All File Changes

v467_preview to v467_preview2 (2024-06-10 to 2024-06-17) v467

• src/hg/checkHgFindSpec/checkHgFindSpec.c
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    b26ab6189278b9fa735672d1aac2b290392cc305 Fri Jun 14 16:27:51 2024 -0700
    Remove mistaken dependency on gbMeta from checkHgFindSpec, refs Novartis email
• src/hg/hgPhyloPlace/vcfFromFasta.c
  • lines changed 38, context: html, text, full: html, text
    0c0fe3658fc96b44ea96c2b30f58194779569961 Mon Jun 10 18:17:25 2024 -0700
    Fix: was forgetting to explicitly set reference alleles when making VCF from nextclade output, resulting in way too many no-calls which made usher-sampled way too slow. Thanks @aviczhl2 for reporting the slowness.
• src/hg/hgTables/filterFields.c
  • lines changed 8, context: html, text, full: html, text
    c2f76a8b519313e22f6c91ee7745e86e4dc660bc Mon Jun 17 10:56:57 2024 -0700
    Switching more hgTracks and hgTables buttons/labels to sentence case, refs #25787
• src/hg/hgTables/identifiers.c
  • lines changed 5, context: html, text, full: html, text
    c2f76a8b519313e22f6c91ee7745e86e4dc660bc Mon Jun 17 10:56:57 2024 -0700
    Switching more hgTracks and hgTables buttons/labels to sentence case, refs #25787
• src/hg/hgTables/mainPage.c
  • lines changed 55, context: html, text, full: html, text
    ec8e394fe288b94187c9258a0aa02a396d7c3ab0 Fri Jun 14 18:41:29 2024 -0700
    Switching hgTables buttons and labels to sentence case, refs #25787
• src/hg/hgTables/usage.c
  • lines changed 25, context: html, text, full: html, text
    ec8e394fe288b94187c9258a0aa02a396d7c3ab0 Fri Jun 14 18:41:29 2024 -0700
    Switching hgTables buttons and labels to sentence case, refs #25787
• src/hg/hgTables/userRegions.c
  • lines changed 3, context: html, text, full: html, text
    c2f76a8b519313e22f6c91ee7745e86e4dc660bc Mon Jun 17 10:56:57 2024 -0700
    Switching more hgTracks and hgTables buttons/labels to sentence case, refs #25787
• src/hg/hgTracks/config.c
  • lines changed 16, context: html, text, full: html, text
    c2f76a8b519313e22f6c91ee7745e86e4dc660bc Mon Jun 17 10:56:57 2024 -0700
    Switching more hgTracks and hgTables buttons/labels to sentence case, refs #25787
• src/hg/hgTracks/extTools.ra
  • lines changed 1, context: html, text, full: html, text
    f66ab9141018bb7d7e5f889489cd77eebfb06404 Tue Jun 11 06:22:57 2024 -0700
    extending primer3 max seq size
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    b3d121a8a7def35ab27b02fd119440a687f2ec15 Wed Jun 12 06:04:29 2024 -0700
    Revert "extending primer3 max seq size". Primer3 really has a hard 10kb limit. This reverts commit f66ab9141018bb7d7e5f889489cd77eebfb06404.
• src/hg/hgTracks/hgTracks.c
  • lines changed 26, context: html, text, full: html, text
    8125e1ea14a9c8b3ab7e6ad879c82c757a539243 Fri Jun 14 17:40:32 2024 -0700
    Switching hgTracks buttons and labels to sentence case, refs #25787
• src/hg/hgTracks/menu.c
  • lines changed 1, context: html, text, full: html, text
    bf337e7ac5646c4a7f7d19a8d577eeff63e27c22 Thu Jun 13 01:16:49 2024 -0700
    changing DNA to DNA sequence in menu, email from user and ML ticket by Sandy Sharp, refs #33589
• src/hg/hgc/bamClick.c
  • lines changed 10, context: html, text, full: html, text
    5add048a3ba033e17e6c0f5643e9985ef8a15f44 Thu Jun 13 02:59:16 2024 -0700
    adding legend under cigar display on bam hgc page, refs #33292
• src/hg/htdocs/goldenPath/help/publicHubGuidelines.html
  • lines changed 3, context: html, text, full: html, text
    4cd0e9c303bb97128ad71a8e236602ca0fbcadae Tue Jun 11 16:27:00 2024 -0700
    Adding 'Labeling tracks with informative labels will help users.' to publicHubGuidelines.html per user request, refs #33768
• src/hg/htdocs/indexMeetings.html
  • lines changed 12, context: html, text, full: html, text
    25262196065274836a9b8c5195c602da8b63bf76 Tue Jun 11 08:35:22 2024 -0700
    Updating training schedule.
• src/hg/hubApi/apiUtils.c
  • lines changed 3, context: html, text, full: html, text
    efe42f68b1889404cfa56bbc020c273ebdb5fc8d Wed Jun 12 12:05:02 2024 -0700
    now supporting bigDbSnp bigMaf and bigChain refs #24430
  • lines changed 40, context: html, text, full: html, text
    3ccd2b6675cc1955d74aec568ef2fdc852bd3fd7 Fri Jun 14 12:12:57 2024 -0700
    adding a /list/genarkGenomes endpoint refs #23589
• src/hg/hubApi/dataApi.h
  • lines changed 8, context: html, text, full: html, text
    3ccd2b6675cc1955d74aec568ef2fdc852bd3fd7 Fri Jun 14 12:12:57 2024 -0700
    adding a /list/genarkGenomes endpoint refs #23589
  • lines changed 1, context: html, text, full: html, text
    ee5f1773270f1662bbea9a28017cf88080e40793 Fri Jun 14 13:28:36 2024 -0700
    add new option to getSeq -revComp to reverse complement sequence output refs #26691
• src/hg/hubApi/getData.c
  • lines changed 24, context: html, text, full: html, text
    ee5f1773270f1662bbea9a28017cf88080e40793 Fri Jun 14 13:28:36 2024 -0700
    add new option to getSeq -revComp to reverse complement sequence output refs #26691
• src/hg/hubApi/hubApi.c
  • lines changed 11, context: html, text, full: html, text
    2ea6e837990eb39bc317f2b1aacacfe4ff77a7ce Tue Jun 11 18:00:29 2024 -0700
    correctly check boolean CGI variable and ouput the tracks in a single file track hub while in html mode no redmine
  • lines changed 21, context: html, text, full: html, text
    efe42f68b1889404cfa56bbc020c273ebdb5fc8d Wed Jun 12 12:05:02 2024 -0700
    now supporting bigDbSnp bigMaf and bigChain refs #24430
  • lines changed 2, context: html, text, full: html, text
    628a3a8a4dd8529eb3ab160d67f934da6595ebdb Wed Jun 12 14:26:58 2024 -0700
    display the source version in the html page title refs #24430
  • lines changed 1, context: html, text, full: html, text
    3ccd2b6675cc1955d74aec568ef2fdc852bd3fd7 Fri Jun 14 12:12:57 2024 -0700
    adding a /list/genarkGenomes endpoint refs #23589
  • lines changed 1, context: html, text, full: html, text
    ee5f1773270f1662bbea9a28017cf88080e40793 Fri Jun 14 13:28:36 2024 -0700
    add new option to getSeq -revComp to reverse complement sequence output refs #26691
• src/hg/hubApi/list.c
  • lines changed 64, context: html, text, full: html, text
    3ccd2b6675cc1955d74aec568ef2fdc852bd3fd7 Fri Jun 14 12:12:57 2024 -0700
    adding a /list/genarkGenomes endpoint refs #23589
• src/hg/hubApi/tests/expected/bigChain.gz
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    2561e20e2d24e53c562c67c64adc01e19a44f7cb Wed Jun 12 15:00:00 2024 -0700
    adding tests for bigDbSnp bigMaf and bigChain refs #24430
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    b538830cb5a8eb5ffce539343a863b2a1bf4df08 Wed Jun 12 15:14:15 2024 -0700
    correct bigChain example refs #24430
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    57be7c2fe6ad00cc149bce423c6050b0aee877d8 Wed Jun 12 15:33:06 2024 -0700
    correctly eliminate the server for the results compare refs #24430
• src/hg/hubApi/tests/expected/bigDbSnp.gz
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    2561e20e2d24e53c562c67c64adc01e19a44f7cb Wed Jun 12 15:00:00 2024 -0700
    adding tests for bigDbSnp bigMaf and bigChain refs #24430
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    57be7c2fe6ad00cc149bce423c6050b0aee877d8 Wed Jun 12 15:33:06 2024 -0700
    correctly eliminate the server for the results compare refs #24430
• src/hg/hubApi/tests/expected/bigMaf.gz
  • lines changed 0, context: html, text, full: html, text
    2561e20e2d24e53c562c67c64adc01e19a44f7cb Wed Jun 12 15:00:00 2024 -0700
    adding tests for bigDbSnp bigMaf and bigChain refs #24430
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    57be7c2fe6ad00cc149bce423c6050b0aee877d8 Wed Jun 12 15:33:06 2024 -0700
    correctly eliminate the server for the results compare refs #24430
• src/hg/hubApi/tests/expected/getSeq06.gz
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    87ec277a5cc1915db16b58a4107b7a39e7a5da70 Fri Jun 14 13:34:16 2024 -0700
    add new option to getSeq -revComp to reverse complement sequence output refs #26691
• src/hg/hubApi/tests/expected/getSeq07.gz
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    87ec277a5cc1915db16b58a4107b7a39e7a5da70 Fri Jun 14 13:34:16 2024 -0700
    add new option to getSeq -revComp to reverse complement sequence output refs #26691
• src/hg/hubApi/tests/expected/list20.gz
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    188036292f01c867ee6ba195e919c6b91071592e Wed Jun 12 12:03:30 2024 -0700
    updated expected results for api test refs #24430
• src/hg/hubApi/tests/expected/list22.gz
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    188036292f01c867ee6ba195e919c6b91071592e Wed Jun 12 12:03:30 2024 -0700
    updated expected results for api test refs #24430
• src/hg/hubApi/tests/expected/list23.gz
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    188036292f01c867ee6ba195e919c6b91071592e Wed Jun 12 12:03:30 2024 -0700
    updated expected results for api test refs #24430
• src/hg/hubApi/tests/expected/list26.gz
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    d4f37ab805653c217758293128fe54557f4ec370 Fri Jun 14 12:13:51 2024 -0700
    adding a /list/genarkGenomes endpoint refs #23589
• src/hg/hubApi/tests/expected/list27.gz
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    d4f37ab805653c217758293128fe54557f4ec370 Fri Jun 14 12:13:51 2024 -0700
    adding a /list/genarkGenomes endpoint refs #23589
• src/hg/hubApi/tests/expected/test0.gz
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    188036292f01c867ee6ba195e919c6b91071592e Wed Jun 12 12:03:30 2024 -0700
    updated expected results for api test refs #24430
• src/hg/hubApi/tests/expected/test41.gz
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    188036292f01c867ee6ba195e919c6b91071592e Wed Jun 12 12:03:30 2024 -0700
    updated expected results for api test refs #24430
• src/hg/hubApi/tests/jsonConsumer.pl
  • lines changed 9, context: html, text, full: html, text
    9512d9e92adf96a6e857ebad9385420a131b41a0 Fri Jun 14 12:19:11 2024 -0700
    correctly form URL when no standard arguments refs #23589
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    2f5ab86dbe1725b58789a00b199c64e0a68b2cff Fri Jun 14 13:35:06 2024 -0700
    add new option to getSeq -revComp to reverse complement sequence output refs #26691
• src/hg/hubApi/tests/makefile
  • lines changed 44, context: html, text, full: html, text
    2561e20e2d24e53c562c67c64adc01e19a44f7cb Wed Jun 12 15:00:00 2024 -0700
    adding tests for bigDbSnp bigMaf and bigChain refs #24430
  • lines changed 8, context: html, text, full: html, text
    1fa309a4080795a05783d3255631e8991eb18e04 Wed Jun 12 15:14:52 2024 -0700
    correct bigChain example refs #24430
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    57be7c2fe6ad00cc149bce423c6050b0aee877d8 Wed Jun 12 15:33:06 2024 -0700
    correctly eliminate the server for the results compare refs #24430
  • lines changed 13, context: html, text, full: html, text
    d4f37ab805653c217758293128fe54557f4ec370 Fri Jun 14 12:13:51 2024 -0700
    adding a /list/genarkGenomes endpoint refs #23589
  • lines changed 12, context: html, text, full: html, text
    87ec277a5cc1915db16b58a4107b7a39e7a5da70 Fri Jun 14 13:34:16 2024 -0700
    add new option to getSeq -revComp to reverse complement sequence output refs #26691
• src/hg/inc/bigChain.h
  • lines changed 3, context: html, text, full: html, text
    4ac9486a77f0ed4e87de2e946f29e203b354398b Thu Jun 13 13:56:46 2024 -0700
    added chainToBigChain command
• src/hg/inc/bigLink.h
  • lines changed 70, context: html, text, full: html, text
    4ac9486a77f0ed4e87de2e946f29e203b354398b Thu Jun 13 13:56:46 2024 -0700
    added chainToBigChain command
• src/hg/inc/customTrack.h
  • lines changed 1, context: html, text, full: html, text
    c2f76a8b519313e22f6c91ee7745e86e4dc660bc Mon Jun 17 10:56:57 2024 -0700
    Switching more hgTracks and hgTables buttons/labels to sentence case, refs #25787
• src/hg/inc/hui.h
  • lines changed 1, context: html, text, full: html, text
    c2f76a8b519313e22f6c91ee7745e86e4dc660bc Mon Jun 17 10:56:57 2024 -0700
    Switching more hgTracks and hgTables buttons/labels to sentence case, refs #25787
• src/hg/inc/search.h
  • lines changed 1, context: html, text, full: html, text
    c2f76a8b519313e22f6c91ee7745e86e4dc660bc Mon Jun 17 10:56:57 2024 -0700
    Switching more hgTracks and hgTables buttons/labels to sentence case, refs #25787
• src/hg/inc/web.h
  • lines changed 3, context: html, text, full: html, text
    a9e106ea5ddcac6b0eb1a25ad7b50b4d98b2f84e Fri Jun 14 07:02:18 2024 -0700
    forgot to include file in previous commit, accidentally committed code that should have been in a separate commit, for genome-china, no redmine
• src/hg/js/hgTracks.js
  • lines changed 2, context: html, text, full: html, text
    c4d3223408b33ddadb3f0ca8b5e492bb3773b868 Fri Jun 14 02:45:33 2024 -0700
    restoring title from recommended track sets window, refs #33974
• src/hg/js/utils.js
  • lines changed 2, context: html, text, full: html, text
    7f1fa012784d2a54bfacd8b1e98045dedceb3c29 Fri Jun 14 16:18:33 2024 -0700
    Make some of the less helpful tooltips have a shorter delay, refs #33540
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    3c44fbeeb6ef05447f7caff6d4156f4b3083c4b1 Fri Jun 14 16:21:43 2024 -0700
    Remove 'drag select or click to zoom' tooltip, refs #33540
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    ba0e2c3758d46d1e85865f5c2730cd842515d73c Fri Jun 14 16:23:23 2024 -0700
    Woops forgot a line, refs #33540
• src/hg/lib/bigChain.c
  • lines changed 12, context: html, text, full: html, text
    4ac9486a77f0ed4e87de2e946f29e203b354398b Thu Jun 13 13:56:46 2024 -0700
    added chainToBigChain command
• src/hg/lib/bigLink.c
  • lines changed 152, context: html, text, full: html, text
    4ac9486a77f0ed4e87de2e946f29e203b354398b Thu Jun 13 13:56:46 2024 -0700
    added chainToBigChain command
• src/hg/lib/chainNetDbLoad.c
  • lines changed 1, context: html, text, full: html, text
    14f06e520a97d5e7d68df145edd88b642200e007 Thu Jun 13 22:56:52 2024 -0700
    fixed decoding of chain scores, which is a double in the data structures; it still displays as an int in hgc
• src/hg/lib/decoratorUi.c
  • lines changed 5, context: html, text, full: html, text
    cf699e14f89d5306a6d136facca8f135f3d81814 Tue Jun 11 05:09:42 2024 -0700
    adding decorator help text, no redmine, email with Mark and Jonathan
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    4ac9486a77f0ed4e87de2e946f29e203b354398b Thu Jun 13 13:56:46 2024 -0700
    added chainToBigChain command
• src/hg/lib/web.c
  • lines changed 16, context: html, text, full: html, text
    5ee63c17bf3324e22fba3ab16c2bb21415b102d7 Fri Jun 14 07:00:44 2024 -0700
    increasing buffer for connected hubs, refs #33973
• src/hg/makeDb/doc/asmHubs/commonNames.pl
  • lines changed 6, context: html, text, full: html, text
    001fb580a2cea33c231639073694e698dbb49a09 Mon Jun 10 11:48:35 2024 -0700
    manage the general name of bony fish, eudicots birds snakes bats refs #29545
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 17, context: html, text, full: html, text
    a430f85c0f9ce1dab0605b6baf041660c6cade4c Mon Jun 10 15:25:46 2024 -0700
    VGP alternate update adding 17 assemblies refs #20545
• src/hg/makeDb/doc/bigDbSnp.txt
  • lines changed 11, context: html, text, full: html, text
    01e5d8c767c5913b35cdc11e66ceef943dcb1906 Mon Jun 10 17:18:34 2024 -0700
    note about h3africa added to bigDbsSnp.txt make doc
• src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv
  • lines changed 5, context: html, text, full: html, text
    a430f85c0f9ce1dab0605b6baf041660c6cade4c Mon Jun 10 15:25:46 2024 -0700
    VGP alternate update adding 17 assemblies refs #20545
• src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    a430f85c0f9ce1dab0605b6baf041660c6cade4c Mon Jun 10 15:25:46 2024 -0700
    VGP alternate update adding 17 assemblies refs #20545
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 6, context: html, text, full: html, text
    a430f85c0f9ce1dab0605b6baf041660c6cade4c Mon Jun 10 15:25:46 2024 -0700
    VGP alternate update adding 17 assemblies refs #20545
• src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv
  • lines changed 5, context: html, text, full: html, text
    a430f85c0f9ce1dab0605b6baf041660c6cade4c Mon Jun 10 15:25:46 2024 -0700
    VGP alternate update adding 17 assemblies refs #20545
• src/hg/makeDb/doc/vgpAsmHub/vgp.alternate.orderList.tsv
  • lines changed 18, context: html, text, full: html, text
    ce4c9616023304d8f391945196866c465c054fb5 Wed Jun 12 20:17:42 2024 -0700
    updating 17 for VGP alternate
• src/hg/makeDb/doc/vgpAsmHub/vgp.taxId.asmId.class.txt
  • lines changed 17, context: html, text, full: html, text
    ce4c9616023304d8f391945196866c465c054fb5 Wed Jun 12 20:17:42 2024 -0700
    updating 17 for VGP alternate
• src/hg/makeDb/trackDb/human/hg38/gnomad.alpha.ra
  • lines changed 2, context: html, text, full: html, text
    7c02cf1265ed37c56e57aef0c6202ddea4d7fd9c Mon Jun 10 16:43:36 2024 -0700
    Add allele frequency information to gnomad v4.1 mouseovers, refs Ana email
• src/hg/makeDb/trackDb/human/hg38/knownGene.alpha.ra
  • lines changed 10, context: html, text, full: html, text
    6e18f171e1ea3a6bf1f09e7b3eea96936fe11fc1 Thu Jun 13 05:06:33 2024 -0700
    initial commit for knownGene NMD decorators, refs #33737
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    6e18f171e1ea3a6bf1f09e7b3eea96936fe11fc1 Thu Jun 13 05:06:33 2024 -0700
    initial commit for knownGene NMD decorators, refs #33737
• src/hg/near/hgNearTest/hgNearTest.c
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    b510e09f43330d387df999db278d44fe717e9dd2 Mon Jun 17 11:02:19 2024 -0700
    Fix for hgNearTest crashing with the new more restrictive db string constraints. We expect 0 for a missing database in hgNear; the test should supply 0. No ticket.
• src/hg/pslToChain/pslToChain.c
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    4ac9486a77f0ed4e87de2e946f29e203b354398b Thu Jun 13 13:56:46 2024 -0700
    added chainToBigChain command
• src/hg/pslToChain/tests/expected/error
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    4ac9486a77f0ed4e87de2e946f29e203b354398b Thu Jun 13 13:56:46 2024 -0700
    added chainToBigChain command
• src/hg/pslToChain/tests/expected/example3.chain
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    bfad6170abfeb8f1e3c38200acc6acb50ae70a5a Thu Jun 13 14:01:04 2024 -0700
    added pslToChain -fixStrand option to correct negative target strands rather than abort or ignore psl
• src/hg/pslToChain/tests/input/mtor.psl
  • lines changed 2, context: html, text, full: html, text
    bfad6170abfeb8f1e3c38200acc6acb50ae70a5a Thu Jun 13 14:01:04 2024 -0700
    added pslToChain -fixStrand option to correct negative target strands rather than abort or ignore psl
• src/hg/pslToChain/tests/input/mtor.psl.gz
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    bfad6170abfeb8f1e3c38200acc6acb50ae70a5a Thu Jun 13 14:01:04 2024 -0700
    added pslToChain -fixStrand option to correct negative target strands rather than abort or ignore psl
• src/hg/pslToChain/tests/makefile
  • lines changed 9, context: html, text, full: html, text
    4ac9486a77f0ed4e87de2e946f29e203b354398b Thu Jun 13 13:56:46 2024 -0700
    added chainToBigChain command
• src/hg/utils/automation/doSimpleRepeat.pl
  • lines changed 4, context: html, text, full: html, text
    405a64d015eb7dd55a4bbfb533f463f7b9a4c23c Tue Jun 11 10:32:25 2024 -0700
    prevent this procedure from running on top of an existing process no redmine
• src/hg/utils/chainToBigChain/chainToBigChain.c
  • lines changed 128, context: html, text, full: html, text
    4ac9486a77f0ed4e87de2e946f29e203b354398b Thu Jun 13 13:56:46 2024 -0700
    added chainToBigChain command
• src/hg/utils/chainToBigChain/makefile
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    4ac9486a77f0ed4e87de2e946f29e203b354398b Thu Jun 13 13:56:46 2024 -0700
    added chainToBigChain command
• src/hg/utils/chainToBigChain/tests/expected/simpleTest.bigChain
  • lines changed 4, context: html, text, full: html, text
    4ac9486a77f0ed4e87de2e946f29e203b354398b Thu Jun 13 13:56:46 2024 -0700
    added chainToBigChain command
• src/hg/utils/chainToBigChain/tests/expected/simpleTest.bigChainLink
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    4ac9486a77f0ed4e87de2e946f29e203b354398b Thu Jun 13 13:56:46 2024 -0700
    added chainToBigChain command
• src/hg/utils/chainToBigChain/tests/input/hg38.chrom.sizes
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    4ac9486a77f0ed4e87de2e946f29e203b354398b Thu Jun 13 13:56:46 2024 -0700
    added chainToBigChain command
• src/hg/utils/chainToBigChain/tests/input/hg38.mm10.test.chain
  • lines changed 19, context: html, text, full: html, text
    4ac9486a77f0ed4e87de2e946f29e203b354398b Thu Jun 13 13:56:46 2024 -0700
    added chainToBigChain command
• src/hg/utils/chainToBigChain/tests/makefile
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    4ac9486a77f0ed4e87de2e946f29e203b354398b Thu Jun 13 13:56:46 2024 -0700
    added chainToBigChain command
• src/hg/utils/makefile
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    4ac9486a77f0ed4e87de2e946f29e203b354398b Thu Jun 13 13:56:46 2024 -0700
    added chainToBigChain command
• src/hg/utils/otto/geneReviews/geneReviewsWrapper.sh
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    7e203f571903324078fe784c15d9e753eac2ceb4 Thu Jun 13 15:56:30 2024 -0700
    Adding the -E flag, we recently silenced this otto job to have an empty body when no output is going out but now it is sending emails with that subject and no content when there is no update. This should cause it to discard the email when no body is found.
• src/utils/bigBedInfo/bigBedInfo.c
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    04e01b72c197e97a044533aaba91fb328061615a Thu Jun 13 02:28:49 2024 -0700
    outputting defined and extra fields in bigBedInfo, no redmine, needed later for hubMake and bedmethyl support
• src/utils/qa/checkSessionsFromRR.py
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    8e415e6f438aac63ed1feb3865c757a74c606606 Tue Jun 11 12:07:22 2024 -0700
    Code review edits, refs #33833
• src/utils/qa/jasparUpdate.py
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    9b025ae8f9ec2c72f1c7d72e2b3b9c25be099e05 Tue Jun 11 11:46:05 2024 -0700
    Adding a usage statement to the updateJaspar.py script. Now prints the usage statement when no arguments are given and runs the script when using a -e flag to run the script. refs #32537
• src/utils/qa/weeklybld/buildEnv.csh
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    d192b4f117a5c9e353f4c1d02cf60f4006fc66f4 Mon Jun 17 11:12:29 2024 -0700
    v467 preview2, refs #33949

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• files changed: 98