All File Changes

v467_base to v468_preview (2024-06-24 to 2024-07-01) v468

• src/hg/cgilib/bedCart.c
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    323b67fc39bc7c1c8763632df94590c44fa61cfe Tue Jun 25 01:34:18 2024 -0700
    null pointer fix, refs #28498
• src/hg/cgilib/cartEdit3.c
  • lines changed 39, context: html, text, full: html, text
    836a45a3110e74d7880d674826515ba3d7065297 Wed Jun 26 10:11:49 2024 -0700
    cart rewrites for #32813
• src/hg/cgilib/cartRewrite.c
  • lines changed 2, context: html, text, full: html, text
    836a45a3110e74d7880d674826515ba3d7065297 Wed Jun 26 10:11:49 2024 -0700
    cart rewrites for #32813
• src/hg/cgilib/makefile
  • lines changed 1, context: html, text, full: html, text
    836a45a3110e74d7880d674826515ba3d7065297 Wed Jun 26 10:11:49 2024 -0700
    cart rewrites for #32813
• src/hg/hgBlat/hgBlat.c
  • lines changed 2, context: html, text, full: html, text
    b8d36ce63fd4a9803ad058357a8aaf16529837ed Tue Jun 25 02:42:41 2024 -0700
    Setting back the hgBlat internal minscore, for some reason it had no effect on hg38, worked only on hg18. refs #32918
• src/hg/hgGene/hgGene.c
  • lines changed 1, context: html, text, full: html, text
    524ac3f3ff7186be84767ce63339baf61ded1356 Thu Jun 27 12:31:32 2024 -0700
    permenantly remove GAD section
• src/hg/hgPcr/hgPcr.c
  • lines changed 10, context: html, text, full: html, text
    4168de92d951347d6c0468a4e4f65c0a4cd953f5 Mon Jul 1 00:55:39 2024 -0700
    adding more text to hgPcr, refs #34003
• src/hg/hgSession/hgSession.c
  • lines changed 1, context: html, text, full: html, text
    56d97da433dfe0e26ec12a9818a521665fa3d295 Tue Jun 25 14:25:49 2024 -0700
    Switching hgSession 'Copy To Clipboard' button to sentence case, #25787
• src/hg/hgTracks/hgTracks.c
  • lines changed 1, context: html, text, full: html, text
    f56632e7b85670970f6cbf914fbf9afbaf359cf8 Fri Jun 28 14:06:45 2024 -0700
    Make 'download tracks in view' menu option present by default. Can still be turned off via hg.conf
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    b591cd270410e8f3eaa03135b39d0bbf14d1297b Sun Jun 30 18:10:59 2024 -0700
    Switching hgTracks 'disconnect' hub button to sentence case, #25787
• src/hg/hgTracks/recTrackSets.c
  • lines changed 1, context: html, text, full: html, text
    0c423c0be4557635f720250e92c4e9f48b014242 Wed Jun 26 13:41:45 2024 -0700
    make canSnake and mergeRecommend to be on by default
• src/hg/hgTracks/simpleTracks.c
  • lines changed 29, context: html, text, full: html, text
    c9aa9c0f8bd30426080ca5a2d5546d1f05befe9b Wed Jun 26 15:51:39 2024 -0700
    Fix for drawing wrong exon numbers in codon mouseovers, refs #33742
• src/hg/hgc/hgc.c
  • lines changed 1, context: html, text, full: html, text
    0c423c0be4557635f720250e92c4e9f48b014242 Wed Jun 26 13:41:45 2024 -0700
    make canSnake and mergeRecommend to be on by default
  • lines changed 31, context: html, text, full: html, text
    352e4a03ec0521929355c33f57b113e3ce890afc Mon Jul 1 01:25:22 2024 -0700
    adding hub tracks to DNA color options, refs #34009
• src/hg/htdocs/cauldron/breakTable.html
  • lines changed 0, context: html, text, full: html, text
    69dcf9c335101bd27b2522a12ba4fed0650f0657 Tue Jun 25 15:31:51 2024 -0700
    Replacing DOS CRLF with Unix-style to clear some build warnings, no ticket
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 72, context: html, text, full: html, text
    61547c79190553a311776b9a309bcb5dafada237 Mon Jul 1 01:23:58 2024 -0700
    Adding documentation on adding groups to a Track Hub, refs #33580
• src/hg/htdocs/style/HGStyle.css
  • lines changed 2, context: html, text, full: html, text
    976c3c1600cd2f0dde8b0579fed17835bf30fe6f Tue Jun 25 04:48:09 2024 -0700
    making font-size on rec track sets popup a little bit larger, came up in ticket with the new tutorial refs #33732
• src/hg/hubApi/dbDb.name.clade.tsv
  • lines changed 239, context: html, text, full: html, text
    733bfccc6366eca9cdb40718caff16406b38efee Wed Jun 26 14:41:14 2024 -0700
    creating file to load into genomePriority.hgcentral for search purpose refs #32897
• src/hg/hubApi/genomePriority.py
  • lines changed 495, context: html, text, full: html, text
    733bfccc6366eca9cdb40718caff16406b38efee Wed Jun 26 14:41:14 2024 -0700
    creating file to load into genomePriority.hgcentral for search purpose refs #32897
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    c1f3643c3e308c7819a375ee5ea4170a45c679e5 Wed Jun 26 14:51:38 2024 -0700
    clean up cruft refs #32897
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    54748ed558ead689973cb71209e4367d16f8450b Thu Jun 27 23:20:53 2024 -0700
    more specific sorting of primates and mammals database vs GenArk listings refs #32897
• src/hg/hubApi/list.c
  • lines changed 4, context: html, text, full: html, text
    c3786681696b93476299dfbfb832b355035861b1 Sat Jun 29 15:13:45 2024 -0700
    ready for an upgrade to the genark table to add columns currently maintain compatible behavior with previous genark table refs #32596;
• src/hg/hubApi/tests/expected/list26.gz
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    c3786681696b93476299dfbfb832b355035861b1 Sat Jun 29 15:13:45 2024 -0700
    ready for an upgrade to the genark table to add columns currently maintain compatible behavior with previous genark table refs #32596;
• src/hg/hubApi/tests/expected/list27.gz
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    c3786681696b93476299dfbfb832b355035861b1 Sat Jun 29 15:13:45 2024 -0700
    ready for an upgrade to the genark table to add columns currently maintain compatible behavior with previous genark table refs #32596;
• src/hg/inc/genark.h
  • lines changed 11, context: html, text, full: html, text
    c3786681696b93476299dfbfb832b355035861b1 Sat Jun 29 15:13:45 2024 -0700
    ready for an upgrade to the genark table to add columns currently maintain compatible behavior with previous genark table refs #32596;
• src/hg/js/utils.js
  • lines changed 52, context: html, text, full: html, text
    eedf621b1bb9fc52351772ddf4b87a26211449f2 Fri Jun 21 10:07:16 2024 -0700
    Fix tooltip mouseover event firing while mouse is still moving, refs #34007
  • lines changed 59, context: html, text, full: html, text
    2102d096150eb0ea18eb2b935dc1d837cf252184 Fri Jun 28 12:39:45 2024 -0700
    Fix a few bugs in the tooltip implementation revealed when making some tooltips have longer wait timers: 1. Get item coordinates that was moused over correctly. 2. Set up the scroll and mouse move events and their signals on mouseover, and not in both mouseover and upon actually showing the text, the competing functions were causing events to not get removed and then other events could not fire appropriately, refs #34007
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    c4b624d0e2d2a78be9808dc4f0dd9d415c45eb4e Mon Jul 1 09:29:06 2024 -0700
    Remove informational message on all tooltips cause it is annoying, refs #34007
• src/hg/lib/cart.c
  • lines changed 1, context: html, text, full: html, text
    75b3dceab13809205cd0f7f3671b4701333f9ee4 Tue Jun 25 07:51:33 2024 -0700
    setting showEarlyErrors to on by default, refs #33992
• src/hg/lib/genark.as
  • lines changed 3, context: html, text, full: html, text
    c3786681696b93476299dfbfb832b355035861b1 Sat Jun 29 15:13:45 2024 -0700
    ready for an upgrade to the genark table to add columns currently maintain compatible behavior with previous genark table refs #32596;
• src/hg/lib/genark.c
  • lines changed 66, context: html, text, full: html, text
    c3786681696b93476299dfbfb832b355035861b1 Sat Jun 29 15:13:45 2024 -0700
    ready for an upgrade to the genark table to add columns currently maintain compatible behavior with previous genark table refs #32596;
• src/hg/lib/genark.sql
  • lines changed 2, context: html, text, full: html, text
    c3786681696b93476299dfbfb832b355035861b1 Sat Jun 29 15:13:45 2024 -0700
    ready for an upgrade to the genark table to add columns currently maintain compatible behavior with previous genark table refs #32596;
• src/hg/lib/genomePriority.as
  • lines changed 10, context: html, text, full: html, text
    6afca455c54a8978418619a55933beb76897e09c Wed Jun 26 14:59:55 2024 -0700
    code to work with genomePriority.hgcentral table refs #32897
• src/hg/lib/genomePriority.c
  • lines changed 238, context: html, text, full: html, text
    6afca455c54a8978418619a55933beb76897e09c Wed Jun 26 14:59:55 2024 -0700
    code to work with genomePriority.hgcentral table refs #32897
• src/hg/lib/genomePriority.h
  • lines changed 86, context: html, text, full: html, text
    6afca455c54a8978418619a55933beb76897e09c Wed Jun 26 14:59:55 2024 -0700
    code to work with genomePriority.hgcentral table refs #32897
• src/hg/lib/genomePriority.sql
  • lines changed 16, context: html, text, full: html, text
    6afca455c54a8978418619a55933beb76897e09c Wed Jun 26 14:59:55 2024 -0700
    code to work with genomePriority.hgcentral table refs #32897
• src/hg/lib/hubConnect.c
  • lines changed 1, context: html, text, full: html, text
    c5d5fcb2a53e4c1c3b7a848fbbd73c9bc2727d4c Tue Jun 25 14:41:53 2024 -0700
    change a buffer that was 64k to 1mg.
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    f029db9758ac06ef95a5b31cc5cd89197620e22d Thu Jun 27 11:35:42 2024 -0700
    replace /gbdb on GBiB with curated hubs
• src/hg/lib/hui.c
  • lines changed 1, context: html, text, full: html, text
    0c423c0be4557635f720250e92c4e9f48b014242 Wed Jun 26 13:41:45 2024 -0700
    make canSnake and mergeRecommend to be on by default
• src/hg/makeDb/dbDbToHubTxt/dbDbToHubTxt.c
  • lines changed 29, context: html, text, full: html, text
    0aeb65a35dee3f20e536516fa2a824a1f3d7314f Thu Jun 6 09:00:00 2024 -0700
    Revert "in the absence of a 2bit file assume it is a track hub attach to a GenArk hub" This reverts commit 8cf5d084511a9bbd9d28edf8f5508d9df1ff98eb.
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 6, context: html, text, full: html, text
    4da4e0f781b1bd70efc468ff3217951408ad087f Mon Jun 24 16:35:44 2024 -0700
    adding some algae sequences per user request refs #29545
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    858f679f166bccf06aca0a82267afa3193feeb1c Tue Jun 25 17:56:02 2024 -0700
    adding five bacteria per user requests refs #29545
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    c269976e78f8b2fe44cd6e64d639a84da13ff4f3 Sun Jun 30 23:36:34 2024 -0700
    adding 2 to catch up with the fish group alignment set refs #29545
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    437a749af8e09f831e84acbbde0d43928e01fd45 Mon Jul 1 09:30:49 2024 -0700
    adding two mouse T2T assemblies per Thomas Keane request refs #29545
• src/hg/makeDb/doc/bacteriaAsmHub/bacteria.orderList.tsv
  • lines changed 5, context: html, text, full: html, text
    858f679f166bccf06aca0a82267afa3193feeb1c Tue Jun 25 17:56:02 2024 -0700
    adding five bacteria per user requests refs #29545
• src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    c269976e78f8b2fe44cd6e64d639a84da13ff4f3 Sun Jun 30 23:36:34 2024 -0700
    adding 2 to catch up with the fish group alignment set refs #29545
• src/hg/makeDb/doc/hg38/gnomad.txt
  • lines changed 72, context: html, text, full: html, text
    9af983b83acb335907ac9bf3da0873cb6e06c48d Wed Jun 26 10:55:48 2024 -0700
    Add updates for gnomad v4.1 genomes and exomes to makedoc
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
  • lines changed 4, context: html, text, full: html, text
    4da4e0f781b1bd70efc468ff3217951408ad087f Mon Jun 24 16:35:44 2024 -0700
    adding some algae sequences per user request refs #29545
  • lines changed 6, context: html, text, full: html, text
    08ebbbe8912ac1a5a38c3630162855827975f4c4 Sat Jun 29 20:52:13 2024 -0700
    better common names from user for the algae refs #29545
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 4, context: html, text, full: html, text
    437a749af8e09f831e84acbbde0d43928e01fd45 Mon Jul 1 09:30:49 2024 -0700
    adding two mouse T2T assemblies per Thomas Keane request refs #29545
• src/hg/makeDb/doc/mm39/lastzRuns.txt
  • lines changed 399, context: html, text, full: html, text
    089042f2c2941c58f286665e236311bddb6bed46 Wed Jun 26 08:40:58 2024 -0700
    Adding lastz run with GCA_921999865.2, refs #33195
• src/hg/makeDb/outside/bayesDel/hg19/createMaxAFBayesDelWig.py
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    69dcf9c335101bd27b2522a12ba4fed0650f0657 Tue Jun 25 15:31:51 2024 -0700
    Replacing DOS CRLF with Unix-style to clear some build warnings, no ticket
• src/hg/makeDb/outside/bayesDel/hg19/createNoAFBayesDelWig.py
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    69dcf9c335101bd27b2522a12ba4fed0650f0657 Tue Jun 25 15:31:51 2024 -0700
    Replacing DOS CRLF with Unix-style to clear some build warnings, no ticket
• src/hg/makeDb/schema/all.joiner
  • lines changed 18, context: html, text, full: html, text
    75e232bbeda2dd0d3a81e927e7c5c1dde9d6d9df Fri Jun 7 12:08:22 2024 -0700
    dropping assocations to hg19 knownGene that aren't applicable anymore
• src/hg/makeDb/trackDb/human/covidTracks.alpha.ra
  • lines changed 1, context: html, text, full: html, text
    836a45a3110e74d7880d674826515ba3d7065297 Wed Jun 26 10:11:49 2024 -0700
    cart rewrites for #32813
• src/hg/makeDb/trackDb/human/hg38/assemblyTracks.alpha.ra
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    836a45a3110e74d7880d674826515ba3d7065297 Wed Jun 26 10:11:49 2024 -0700
    cart rewrites for #32813
• src/hg/makeDb/trackDb/human/hg38/knownGeneV46.html
  • lines changed 3, context: html, text, full: html, text
    8b84dbd02901e6288237476bb410eaa6199518fb Mon Jun 24 16:30:00 2024 -0700
    Updating knownGene HTML color descriptions to include a mention of MANE, refs #33479
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    ebf40466cfe38e6585d453b19bc17bc96f147c43 Wed Jun 26 12:34:20 2024 -0700
    Tweaking the mane select plus clinical wording to be simpler, refs #33479
• src/hg/makeDb/trackDb/human/spliceAI.html
  • lines changed 1, context: html, text, full: html, text
    9418b6ff8004c4aea32c66cfb58cb821a072f94d Thu Jun 27 17:30:26 2024 -0700
    Adding dataVersion and consistent Broad wording as per feedback from Max refs #27141
• src/hg/makeDb/trackDb/human/spliceAI.ra
  • lines changed 22, context: html, text, full: html, text
    c07fbc7c04f212534a8cbe6b22d8a71e3e76e20c Wed Jun 26 16:57:06 2024 -0700
    Turning SpliceAI into a superTrack, refs #27141
  • lines changed 1, context: html, text, full: html, text
    9418b6ff8004c4aea32c66cfb58cb821a072f94d Thu Jun 27 17:30:26 2024 -0700
    Adding dataVersion and consistent Broad wording as per feedback from Max refs #27141
• src/hg/makeDb/trackDb/trackDb.mgc-orfeome.ra
  • lines changed 1, context: html, text, full: html, text
    836a45a3110e74d7880d674826515ba3d7065297 Wed Jun 26 10:11:49 2024 -0700
    cart rewrites for #32813
• src/hg/utils/otto/knownGene/buildCore.sh
  • lines changed 6, context: html, text, full: html, text
    f792205c4ed7244a9ce7db761de77f21f1af7307 Mon Jun 24 16:32:07 2024 -0700
    KnownGene pipeline will now mark MANE transcripts in a separate color, refs #33479
• src/hg/utils/otto/knownGene/buildTo.sh
  • lines changed 1, context: html, text, full: html, text
    b209ddecd094d68684158d3b22c7ba1a23c06f8c Thu Jun 27 12:58:43 2024 -0700
    strip off _# at end of id for knownToEnsembl if it's there (like it is on hg19)
• src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv
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    80f940b522ef43a3f01324209689f644a6b3aa5b Thu Jun 27 11:47:33 2024 -0700
    Correction to path for JN.1.1.3; KR.2 renamed to LT.1; new lineages. pango-designation release v1.28.
• src/utils/qa/weeklybld/buildEnv.csh
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    b80b2f6a0b21b3379d3c38d2168d6c103cb3ee75 Mon Jul 1 10:12:07 2024 -0700
    v468 preview1, refs #33949

• lines changed: 2246
• files changed: 66