All File Changes

v430_preview2 to v430_base (2022-04-18 to 2022-04-25) v430

• LICENSE
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    5297524cd0b7507aa3cce8a0bfddc8baa0e8fc8e Tue Apr 19 02:52:34 2022 -0700
    trying to make the LICENSE file easier to read, after email discussion with IATC
• confs/asia.hg.conf
  • lines changed 8, context: html, text, full: html, text
    e3ebdd69c0eb45cccd5d8564db3f5770b897d22c Sun Apr 24 01:11:51 2022 -0700
    Installing updated hg.conf files from UCSC servers
• confs/euro.hg.conf
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    e3ebdd69c0eb45cccd5d8564db3f5770b897d22c Sun Apr 24 01:11:51 2022 -0700
    Installing updated hg.conf files from UCSC servers
• confs/hgwdev.hg.conf
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    e3ebdd69c0eb45cccd5d8564db3f5770b897d22c Sun Apr 24 01:11:51 2022 -0700
    Installing updated hg.conf files from UCSC servers
• confs/rr.hg.conf
  • lines changed 8, context: html, text, full: html, text
    e3ebdd69c0eb45cccd5d8564db3f5770b897d22c Sun Apr 24 01:11:51 2022 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/gar/gar.cgi.pl
  • lines changed 1, context: html, text, full: html, text
    634ca65b0681b7d39e93c452e9c1d28aa8b3ac3e Tue Apr 19 12:37:53 2022 -0700
    add clay email to recipient list refs #28930
• src/hg/gar/garTable.sh
  • lines changed 3, context: html, text, full: html, text
    6cfdc4a871b565db2b9152612d147877b4a9783b Tue Apr 19 12:52:47 2022 -0700
    add link to blog post refs #29237
• src/hg/gar/makefile
  • lines changed 24, context: html, text, full: html, text
    15b08d18cac716bb9f09d873f1df06787fab3dfc Tue Apr 19 13:11:01 2022 -0700
    bare minimum to satisify build system refs #29237
  • lines changed 6, context: html, text, full: html, text
    311012f072535713c144bfe39436acd835eca9ef Tue Apr 19 13:32:41 2022 -0700
    adding gar to the build system refs #29237
• src/hg/hgTracks/hgTracks.h
  • lines changed 1, context: html, text, full: html, text
    b175287d55a36634edae44819e36c1cfafaeba65 Tue Apr 19 08:40:50 2022 -0700
    increase maxItems in bigBeds to 1,000,000 from 100,000
• src/hg/hgc/hgc.c
  • lines changed 35, context: html, text, full: html, text
    7584b9d77bf4ca1bb60af851d70f12dd6bb4e670 Thu Apr 21 12:35:05 2022 -0700
    pay attention to block structure in bigBed 12+ when generating featureBit structure
• src/hg/htdocs/FAQ/FAQreleases.html
  • lines changed 11, context: html, text, full: html, text
    483ee22a127c4f2fc29aca3752227232df09f2ab Fri Apr 22 09:21:31 2022 -0700
    Adding a note about the new assemblyRequest.html page on the FAQ about genomes refs #29237
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
  • lines changed 15, context: html, text, full: html, text
    d291406142c21bb493b06379be1d6141be9bec94 Thu Apr 21 14:23:02 2022 -0700
    Adding docs for barChartFacets, barChartStatsUrl, and barChartMerge tags.
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html
  • lines changed 12, context: html, text, full: html, text
    d243250b9dbaede757b5b66dbf2514ab6f95d926 Thu Apr 21 13:31:25 2022 -0700
    Adding some new settings under bigPsl in Track Hub doc as noted work with CHM13 hub refs #29278
  • lines changed 18, context: html, text, full: html, text
    d291406142c21bb493b06379be1d6141be9bec94 Thu Apr 21 14:23:02 2022 -0700
    Adding docs for barChartFacets, barChartStatsUrl, and barChartMerge tags.
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 39, context: html, text, full: html, text
    f402b5964c965234fa4663f6a24ea683a62ca48c Tue Apr 19 18:51:20 2022 -0700
    Adjusting the html section of trackDbLibrary.shtml to be more friendly for Track Hubs, refs #28817
  • lines changed 1, context: html, text, full: html, text
    095fd548bd90afdb940e6f8edaae8098e271bb9e Thu Apr 21 11:20:31 2022 -0700
    Fix typo from code review ,refs #29291
  • lines changed 3, context: html, text, full: html, text
    d243250b9dbaede757b5b66dbf2514ab6f95d926 Thu Apr 21 13:31:25 2022 -0700
    Adding some new settings under bigPsl in Track Hub doc as noted work with CHM13 hub refs #29278
  • lines changed 48, context: html, text, full: html, text
    d291406142c21bb493b06379be1d6141be9bec94 Thu Apr 21 14:23:02 2022 -0700
    Adding docs for barChartFacets, barChartStatsUrl, and barChartMerge tags.
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 27, context: html, text, full: html, text
    84b75d01f40d943cd0ce7ea69b0f85d7bf61ccfd Fri Apr 22 15:16:09 2022 -0700
    Announcing EVA tracks and minor change to settings refs #29031
• src/hg/htdocs/images/dm6ReMap.png
  • lines changed 0, context: html, text, full: html, text
    ad01cd9f5957d4c94a443940fc40e5f7323a8654 Fri Apr 22 01:51:17 2022 -0700
    Adding images for the ReMap track, refs #28960
• src/hg/htdocs/images/humanReMap.png
  • lines changed 0, context: html, text, full: html, text
    ad01cd9f5957d4c94a443940fc40e5f7323a8654 Fri Apr 22 01:51:17 2022 -0700
    Adding images for the ReMap track, refs #28960
• src/hg/htdocs/images/mouseReMap.png
  • lines changed 0, context: html, text, full: html, text
    ad01cd9f5957d4c94a443940fc40e5f7323a8654 Fri Apr 22 01:51:17 2022 -0700
    Adding images for the ReMap track, refs #28960
• src/hg/htdocs/images/reMap_schema_datatype.png
  • lines changed 0, context: html, text, full: html, text
    ad01cd9f5957d4c94a443940fc40e5f7323a8654 Fri Apr 22 01:51:17 2022 -0700
    Adding images for the ReMap track, refs #28960
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    84b75d01f40d943cd0ce7ea69b0f85d7bf61ccfd Fri Apr 22 15:16:09 2022 -0700
    Announcing EVA tracks and minor change to settings refs #29031
• src/hg/htdocs/makefile
  • lines changed 1, context: html, text, full: html, text
    d5cafae5e0dce22ad6ca2639a8bb3896f1059412 Wed Apr 20 12:30:45 2022 -0700
    get the assemblyRequest.html to htdocs-beta during a make beta refs #29237
  • lines changed 2, context: html, text, full: html, text
    e92e04e2d6dcf943fb7977d8591817233803fe54 Wed Apr 20 12:49:11 2022 -0700
    do the copy of assemblyRequest.html to htdocs-beta before the rsync to hgwbeta statements refs #29237
  • lines changed 1, context: html, text, full: html, text
    5dc00f0f294eac72fdf688556698487c1547ceec Thu Apr 21 09:02:46 2022 -0700
    add the rsync command that will get the assemblyRequest.html file to hgwbeta refs #29237
• src/hg/htdocs/training/coming.html
  • lines changed 86, context: html, text, full: html, text
    be357dc1bda00f69f9a7739fb5c449822c681d41 Fri Apr 22 14:22:59 2022 -0700
    change include filename to something easier to remember
• src/hg/htdocs/training/index.html
  • lines changed 1, context: html, text, full: html, text
    be357dc1bda00f69f9a7739fb5c449822c681d41 Fri Apr 22 14:22:59 2022 -0700
    change include filename to something easier to remember
• src/hg/htdocs/training/upcoming.html
  • lines changed 86, context: html, text, full: html, text
    be357dc1bda00f69f9a7739fb5c449822c681d41 Fri Apr 22 14:22:59 2022 -0700
    change include filename to something easier to remember
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    d2487ecf0f6491fcec2d901b6e64c9961572df64 Mon Apr 25 10:12:42 2022 -0700
    New version number v430
• src/hg/js/hgGateway.js
  • lines changed 1, context: html, text, full: html, text
    9be317c966b0eb4c05cfee143db116bb8def08a0 Tue Apr 19 14:08:17 2022 -0700
    ignore taxId from hubs when user clicks on one of the native organisms
• src/hg/lib/featureBits.c
  • lines changed 1, context: html, text, full: html, text
    4c1f727a9e15bed8ab103072f3e320c1d0fb02ed Wed Apr 20 17:15:15 2022 -0700
    don't treat bigWigs like all the other big* files which are based on bigBed
  • lines changed 1, context: html, text, full: html, text
    d1f536096d7ac957747ccc64a3b0eaa27981d7ab Thu Apr 21 12:55:59 2022 -0700
    fix in response to code review to restore original functionality
• src/hg/lib/hdb.c
  • lines changed 1, context: html, text, full: html, text
    b66cc3a556c36eea0a6575b1a84a8525c7d117d4 Wed Apr 20 15:19:15 2022 -0700
    clone a string that some code decides to free
• src/hg/makeDb/doc/canFam4/initialBuild.txt
  • lines changed 52, context: html, text, full: html, text
    29497c1dca3c7480705e178357dac9a7fa49cfb5 Mon Apr 18 20:16:35 2022 -0700
    add make doc for ncbiRefSeq build refs #29128
• src/hg/makeDb/doc/chm13v2.0/html/GCA_009914755.4_T2T-CHM13v2.0.description.html
  • lines changed 1, context: html, text, full: html, text
    82f90a52db4e8366bc85d4f42370da8a9827ef1b Thu Apr 21 12:35:01 2022 -0700
    include download link for NCBI RefSeq gene gtf file refs #29278
• src/hg/makeDb/doc/chm13v2.0/html/GCA_009914755.4_T2T-CHM13v2.0.refSeqComposite.html
  • lines changed 186, context: html, text, full: html, text
    a023c503eab0b9d165895f236f2614fac4f15723 Thu Apr 21 11:55:14 2022 -0700
    adding NCBI RefSeq genes refs #29278
• src/hg/makeDb/doc/chm13v2.0/hub/GCA_009914755.4_T2T-CHM13v2.0.chromAlias.txt
  • lines changed 25, context: html, text, full: html, text
    fc070c60b3b5baf1aba50372f28ea8788829605a Thu Apr 21 12:50:41 2022 -0700
    adding the RefSeq sequence names refs #29278
• src/hg/makeDb/doc/chm13v2.0/makefile
  • lines changed 1, context: html, text, full: html, text
    8cbdb800a1d6e5a699372b44567f77ef6ff4cc37 Thu Apr 21 12:21:36 2022 -0700
    adding NCBI RefSeq genes refs #29278
• src/hg/makeDb/doc/chm13v2.0/trackDb/GCA_009914755.4_T2T-CHM13v2.0.trackDb.txt
  • lines changed 88, context: html, text, full: html, text
    5e9b63de5fab122065dfe346d39d70148644226e Thu Apr 21 10:34:46 2022 -0700
    moving liftOver tracks from chains/nets to liftover composite track, refs #29266
  • lines changed 93, context: html, text, full: html, text
    8cbdb800a1d6e5a699372b44567f77ef6ff4cc37 Thu Apr 21 12:21:36 2022 -0700
    adding NCBI RefSeq genes refs #29278
• src/hg/makeDb/doc/chm13v2.0userData/build.txt
  • lines changed 24, context: html, text, full: html, text
    41f199e88fc710d1f86b96b606d15a5b975dda71 Tue Apr 19 22:05:14 2022 -0700
    fixed chain ids in hgLiftOver
  • lines changed 9, context: html, text, full: html, text
    3442f799e4ddde42dfc0257e514ea1831a514f97 Sun Apr 24 21:03:28 2022 -0700
    add score to T2T supplied liftOver chains
• src/hg/makeDb/doc/chm13v2.0userData/html/hgLiftOver.html
  • lines changed 131, context: html, text, full: html, text
    5e9b63de5fab122065dfe346d39d70148644226e Thu Apr 21 10:34:46 2022 -0700
    moving liftOver tracks from chains/nets to liftover composite track, refs #29266
  • lines changed 42, context: html, text, full: html, text
    9b720294543d666256e90f482ac9199cb77016a9 Sat Apr 23 06:18:00 2022 -0700
    adding more details to t2t liftover track after emails from Mark and Jim, refs #29266
  • lines changed 6, context: html, text, full: html, text
    4784eb35355907aa0b17327ccf0fb2c24fb00cce Sat Apr 23 07:07:42 2022 -0700
    adding one more sentence to prevous commit on t2t liftOver docs file
  • lines changed 3, context: html, text, full: html, text
    aa7883549df982bdba5d42f6bf31d64591ffb01b Sun Apr 24 21:17:15 2022 -0700
    moved various liftover tracks to mapping and sequencing group
• src/hg/makeDb/doc/chm13v2.0userData/makefile
  • lines changed 2, context: html, text, full: html, text
    3442f799e4ddde42dfc0257e514ea1831a514f97 Sun Apr 24 21:03:28 2022 -0700
    add score to T2T supplied liftOver chains
• src/hg/makeDb/doc/chm13v2.0userData/trackDb/hgLiftOver.trackDb.txt
  • lines changed 46, context: html, text, full: html, text
    5e9b63de5fab122065dfe346d39d70148644226e Thu Apr 21 10:34:46 2022 -0700
    moving liftOver tracks from chains/nets to liftover composite track, refs #29266
  • lines changed 3, context: html, text, full: html, text
    462c63760f1a1ce868b8c94d1f2c8da74a3d906c Thu Apr 21 10:39:06 2022 -0700
    small fixes to liftOver tracks, refs #29266
  • lines changed 4, context: html, text, full: html, text
    aa7883549df982bdba5d42f6bf31d64591ffb01b Sun Apr 24 21:17:15 2022 -0700
    moved various liftover tracks to mapping and sequencing group
• src/hg/makeDb/doc/evaSnp3.txt
  • lines changed 377, context: html, text, full: html, text
    26aac34f999f66703d253baef1ff5f084c2d5007 Tue Apr 19 17:12:41 2022 -0700
    EVA SNP3 track now QA ready, refs #29031
• src/hg/makeDb/doc/hg19.txt
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    3442f799e4ddde42dfc0257e514ea1831a514f97 Sun Apr 24 21:03:28 2022 -0700
    add score to T2T supplied liftOver chains
• src/hg/makeDb/doc/hg38/chm13LiftOver.txt
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    3442f799e4ddde42dfc0257e514ea1831a514f97 Sun Apr 24 21:03:28 2022 -0700
    add score to T2T supplied liftOver chains
• src/hg/makeDb/trackDb/drosophila/dm6/reMap.html
  • lines changed 11, context: html, text, full: html, text
    e9cb8eda87388e889a16f5737ea831979118445e Thu Apr 21 12:48:29 2022 -0700
    Code review edits for the ReMap track, refs #29293
  • lines changed 8, context: html, text, full: html, text
    951a2f1ae953b7f284a8865ba7c6810823142b61 Fri Apr 22 09:53:56 2022 -0700
    Updating ReMap track images, refs #28960
• src/hg/makeDb/trackDb/drosophila/dm6/reMap.ra
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    e9cb8eda87388e889a16f5737ea831979118445e Thu Apr 21 12:48:29 2022 -0700
    Code review edits for the ReMap track, refs #29293
• src/hg/makeDb/trackDb/evaSnp.html
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    26aac34f999f66703d253baef1ff5f084c2d5007 Tue Apr 19 17:12:41 2022 -0700
    EVA SNP3 track now QA ready, refs #29031
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    3e99f46ae896bf28c1fe300b5176ded59a73632e Thu Apr 21 16:53:24 2022 -0700
    Minor edits to eva track, refs #29031
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    84b75d01f40d943cd0ce7ea69b0f85d7bf61ccfd Fri Apr 22 15:16:09 2022 -0700
    Announcing EVA tracks and minor change to settings refs #29031
• src/hg/makeDb/trackDb/human/hg19/reMap.ra
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    e9cb8eda87388e889a16f5737ea831979118445e Thu Apr 21 12:48:29 2022 -0700
    Code review edits for the ReMap track, refs #29293
• src/hg/makeDb/trackDb/human/hg38/chm13LiftOver.ra
  • lines changed 1, context: html, text, full: html, text
    462c63760f1a1ce868b8c94d1f2c8da74a3d906c Thu Apr 21 10:39:06 2022 -0700
    small fixes to liftOver tracks, refs #29266
• src/hg/makeDb/trackDb/human/hg38/reMap.ra
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    e9cb8eda87388e889a16f5737ea831979118445e Thu Apr 21 12:48:29 2022 -0700
    Code review edits for the ReMap track, refs #29293
• src/hg/makeDb/trackDb/human/reMap.html
  • lines changed 7, context: html, text, full: html, text
    e9cb8eda87388e889a16f5737ea831979118445e Thu Apr 21 12:48:29 2022 -0700
    Code review edits for the ReMap track, refs #29293
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    951a2f1ae953b7f284a8865ba7c6810823142b61 Fri Apr 22 09:53:56 2022 -0700
    Updating ReMap track images, refs #28960
• src/hg/makeDb/trackDb/human/trackDb.ra
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    05eac053d3e77b852b0d8d3c4db896adabcf24b2 Wed Apr 20 05:12:54 2022 -0700
    fixing maxWindowCoverage on the genomenom track, refs #29271
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    b64ef884f050be442eb523c85d9084ae222078b0 Wed Apr 20 17:45:34 2022 -0700
    fix filters on Mastermind
• src/hg/makeDb/trackDb/mouse/mm10/reMap.ra
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    e9cb8eda87388e889a16f5737ea831979118445e Thu Apr 21 12:48:29 2022 -0700
    Code review edits for the ReMap track, refs #29293
• src/hg/makeDb/trackDb/mouse/mm39/reMap.ra
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    e9cb8eda87388e889a16f5737ea831979118445e Thu Apr 21 12:48:29 2022 -0700
    Code review edits for the ReMap track, refs #29293
• src/hg/makeDb/trackDb/mouse/reMap.html
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    e9cb8eda87388e889a16f5737ea831979118445e Thu Apr 21 12:48:29 2022 -0700
    Code review edits for the ReMap track, refs #29293
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    951a2f1ae953b7f284a8865ba7c6810823142b61 Fri Apr 22 09:53:56 2022 -0700
    Updating ReMap track images, refs #28960
• src/hg/makeDb/trackDb/mouse/trackDb.ra
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    3e99f46ae896bf28c1fe300b5176ded59a73632e Thu Apr 21 16:53:24 2022 -0700
    Minor edits to eva track, refs #29031
• src/hg/makeDb/trackDb/tagTypes.tab
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    c4bb3841cc5f44b891d4825064753fa0710566bb Thu Apr 21 14:21:34 2022 -0700
    Making multiRegionsBedUrl tab be alphabetical like everything else.
• src/hg/makeDb/trackDb/trackDb.ra
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    26aac34f999f66703d253baef1ff5f084c2d5007 Tue Apr 19 17:12:41 2022 -0700
    EVA SNP3 track now QA ready, refs #29031
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    652d4ef894e0ad94ea0ee1be0f2b54e5ad3398c7 Wed Apr 20 09:54:20 2022 -0700
    Tweaking visibility and setting maxWindowCoverage which now acts like maxItems, refs #29031
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    0f349610f7a4c045796508d7e8160576d6cb6fcc Wed Apr 20 17:09:13 2022 -0700
    Adding density view to evaSnp track, refs #29031
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    3e99f46ae896bf28c1fe300b5176ded59a73632e Thu Apr 21 16:53:24 2022 -0700
    Minor edits to eva track, refs #29031
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    84b75d01f40d943cd0ce7ea69b0f85d7bf61ccfd Fri Apr 22 15:16:09 2022 -0700
    Announcing EVA tracks and minor change to settings refs #29031
• src/hg/makeDb/trackDb/virus/wuhCor1/galaxyEna.html
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    314549e546f7eb6159ec55c6201bcc22e9a4cea6 Thu Apr 21 16:21:07 2022 -0700
    Releasing galaxy ENA track, refs #29069
• src/hg/makeDb/trackDb/virus/wuhCor1/galaxyEna.ra
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    314549e546f7eb6159ec55c6201bcc22e9a4cea6 Thu Apr 21 16:21:07 2022 -0700
    Releasing galaxy ENA track, refs #29069
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra
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    314549e546f7eb6159ec55c6201bcc22e9a4cea6 Thu Apr 21 16:21:07 2022 -0700
    Releasing galaxy ENA track, refs #29069
• src/hg/makeDb/trackDb/virus/wuhCor1/variantMuts.ra
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    80d5d4379047697b040ae460146a73e558b0abb3 Tue Apr 19 06:33:17 2022 -0700
    fixing tdb bug that I introduced with a braindead commit, found by cron job, no redmine
• src/hg/makefile
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    311012f072535713c144bfe39436acd835eca9ef Tue Apr 19 13:32:41 2022 -0700
    adding gar to the build system refs #29237
• src/hg/pyLib/hgLib.py
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    4cf631b8c17695efbef6ba6fd005e33f09ea16af Tue Apr 19 09:52:41 2022 -0700
    Fix pyLib hg.conf parser to account for the new what is this assembly section
• src/inc/srcVersion.h
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    d2487ecf0f6491fcec2d901b6e64c9961572df64 Mon Apr 25 10:12:42 2022 -0700
    New version number v430
• src/utils/qa/weeklybld/buildEnv.csh
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    4bea9b8593cfc3ef2e471f9107d9a10892cee2d4 Mon Apr 25 10:11:24 2022 -0700
    v430 final build, refs #29240

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• files changed: 88