4.1 tracks, #34511
• src/hg/makeDb/trackDb/human/hg38/gnomad.constraint.public.ra
  • lines changed 4, context: html, text, full: html, text
    7e865ba003ca775541643d5eeeb56c597f3417e7 Fri Sep 27 15:36:02 2024 -0700
    Releasing the six new gnomAD v4.1 tracks, #34511
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    42a90b406e18f8eb88ecf4ee3ee96f54a5814f75 Fri Sep 27 17:07:16 2024 -0700
    Revert "Releasing the six new gnomAD v4.1 tracks, #34511" This reverts commit 7e865ba003ca775541643d5eeeb56c597f3417e7.
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    5d9669325edefa6193f94910b74dc48f9655ffc7 Sun Sep 29 17:50:32 2024 -0700
    Releasing the six new gnomAD v4.1 tracks, #34511
• src/hg/makeDb/trackDb/human/hg38/gnomad.ra
  • lines changed 46, context: html, text, full: html, text
    fbc578a21b2fedcc007d98964cced9a0a5b3d410 Thu Sep 26 14:58:45 2024 -0700
    Staging the gnomAD v4.1 SV and CNVs tracks, refs #33823 #34253
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    7e865ba003ca775541643d5eeeb56c597f3417e7 Fri Sep 27 15:36:02 2024 -0700
    Releasing the six new gnomAD v4.1 tracks, #34511
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    42a90b406e18f8eb88ecf4ee3ee96f54a5814f75 Fri Sep 27 17:07:16 2024 -0700
    Revert "Releasing the six new gnomAD v4.1 tracks, #34511" This reverts commit 7e865ba003ca775541643d5eeeb56c597f3417e7.
  • lines changed 156, context: html, text, full: html, text
    5d9669325edefa6193f94910b74dc48f9655ffc7 Sun Sep 29 17:50:32 2024 -0700
    Releasing the six new gnomAD v4.1 tracks, #34511
• src/hg/makeDb/trackDb/human/hg38/gnomadCNV.html
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    70a4785a3f116a48ccf18c302a68de4d47ea2f0c Wed Sep 25 10:58:36 2024 -0700
    Making edits to the gnomAD v4.1 CNV track from Lou's feedback, refs #34253
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    bb04c8d48c3857e75ddbc762546e3f17c72a4afa Wed Sep 25 11:34:00 2024 -0700
    Updating the mouseover description for the gnomAD v4.1 CNV track, refs #34253
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    0f99f0096e71788dc16530884fe75171d5eb5c28 Wed Sep 25 16:13:49 2024 -0700
    Making small tweaks to gnomAD CNV track, upper case the short label and more information on the desc page. Refs #34253
• src/hg/makeDb/trackDb/human/hg38/knownGeneArchive.ra
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    4251a33256fefa88dbf91845b4fda2e53e3ef6bf Wed Sep 25 15:17:08 2024 -0700
    Changing the order of the tracks to show the most recent at the top, refs #33232
• src/hg/makeDb/trackDb/human/hg38/nuMtSeq.html
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    17faa1a197875dfb6c38efce05e68740b2c23c32 Mon Sep 23 16:08:49 2024 -0700
    Fixing a run on sentence. refs #34303
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
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    7e865ba003ca775541643d5eeeb56c597f3417e7 Fri Sep 27 15:36:02 2024 -0700
    Releasing the six new gnomAD v4.1 tracks, #34511
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    42a90b406e18f8eb88ecf4ee3ee96f54a5814f75 Fri Sep 27 17:07:16 2024 -0700
    Revert "Releasing the six new gnomAD v4.1 tracks, #34511" This reverts commit 7e865ba003ca775541643d5eeeb56c597f3417e7.
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    5d9669325edefa6193f94910b74dc48f9655ffc7 Sun Sep 29 17:50:32 2024 -0700
    Releasing the six new gnomAD v4.1 tracks, #34511
• src/hg/utils/automation/doAssemblyHub.pl
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    22125620d4dc7d776599c3bf6e99932ba43a6db5 Thu Sep 26 10:28:21 2024 -0700
    allow an assembly to work even if it has no repeatMasker result refs #34337
• src/hg/utils/otto/genArk/README
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    736e0d588f220cef8093cf1ba6ea3bb4f376baf4 Fri Sep 27 11:25:40 2024 -0700
    now loading up the new expanded genark.hgcentral table refs #32596
• src/hg/utils/otto/genArk/addAssemblyList.sh
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    736e0d588f220cef8093cf1ba6ea3bb4f376baf4 Fri Sep 27 11:25:40 2024 -0700
    now loading up the new expanded genark.hgcentral table refs #32596
• src/hg/utils/otto/genArk/dbDb.clade.year.acc.tsv
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    736e0d588f220cef8093cf1ba6ea3bb4f376baf4 Fri Sep 27 11:25:40 2024 -0700
    now loading up the new expanded genark.hgcentral table refs #32596
• src/inc/udc.h
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    1d351c15d3e2f6c7e3cb5e9773d2d38327bc9a36 Tue Sep 24 17:24:02 2024 -0700
    It turns out that parallelFetch.timeout already implements this Revert "add ability to set a timeout on remote loads" This reverts commit 6afa9dd4343c3b66ff09f39735170ec8be5f282e.
• src/lib/udc.c
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    1d351c15d3e2f6c7e3cb5e9773d2d38327bc9a36 Tue Sep 24 17:24:02 2024 -0700
    It turns out that parallelFetch.timeout already implements this Revert "add ability to set a timeout on remote loads" This reverts commit 6afa9dd4343c3b66ff09f39735170ec8be5f282e.
• src/utils/qa/weeklybld/buildEnv.csh
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    403210e7ca02e32cca286934165ae415a6cb926e Mon Sep 30 11:38:36 2024 -0700
    v472 preview2, refs #34490

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