All File Changes

v431_preview2 to v431_base (2022-05-09 to 2022-05-16) v431

• confs/asia.hg.conf
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    8ca30814adfb87316b41ad7aff4f5b55036a13ee Sun May 15 01:12:06 2022 -0700
    Installing updated hg.conf files from UCSC servers
• confs/euro.hg.conf
  • lines changed 3, context: html, text, full: html, text
    8ca30814adfb87316b41ad7aff4f5b55036a13ee Sun May 15 01:12:06 2022 -0700
    Installing updated hg.conf files from UCSC servers
• confs/hgwbeta.hg.conf
  • lines changed 3, context: html, text, full: html, text
    8ca30814adfb87316b41ad7aff4f5b55036a13ee Sun May 15 01:12:06 2022 -0700
    Installing updated hg.conf files from UCSC servers
• confs/rr.hg.conf
  • lines changed 3, context: html, text, full: html, text
    8ca30814adfb87316b41ad7aff4f5b55036a13ee Sun May 15 01:12:06 2022 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/gar/garTable.pl
  • lines changed 32, context: html, text, full: html, text
    b313555b67a1aff99cd940e4bca28677b35b608d Mon May 9 15:58:39 2022 -0700
    fixup note about how to search, better include almost all GenArk assemblies no redmine
  • lines changed 12, context: html, text, full: html, text
    d10d359c47f9f4a1245111f8b75b4c25c483c9ee Tue May 10 14:52:17 2022 -0700
    fixup some types for cleaner html vs. W3C validator no redmine
• src/hg/gar/garTable.sh
  • lines changed 3, context: html, text, full: html, text
    b313555b67a1aff99cd940e4bca28677b35b608d Mon May 9 15:58:39 2022 -0700
    fixup note about how to search, better include almost all GenArk assemblies no redmine
  • lines changed 2, context: html, text, full: html, text
    d10d359c47f9f4a1245111f8b75b4c25c483c9ee Tue May 10 14:52:17 2022 -0700
    fixup some types for cleaner html vs. W3C validator no redmine
• src/hg/hgBeacon/hgBeacon
  • lines changed 1, context: html, text, full: html, text
    cf97ccb00abb86e63f732e4ca0a7de0faacc7f8f Fri May 13 03:07:05 2022 -0700
    fixing hgBeacon bug when hg.conf contains equal signs, refs #29419
• src/hg/hgSession/hgSession.c
  • lines changed 3, context: html, text, full: html, text
    9c94fbc11c1bb90ea92e216b5c65d908b2c79b0d Fri May 13 18:56:18 2022 -0700
    Fixing oddly encoded firstBuf in hgSession. refs #29274, #29373
• src/hg/hgTables/filterFields.c
  • lines changed 24, context: html, text, full: html, text
    e9e437a0c661134140b0fd92c83261a70b238c73 Fri May 13 14:51:46 2022 -0700
    Fixing issue for %-s with secure operators in hgTables filterFields.c. refs #29274
• src/hg/hgTables/hgTables.c
  • lines changed 1, context: html, text, full: html, text
    c98ab6c8d2b3a44f447f3f6847129b9840c1749d Fri May 13 01:39:42 2022 -0700
    Fixing #filter in hgTables/joining.c for improved SQL Injection protections. refs #29274
• src/hg/hgTables/joining.c
  • lines changed 3, context: html, text, full: html, text
    c98ab6c8d2b3a44f447f3f6847129b9840c1749d Fri May 13 01:39:42 2022 -0700
    Fixing #filter in hgTables/joining.c for improved SQL Injection protections. refs #29274
• src/hg/hgTracks/barChartTrack.c
  • lines changed 40, context: html, text, full: html, text
    1f5a7c5b430943462e3fed00385b4112a65e5f9d Thu May 12 15:31:45 2022 -0700
    First pass - fixing a barChart draw issue and enabling the trackDb minimum width/padding variables, refs #28062
  • lines changed 29, context: html, text, full: html, text
    fe26ea11179837ba80f1e2dd12b9128eb9058b58 Fri May 13 16:10:49 2022 -0700
    Revised method of barChart width calculation does a better job accounting for padding, refs #29425
• src/hg/hgTracks/hgTracks.c
  • lines changed 10, context: html, text, full: html, text
    b94993d07e5d0ef24f17a40c9ca7f5b2ddb93701 Wed May 11 10:50:56 2022 -0700
    allow hubs to specify a naming authority for the chromosome that's displayed by the browser
• src/hg/hgTracks/hgTracks.h
  • lines changed 1, context: html, text, full: html, text
    b94993d07e5d0ef24f17a40c9ca7f5b2ddb93701 Wed May 11 10:50:56 2022 -0700
    allow hubs to specify a naming authority for the chromosome that's displayed by the browser
• src/hg/hgTracks/simpleTracks.c
  • lines changed 1, context: html, text, full: html, text
    b94993d07e5d0ef24f17a40c9ca7f5b2ddb93701 Wed May 11 10:50:56 2022 -0700
    allow hubs to specify a naming authority for the chromosome that's displayed by the browser
• src/hg/htdocs/goldenPath/help/bigBed.html
  • lines changed 4, context: html, text, full: html, text
    2c23366274517a7468114784c0a924adcf4e7958 Mon May 9 14:43:46 2022 -0700
    Adding a link to bedDetail blog in bigBed.html help page
  • lines changed 5, context: html, text, full: html, text
    6710917f67d227676ec78692cce69b8b6a113285 Tue May 10 11:20:14 2022 -0700
    Adding a link to trix doc in bigBed help, refs #28817
• src/hg/htdocs/goldenPath/help/customTrackText.html
  • lines changed 3, context: html, text, full: html, text
    ce5eff33ee510ad5dd99477ba0b11e2d9168505e Sat May 14 06:59:36 2022 -0700
    Updating other doc references to resetting browser
• src/hg/htdocs/goldenPath/help/hgGenomeHelp.html
  • lines changed 2, context: html, text, full: html, text
    ce5eff33ee510ad5dd99477ba0b11e2d9168505e Sat May 14 06:59:36 2022 -0700
    Updating other doc references to resetting browser
• src/hg/htdocs/goldenPath/help/hgTracksHelp.html
  • lines changed 9, context: html, text, full: html, text
    e8feba7d60f1dcec7cfd9cc94174c66e7dec5102 Wed May 11 12:28:14 2022 -0700
    Adding note about text-size, font, on our configuration descriptions, as look at WashU browser refs #29388
  • lines changed 3, context: html, text, full: html, text
    80cbe376e37323c058df9ea964a567a4ac782343 Fri May 13 15:20:37 2022 -0700
    Updating how to reset browser (after using WashU and not finding how to reset theirs)
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 3, context: html, text, full: html, text
    dd7ed7e51c04a48e71b961c5b3e8de6ea0655447 Tue May 10 12:00:46 2022 -0700
    Adding a link to quickstart searchable hub page for searchTrix, refs #28817
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 2, context: html, text, full: html, text
    eeb5e628dfe53a1bab3e2b0d3cf02aef4cdc38fd Wed May 11 11:38:45 2022 -0700
    Minor grammar edits for CR refs #29399
  • lines changed 36, context: html, text, full: html, text
    3b9576331b05c510b9509f66090a25d9582a0219 Wed May 11 13:53:06 2022 -0700
    Releasing new GENCODE release, refs #29275 #29276 #29277
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    3b9576331b05c510b9509f66090a25d9582a0219 Wed May 11 13:53:06 2022 -0700
    Releasing new GENCODE release, refs #29275 #29276 #29277
• src/hg/inc/chromAlias.h
  • lines changed 5, context: html, text, full: html, text
    b94993d07e5d0ef24f17a40c9ca7f5b2ddb93701 Wed May 11 10:50:56 2022 -0700
    allow hubs to specify a naming authority for the chromosome that's displayed by the browser
• src/hg/inc/trackHub.h
  • lines changed 1, context: html, text, full: html, text
    b94993d07e5d0ef24f17a40c9ca7f5b2ddb93701 Wed May 11 10:50:56 2022 -0700
    allow hubs to specify a naming authority for the chromosome that's displayed by the browser
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    caf9ecd5cc981e03b1d31885abc49f1992873963 Mon May 16 10:17:50 2022 -0700
    New version number v431
• src/hg/js/gar.js
  • lines changed 68, context: html, text, full: html, text
    359effbb6588468172f2aba67c930c6992a4585b Tue May 10 14:59:02 2022 -0700
    cleanup old debug code and add wait cursor no redmine
• src/hg/lib/chromAlias.c
  • lines changed 96, context: html, text, full: html, text
    b94993d07e5d0ef24f17a40c9ca7f5b2ddb93701 Wed May 11 10:50:56 2022 -0700
    allow hubs to specify a naming authority for the chromosome that's displayed by the browser
  • lines changed 11, context: html, text, full: html, text
    c13ed07bb8cf97ee53a45a91da18910edbc525d9 Fri May 13 13:46:20 2022 -0700
    support chromAuthority with bigBed chromAlias files
• src/hg/lib/trackHub.c
  • lines changed 1, context: html, text, full: html, text
    b94993d07e5d0ef24f17a40c9ca7f5b2ddb93701 Wed May 11 10:50:56 2022 -0700
    allow hubs to specify a naming authority for the chromosome that's displayed by the browser
• src/hg/makeDb/doc/chm13v2.0/hub/GCA_009914755.4_T2T-CHM13v2.0.genomes.txt
  • lines changed 2, context: html, text, full: html, text
    8525118e8c0e51df0d0326faab5c7b795bfe04d4 Wed May 11 10:35:30 2022 -0700
    better organism and description strings to avoid duplication no redmine
• src/hg/makeDb/doc/chm13v2.0/makefile
  • lines changed 7, context: html, text, full: html, text
    99af29af57ad35acbd405102709d5046bcb32097 Wed May 11 09:10:22 2022 -0700
    do not use -p option on the copy to make sure the files are always new refs #29371
• src/hg/makeDb/doc/chm13v2.0userData/html/hgLiftOver.html
  • lines changed 11, context: html, text, full: html, text
    61ebfa3a2c8203b2612cf54074d12410074d04ee Tue May 10 13:57:32 2022 -0700
    add info about adding chain ids and scores to CHM13 chains
• src/hg/makeDb/doc/dm6/lastzRuns.txt
  • lines changed 95, context: html, text, full: html, text
    55556e2ea3d58d8eb4678fc612302812347ea37d Wed May 11 23:34:22 2022 -0700
    dm6 vs. dp3 lastz/chain/net run for user, refs #29302
• src/hg/makeDb/doc/hg19.txt
  • lines changed 15, context: html, text, full: html, text
    d8df38ba4671d2f98771343bb695cbf49e38bde8 Mon May 9 16:35:30 2022 -0700
    Adding MTR track refs #29152
• src/hg/makeDb/doc/hg38/gencode.txt
  • lines changed 30, context: html, text, full: html, text
    24d69a7106a0e67837d07d860924733c30ba66e2 Fri May 13 12:48:37 2022 -0700
    import of gencode V41 pre-release
  • lines changed 1, context: html, text, full: html, text
    05a3d177bf35df451f750276c274efc25b8acc70 Fri May 13 14:28:34 2022 -0700
    import of gencode VM30 pre-release
• src/hg/makeDb/doc/hg38/gnomadPLI.txt
  • lines changed 42, context: html, text, full: html, text
    e2b40d37a4575d5df1665e85214a387050a1f094 Thu May 12 14:40:19 2022 -0700
    Building gnomAD pLI track on hg38 (prev only on hg19) refs #29358
• src/hg/makeDb/doc/mm10.txt
  • lines changed 98, context: html, text, full: html, text
    64b0cb25a7b19441d238cf5ef7f6c9f5b15a4c02 Wed May 11 23:38:40 2022 -0700
    mm10 vs. GCA_001624535.1 lastz/chain/net run for user, refs #29311
• src/hg/makeDb/doc/mm39/gencode.txt
  • lines changed 33, context: html, text, full: html, text
    05a3d177bf35df451f750276c274efc25b8acc70 Fri May 13 14:28:34 2022 -0700
    import of gencode VM30 pre-release
• src/hg/makeDb/outside/gencode/gencodeLoad.mk
  • lines changed 9, context: html, text, full: html, text
    24d69a7106a0e67837d07d860924733c30ba66e2 Fri May 13 12:48:37 2022 -0700
    import of gencode V41 pre-release
  • lines changed 2, context: html, text, full: html, text
    05a3d177bf35df451f750276c274efc25b8acc70 Fri May 13 14:28:34 2022 -0700
    import of gencode VM30 pre-release
• src/hg/makeDb/outside/gencode/lib/gencode/biotypes.py
  • lines changed 10, context: html, text, full: html, text
    24d69a7106a0e67837d07d860924733c30ba66e2 Fri May 13 12:48:37 2022 -0700
    import of gencode V41 pre-release
• src/hg/makeDb/outside/gencode/lib/gencode/gencodeTags.py
  • lines changed 2, context: html, text, full: html, text
    24d69a7106a0e67837d07d860924733c30ba66e2 Fri May 13 12:48:37 2022 -0700
    import of gencode V41 pre-release
• src/hg/makeDb/schema/all.joiner
  • lines changed 95, context: html, text, full: html, text
    24d69a7106a0e67837d07d860924733c30ba66e2 Fri May 13 12:48:37 2022 -0700
    import of gencode V41 pre-release
  • lines changed 95, context: html, text, full: html, text
    05a3d177bf35df451f750276c274efc25b8acc70 Fri May 13 14:28:34 2022 -0700
    import of gencode VM30 pre-release
• src/hg/makeDb/scripts/mtr/buildMTRbedTrack.py
  • lines changed 64, context: html, text, full: html, text
    d8df38ba4671d2f98771343bb695cbf49e38bde8 Mon May 9 16:35:30 2022 -0700
    Adding MTR track refs #29152
• src/hg/makeDb/scripts/mtr/buildMTRwigTracks.py
  • lines changed 68, context: html, text, full: html, text
    d8df38ba4671d2f98771343bb695cbf49e38bde8 Mon May 9 16:35:30 2022 -0700
    Adding MTR track refs #29152
• src/hg/makeDb/trackDb/human/constraintSuper.html
  • lines changed 76, context: html, text, full: html, text
    d8df38ba4671d2f98771343bb695cbf49e38bde8 Mon May 9 16:35:30 2022 -0700
    Adding MTR track refs #29152
  • lines changed 24, context: html, text, full: html, text
    e3d41cdb5005a8688ce803eca9b0b4fd9574a43f Tue May 10 00:58:13 2022 -0700
    fixing typo in constraint docs page, refs #29152
  • lines changed 69, context: html, text, full: html, text
    6180cce0bc1c3644813d2c0a5a9b5aa2fa82244b Wed May 11 03:00:22 2022 -0700
    fixing merge conflict, refs #29152
• src/hg/makeDb/trackDb/human/constraintSuper.ra
  • lines changed 2, context: html, text, full: html, text
    d8df38ba4671d2f98771343bb695cbf49e38bde8 Mon May 9 16:35:30 2022 -0700
    Adding MTR track refs #29152
• src/hg/makeDb/trackDb/human/hg19/chm13LiftOver.html
  • lines changed 11, context: html, text, full: html, text
    61ebfa3a2c8203b2612cf54074d12410074d04ee Tue May 10 13:57:32 2022 -0700
    add info about adding chain ids and scores to CHM13 chains
• src/hg/makeDb/trackDb/human/hg19/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    c4d51681dcec644ccffb54d40b0ec94e00eb532d Wed May 11 12:27:15 2022 -0700
    Staging new GENCODE release, refs #29275 #29276 #29277
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeSuper.html
  • lines changed 1, context: html, text, full: html, text
    c4d51681dcec644ccffb54d40b0ec94e00eb532d Wed May 11 12:27:15 2022 -0700
    Staging new GENCODE release, refs #29275 #29276 #29277
  • lines changed 4, context: html, text, full: html, text
    daae75ac0c06304b50a86599f7c7cba7b336cdbf Wed May 11 12:29:37 2022 -0700
    Fixing a bad paste command, refs #29275 #29276 #29277
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV39lift37.ra
  • lines changed 1, context: html, text, full: html, text
    c4d51681dcec644ccffb54d40b0ec94e00eb532d Wed May 11 12:27:15 2022 -0700
    Staging new GENCODE release, refs #29275 #29276 #29277
• src/hg/makeDb/trackDb/human/hg38/chm13LiftOver.html
  • lines changed 11, context: html, text, full: html, text
    61ebfa3a2c8203b2612cf54074d12410074d04ee Tue May 10 13:57:32 2022 -0700
    add info about adding chain ids and scores to CHM13 chains
• src/hg/makeDb/trackDb/human/hg38/gnomad.ra
  • lines changed 88, context: html, text, full: html, text
    e2b40d37a4575d5df1665e85214a387050a1f094 Thu May 12 14:40:19 2022 -0700
    Building gnomAD pLI track on hg38 (prev only on hg19) refs #29358
• src/hg/makeDb/trackDb/human/hg38/gnomadPLI.html
  • lines changed 232, context: html, text, full: html, text
    e2b40d37a4575d5df1665e85214a387050a1f094 Thu May 12 14:40:19 2022 -0700
    Building gnomAD pLI track on hg38 (prev only on hg19) refs #29358
• src/hg/makeDb/trackDb/human/hg38/gnomadV3_1_1.html
  • lines changed 2, context: html, text, full: html, text
    eeb5e628dfe53a1bab3e2b0d3cf02aef4cdc38fd Wed May 11 11:38:45 2022 -0700
    Minor grammar edits for CR refs #29399
  • lines changed 4, context: html, text, full: html, text
    e2b40d37a4575d5df1665e85214a387050a1f094 Thu May 12 14:40:19 2022 -0700
    Building gnomAD pLI track on hg38 (prev only on hg19) refs #29358
• src/hg/makeDb/trackDb/human/hg38/knownGene.alpha.ra
  • lines changed 6, context: html, text, full: html, text
    c2a39bfb5cbc74bc5a655c89f5162d38ac59a3f1 Sun May 15 14:15:19 2022 -0700
    GENCODE V41 in da house!
• src/hg/makeDb/trackDb/human/hg38/knownGeneArchive.ra
  • lines changed 25, context: html, text, full: html, text
    dccdda7ba389a2897bd3721de5f45335c5c7cd0b Sun May 15 14:29:43 2022 -0700
    set up archive for V39
• src/hg/makeDb/trackDb/human/hg38/knownGeneV41.html
  • lines changed 140, context: html, text, full: html, text
    c2a39bfb5cbc74bc5a655c89f5162d38ac59a3f1 Sun May 15 14:15:19 2022 -0700
    GENCODE V41 in da house!
• src/hg/makeDb/trackDb/human/hg38/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    c4d51681dcec644ccffb54d40b0ec94e00eb532d Wed May 11 12:27:15 2022 -0700
    Staging new GENCODE release, refs #29275 #29276 #29277
  • lines changed 1, context: html, text, full: html, text
    24d69a7106a0e67837d07d860924733c30ba66e2 Fri May 13 12:48:37 2022 -0700
    import of gencode V41 pre-release
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 10, context: html, text, full: html, text
    ae55889347291dda796b9803256399158f3c82fa Mon May 9 16:22:24 2022 -0700
    add a test of Michael Hillers 483-way
  • lines changed 2, context: html, text, full: html, text
    c2a39bfb5cbc74bc5a655c89f5162d38ac59a3f1 Sun May 15 14:15:19 2022 -0700
    GENCODE V41 in da house!
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeSuper.html
  • lines changed 2, context: html, text, full: html, text
    c4d51681dcec644ccffb54d40b0ec94e00eb532d Wed May 11 12:27:15 2022 -0700
    Staging new GENCODE release, refs #29275 #29276 #29277
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV39.ra
  • lines changed 1, context: html, text, full: html, text
    c4d51681dcec644ccffb54d40b0ec94e00eb532d Wed May 11 12:27:15 2022 -0700
    Staging new GENCODE release, refs #29275 #29276 #29277
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV41.html
  • lines changed 47, context: html, text, full: html, text
    24d69a7106a0e67837d07d860924733c30ba66e2 Fri May 13 12:48:37 2022 -0700
    import of gencode V41 pre-release
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV41.ra
  • lines changed 286, context: html, text, full: html, text
    24d69a7106a0e67837d07d860924733c30ba66e2 Fri May 13 12:48:37 2022 -0700
    import of gencode V41 pre-release
• src/hg/makeDb/trackDb/human/mtr.ra
  • lines changed 75, context: html, text, full: html, text
    d8df38ba4671d2f98771343bb695cbf49e38bde8 Mon May 9 16:35:30 2022 -0700
    Adding MTR track refs #29152
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    dbdbe5dc1eda031e2e3be1ecf8f8db8e91b8b863 Mon May 9 16:37:38 2022 -0700
    Fixing small typo
• src/hg/makeDb/trackDb/human/trackDb.clinvar.ra
  • lines changed 1, context: html, text, full: html, text
    70a6e3b00f64e3a1bc8f800367769fd447e43bcc Thu May 12 01:10:32 2022 -0700
    fixing clinvar trackDb filters, refs #29216
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    020ce5ad874fab8928c2e66b832c52708e7125f1 Fri May 13 04:16:32 2022 -0700
    forgot to change the cnv track, refs #29216
• src/hg/makeDb/trackDb/maybeBuildHub
  • lines changed 17, context: html, text, full: html, text
    6a9336c9f65f85b7d9fdcb8627995d2d4d9c06ed Tue May 10 17:51:54 2022 -0700
    a little script to be called in trackDb makefile to make an assembly hub from a trackDb
• src/hg/makeDb/trackDb/mouse/mm10/refSeqComposite.html
  • lines changed 7, context: html, text, full: html, text
    da878c2cf9a07702c9c72657d326a9d488c77307 Wed May 11 15:39:07 2022 -0700
    Updating the html for the mouse ncbiRefSeqSelect, refs #28130
• src/hg/makeDb/trackDb/mouse/mm39/refSeqComposite.html
  • lines changed 7, context: html, text, full: html, text
    da878c2cf9a07702c9c72657d326a9d488c77307 Wed May 11 15:39:07 2022 -0700
    Updating the html for the mouse ncbiRefSeqSelect, refs #28130
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    c4d51681dcec644ccffb54d40b0ec94e00eb532d Wed May 11 12:27:15 2022 -0700
    Staging new GENCODE release, refs #29275 #29276 #29277
  • lines changed 1, context: html, text, full: html, text
    05a3d177bf35df451f750276c274efc25b8acc70 Fri May 13 14:28:34 2022 -0700
    import of gencode VM30 pre-release
• src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM28.ra
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    c4d51681dcec644ccffb54d40b0ec94e00eb532d Wed May 11 12:27:15 2022 -0700
    Staging new GENCODE release, refs #29275 #29276 #29277
• src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM30.html
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    05a3d177bf35df451f750276c274efc25b8acc70 Fri May 13 14:28:34 2022 -0700
    import of gencode VM30 pre-release
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    05a3d177bf35df451f750276c274efc25b8acc70 Fri May 13 14:28:34 2022 -0700
    import of gencode VM30 pre-release
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    1f5a7c5b430943462e3fed00385b4112a65e5f9d Thu May 12 15:31:45 2022 -0700
    First pass - fixing a barChart draw issue and enabling the trackDb minimum width/padding variables, refs #28062
• src/hg/utils/gencodeGeneSymVerTx/gencodeGeneSymVerTx.c
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    7a5533f3131b50e00f7568767cf837c4c418b6a0 Thu May 12 06:40:55 2022 -0700
    Outputting all genes with same name so get refSeq on both alts and main chromosomes.
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    0957695666775bee81510336f88a2b9dbbef9203 Thu May 12 06:14:05 2022 -0700
    ref #29416 - Making it so that all the genes of a given name (but just for a particular version of genes) are output in the mapping.bed file, rather than just the most recent one added to the hash.
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    2af681b48db9f2763dc35912ecd267a8bae96d8b Thu May 12 08:37:32 2022 -0700
    Making it take most recent GENCODE by preference when -targetDb option is set again.
• src/hg/utils/otto/decipher/checkDecipher.sh
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    e23fb89fb5db425125e18013e6be747164d0599f Thu May 12 20:36:14 2022 -0700
    Updating DECIPHER otto pipeline for new retrieval method, refs #29130
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    8f32273ebe555d15ba642587d79ee7f20c5e2881 Fri May 13 11:58:05 2022 -0700
    Reactivating DECIPHER otto, Jonathan has fixed the automatic data fetching. Refs #29130
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    caf9ecd5cc981e03b1d31885abc49f1992873963 Mon May 16 10:17:50 2022 -0700
    New version number v431
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    c13ed07bb8cf97ee53a45a91da18910edbc525d9 Fri May 13 13:46:20 2022 -0700
    support chromAuthority with bigBed chromAlias files
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    4e8f4786b04d81ae75cab0f10412847cbcf1aa6a Wed May 11 10:30:41 2022 -0700
    change fieldedTable to require the same number of tab separated fields on every line.
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    First cut of bedGraphToWig
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    8a7c71f2356e7d6650a2143064a92bca2bef6580 Thu May 12 10:28:19 2022 -0700
    Adding Redmine check, no RM
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    3b321ac2944265e63fb0f31b2a09d6489319da09 Mon May 16 10:16:01 2022 -0700
    v431 final build, refs #29357

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