All File Changes

v436_preview2 to v436_base (2022-08-22 to 2022-08-29) v436

• src/hg/cgilib/tests/expected/annoGrator/insertions.txt
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    ae5fa46665b19315211b621745d925fb94aa65a0 Wed Aug 24 15:16:45 2022 -0700
    Replacing spaces in some VCF header #CHROM lines with tabs -- this was overlooked when vcf.c was using chopLine instead of chopTabs as it should.
• src/hg/cgilib/tests/input/annoGrator/insertionsPrimary.vcf
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    ae5fa46665b19315211b621745d925fb94aa65a0 Wed Aug 24 15:16:45 2022 -0700
    Replacing spaces in some VCF header #CHROM lines with tabs -- this was overlooked when vcf.c was using chopLine instead of chopTabs as it should.
• src/hg/cgilib/tests/input/annoGrator/insertionsPrimary.vcf.gz
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    ae5fa46665b19315211b621745d925fb94aa65a0 Wed Aug 24 15:16:45 2022 -0700
    Replacing spaces in some VCF header #CHROM lines with tabs -- this was overlooked when vcf.c was using chopLine instead of chopTabs as it should.
• src/hg/cgilib/tests/input/annoGrator/insertionsPrimary.vcf.gz.tbi
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    ae5fa46665b19315211b621745d925fb94aa65a0 Wed Aug 24 15:16:45 2022 -0700
    Replacing spaces in some VCF header #CHROM lines with tabs -- this was overlooked when vcf.c was using chopLine instead of chopTabs as it should.
• src/hg/cgilib/tests/input/annoGrator/insertionsSecondary.vcf
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    ae5fa46665b19315211b621745d925fb94aa65a0 Wed Aug 24 15:16:45 2022 -0700
    Replacing spaces in some VCF header #CHROM lines with tabs -- this was overlooked when vcf.c was using chopLine instead of chopTabs as it should.
• src/hg/cgilib/tests/input/annoGrator/insertionsSecondary.vcf.gz
  • lines changed 0, context: html, text, full: html, text
    ae5fa46665b19315211b621745d925fb94aa65a0 Wed Aug 24 15:16:45 2022 -0700
    Replacing spaces in some VCF header #CHROM lines with tabs -- this was overlooked when vcf.c was using chopLine instead of chopTabs as it should.
• src/hg/cgilib/tests/input/annoGrator/insertionsSecondary.vcf.gz.tbi
  • lines changed 0, context: html, text, full: html, text
    ae5fa46665b19315211b621745d925fb94aa65a0 Wed Aug 24 15:16:45 2022 -0700
    Replacing spaces in some VCF header #CHROM lines with tabs -- this was overlooked when vcf.c was using chopLine instead of chopTabs as it should.
• src/hg/hgPhyloPlace/hgPhyloPlace.c
  • lines changed 103, context: html, text, full: html, text
    afafa0301ea4b14fbe1fbd5aa379c5351ecd640d Tue Aug 2 19:41:44 2022 -0700
    Add support for non-wuhCor1 genomes (e.g. monkeypox GenArk hub). * Search in hgPhyloPlaceData for config.ra files, taking assembly name (minus hub prefix) from directory name. * Add a menu input to the main page for switching between supported genomes if there are more than one. * Replace hardcoded values or global vars with dnaSeq attributes, assembly metadata queries or new config.ra settings. * Separate out SARS-CoV-2-specific help text like GISAID/CNCB descriptions. * Support metadata columns for GenBank-specific stuff & Nextstrain lineages (for MPXV). * also a little refactoring in runUsher in preparation for supporting usher server mode: parse new placement info file so we don't have to parse that data form usher stderr output. TODO: update Nextstrain/Auspice JSON output to use appropriate metadata columns and support monkeypox genes.
• src/hg/hgPhyloPlace/phyloPlace.c
  • lines changed 207, context: html, text, full: html, text
    afafa0301ea4b14fbe1fbd5aa379c5351ecd640d Tue Aug 2 19:41:44 2022 -0700
    Add support for non-wuhCor1 genomes (e.g. monkeypox GenArk hub). * Search in hgPhyloPlaceData for config.ra files, taking assembly name (minus hub prefix) from directory name. * Add a menu input to the main page for switching between supported genomes if there are more than one. * Replace hardcoded values or global vars with dnaSeq attributes, assembly metadata queries or new config.ra settings. * Separate out SARS-CoV-2-specific help text like GISAID/CNCB descriptions. * Support metadata columns for GenBank-specific stuff & Nextstrain lineages (for MPXV). * also a little refactoring in runUsher in preparation for supporting usher server mode: parse new placement info file so we don't have to parse that data form usher stderr output. TODO: update Nextstrain/Auspice JSON output to use appropriate metadata columns and support monkeypox genes.
• src/hg/hgPhyloPlace/phyloPlace.h
  • lines changed 13, context: html, text, full: html, text
    afafa0301ea4b14fbe1fbd5aa379c5351ecd640d Tue Aug 2 19:41:44 2022 -0700
    Add support for non-wuhCor1 genomes (e.g. monkeypox GenArk hub). * Search in hgPhyloPlaceData for config.ra files, taking assembly name (minus hub prefix) from directory name. * Add a menu input to the main page for switching between supported genomes if there are more than one. * Replace hardcoded values or global vars with dnaSeq attributes, assembly metadata queries or new config.ra settings. * Separate out SARS-CoV-2-specific help text like GISAID/CNCB descriptions. * Support metadata columns for GenBank-specific stuff & Nextstrain lineages (for MPXV). * also a little refactoring in runUsher in preparation for supporting usher server mode: parse new placement info file so we don't have to parse that data form usher stderr output. TODO: update Nextstrain/Auspice JSON output to use appropriate metadata columns and support monkeypox genes.
• src/hg/hgPhyloPlace/runUsher.c
  • lines changed 62, context: html, text, full: html, text
    afafa0301ea4b14fbe1fbd5aa379c5351ecd640d Tue Aug 2 19:41:44 2022 -0700
    Add support for non-wuhCor1 genomes (e.g. monkeypox GenArk hub). * Search in hgPhyloPlaceData for config.ra files, taking assembly name (minus hub prefix) from directory name. * Add a menu input to the main page for switching between supported genomes if there are more than one. * Replace hardcoded values or global vars with dnaSeq attributes, assembly metadata queries or new config.ra settings. * Separate out SARS-CoV-2-specific help text like GISAID/CNCB descriptions. * Support metadata columns for GenBank-specific stuff & Nextstrain lineages (for MPXV). * also a little refactoring in runUsher in preparation for supporting usher server mode: parse new placement info file so we don't have to parse that data form usher stderr output. TODO: update Nextstrain/Auspice JSON output to use appropriate metadata columns and support monkeypox genes.
• src/hg/hgPhyloPlace/treeToAuspiceJson.c
  • lines changed 8, context: html, text, full: html, text
    afafa0301ea4b14fbe1fbd5aa379c5351ecd640d Tue Aug 2 19:41:44 2022 -0700
    Add support for non-wuhCor1 genomes (e.g. monkeypox GenArk hub). * Search in hgPhyloPlaceData for config.ra files, taking assembly name (minus hub prefix) from directory name. * Add a menu input to the main page for switching between supported genomes if there are more than one. * Replace hardcoded values or global vars with dnaSeq attributes, assembly metadata queries or new config.ra settings. * Separate out SARS-CoV-2-specific help text like GISAID/CNCB descriptions. * Support metadata columns for GenBank-specific stuff & Nextstrain lineages (for MPXV). * also a little refactoring in runUsher in preparation for supporting usher server mode: parse new placement info file so we don't have to parse that data form usher stderr output. TODO: update Nextstrain/Auspice JSON output to use appropriate metadata columns and support monkeypox genes.
• src/hg/hgPhyloPlace/vcfFromFasta.c
  • lines changed 24, context: html, text, full: html, text
    afafa0301ea4b14fbe1fbd5aa379c5351ecd640d Tue Aug 2 19:41:44 2022 -0700
    Add support for non-wuhCor1 genomes (e.g. monkeypox GenArk hub). * Search in hgPhyloPlaceData for config.ra files, taking assembly name (minus hub prefix) from directory name. * Add a menu input to the main page for switching between supported genomes if there are more than one. * Replace hardcoded values or global vars with dnaSeq attributes, assembly metadata queries or new config.ra settings. * Separate out SARS-CoV-2-specific help text like GISAID/CNCB descriptions. * Support metadata columns for GenBank-specific stuff & Nextstrain lineages (for MPXV). * also a little refactoring in runUsher in preparation for supporting usher server mode: parse new placement info file so we don't have to parse that data form usher stderr output. TODO: update Nextstrain/Auspice JSON output to use appropriate metadata columns and support monkeypox genes.
• src/hg/hgPhyloPlace/writeCustomTracks.c
  • lines changed 41, context: html, text, full: html, text
    afafa0301ea4b14fbe1fbd5aa379c5351ecd640d Tue Aug 2 19:41:44 2022 -0700
    Add support for non-wuhCor1 genomes (e.g. monkeypox GenArk hub). * Search in hgPhyloPlaceData for config.ra files, taking assembly name (minus hub prefix) from directory name. * Add a menu input to the main page for switching between supported genomes if there are more than one. * Replace hardcoded values or global vars with dnaSeq attributes, assembly metadata queries or new config.ra settings. * Separate out SARS-CoV-2-specific help text like GISAID/CNCB descriptions. * Support metadata columns for GenBank-specific stuff & Nextstrain lineages (for MPXV). * also a little refactoring in runUsher in preparation for supporting usher server mode: parse new placement info file so we don't have to parse that data form usher stderr output. TODO: update Nextstrain/Auspice JSON output to use appropriate metadata columns and support monkeypox genes.
• src/hg/hgc/mafClick.c
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    38d43a0662e9cc3d44bd257b4edff456b068a6dd Fri Aug 26 12:20:59 2022 -0700
    use mapped species names on insert blocks
• src/hg/htdocs/bigRmskTrackDesc.html
  • lines changed 10, context: html, text, full: html, text
    cbc09e1a0995aaec42e14f54e796a2b03122d556 Wed Aug 24 17:41:03 2022 -0700
    removed repeat masker build-specific stuff from defautt bigRmsk track description
  • lines changed 208, context: html, text, full: html, text
    a6b50639f42d157408a1dc49512b77546b58afac Thu Aug 25 14:18:37 2022 -0700
    Moving the track description page to a new directory for tidyness, refs #29356
• src/hg/htdocs/goldenPath/help/bigRmsk.html
  • lines changed 3, context: html, text, full: html, text
    991271ccd9dbfe0d95386491f5e5e47b8e52896a Wed Aug 24 21:16:21 2022 -0700
    link bigRmsk to standard bigRmsk track description
  • lines changed 2, context: html, text, full: html, text
    ea975f152d4f10764a49b1f43870a05112566597 Thu Aug 25 13:11:37 2022 -0700
    fixed example of how to reference bigRmskTrackDesc.html
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    9223208a7550e787bf2e76a00aab5cf28f8e184d Thu Aug 25 13:32:05 2022 -0700
    missed place bigRmskTrackDesc.html linked needed to be edited
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    785d965633df1750c9ab1d3361fb0107c7519729 Thu Aug 25 15:22:33 2022 -0700
    updated links to bigRmskTrackDesc.html
• src/hg/htdocs/goldenPath/help/bigRmskTrackDescExample.html
  • lines changed 11, context: html, text, full: html, text
    991271ccd9dbfe0d95386491f5e5e47b8e52896a Wed Aug 24 21:16:21 2022 -0700
    link bigRmsk to standard bigRmsk track description
  • lines changed 1, context: html, text, full: html, text
    785d965633df1750c9ab1d3361fb0107c7519729 Thu Aug 25 15:22:33 2022 -0700
    updated links to bigRmskTrackDesc.html
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
  • lines changed 1, context: html, text, full: html, text
    6d64b09aedb4a36a719c4355629aaee0004fb134 Wed Aug 24 11:18:21 2022 -0700
    documenting the tbNoGenome option refs #29729
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html
  • lines changed 1, context: html, text, full: html, text
    6d64b09aedb4a36a719c4355629aaee0004fb134 Wed Aug 24 11:18:21 2022 -0700
    documenting the tbNoGenome option refs #29729
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 13, context: html, text, full: html, text
    6d64b09aedb4a36a719c4355629aaee0004fb134 Wed Aug 24 11:18:21 2022 -0700
    documenting the tbNoGenome option refs #29729
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 39, context: html, text, full: html, text
    2731937b048d40737f10ece92ceff7bd5251d5a9 Mon Aug 22 16:44:12 2022 -0700
    Updating news for dbSNP build 155 tracks, refs #27751
• src/hg/htdocs/goldenPath/trackDescriptions/bigRmskTrackDesc.html
  • lines changed 208, context: html, text, full: html, text
    a6b50639f42d157408a1dc49512b77546b58afac Thu Aug 25 14:18:37 2022 -0700
    Moving the track description page to a new directory for tidyness, refs #29356
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    2731937b048d40737f10ece92ceff7bd5251d5a9 Mon Aug 22 16:44:12 2022 -0700
    Updating news for dbSNP build 155 tracks, refs #27751
• src/hg/htdocs/staff.html
  • lines changed 2, context: html, text, full: html, text
    10a92c1e45dce9f691c2bcaa1e145ef1f024eb2d Tue Aug 23 14:47:59 2022 -0700
    Adding the widget to staff page since it comes up when searching UCSC Genome Browser email on google. No RM.
• src/hg/inc/trackHub.h
  • lines changed 3, context: html, text, full: html, text
    afafa0301ea4b14fbe1fbd5aa379c5351ecd640d Tue Aug 2 19:41:44 2022 -0700
    Add support for non-wuhCor1 genomes (e.g. monkeypox GenArk hub). * Search in hgPhyloPlaceData for config.ra files, taking assembly name (minus hub prefix) from directory name. * Add a menu input to the main page for switching between supported genomes if there are more than one. * Replace hardcoded values or global vars with dnaSeq attributes, assembly metadata queries or new config.ra settings. * Separate out SARS-CoV-2-specific help text like GISAID/CNCB descriptions. * Support metadata columns for GenBank-specific stuff & Nextstrain lineages (for MPXV). * also a little refactoring in runUsher in preparation for supporting usher server mode: parse new placement info file so we don't have to parse that data form usher stderr output. TODO: update Nextstrain/Auspice JSON output to use appropriate metadata columns and support monkeypox genes.
• src/hg/inc/versionInfo.h
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    03120dc602a76d48ada675d28511ec53a1ecb756 Mon Aug 29 10:10:23 2022 -0700
    New version number v436
• src/hg/lib/hgncBig62.as
  • lines changed 1, context: html, text, full: html, text
    6a81b996d2ba76182a6db75f84b02f346a6204e8 Mon Aug 22 17:08:59 2022 -0700
    change name so cron utilities don't complain
• src/hg/lib/tests/expected/hgvs/validTerms.txt
  • lines changed 1, context: html, text, full: html, text
    fec32cc187d7b42cbac7ee36fef68fa6a150fce8 Wed Aug 24 14:39:51 2022 -0700
    Adding additional HGVS validTerms.txt line of output for new RefSeq transcript.
• src/hg/makeDb/doc/asmHubs/lastzRuns.txt
  • lines changed 84, context: html, text, full: html, text
    fcff537626b716dd2db572b94991b71e7040d426 Tue Aug 23 14:33:05 2022 -0700
    lastz chain net to Asiatic elephant GCF_024166365.1 per user request refs #29905
• src/hg/makeDb/doc/bacteriaAsmHub/bacteria.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    c850f4d308195cb4f8a8e7c9c3c7f2eb5199f382 Tue Aug 23 20:05:03 2022 -0700
    per user request adding GCF_002101785.1_ASM210178v1 Mycobacterium palustre refs #29545
• src/hg/makeDb/doc/hg38/multiz470way.txt
  • lines changed 380, context: html, text, full: html, text
    bf1751d6241da4428178365599c31ce7e876592a Fri Aug 26 10:40:37 2022 -0700
    done with frames construction refs #29898
• src/hg/makeDb/trackDb/human/chainNetPlacental.ra
  • lines changed 26, context: html, text, full: html, text
    3148a2ad3b931f8f9b8412b698ee20a48dd4c391 Tue Aug 23 14:10:38 2022 -0700
    adding lastz/chain/net Asiatic elephant GCF_024166365.1 to hg38 per user request refs #29905
• src/hg/makeDb/trackDb/human/hg19/genotypeArrays.html
  • lines changed 21, context: html, text, full: html, text
    d5aac703468278e28c47cb2c4a30719d8d85b4bc Thu Aug 25 15:34:01 2022 -0700
    Adding a Data Access section and a hyperlink to the description page for hg19, refs #29309
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 5, context: html, text, full: html, text
    032d0580bf423295d14153703b029f1c52c57651 Fri Aug 26 13:46:07 2022 -0700
    Adding priority settings and updating pennantIcons, refs #29309 #29492
• src/hg/makeDb/trackDb/human/hg38/cons470way.html
  • lines changed 3600, context: html, text, full: html, text
    2bb832c4a2fbfec5651fa178a169b1199cafb1b0 Mon Aug 22 16:19:53 2022 -0700
    initial version of a table listing everything refs #29898
  • lines changed 1880, context: html, text, full: html, text
    1c83031fe5697cd4c3108cc0f652f6e576890660 Mon Aug 22 16:41:03 2022 -0700
    improving the table display and refereces refs #29898
  • lines changed 92, context: html, text, full: html, text
    67da9f29d4b081b49d838a39a682fefbcb4063fd Thu Aug 25 15:07:38 2022 -0700
    cleaning up the documentation to match this track refs #29898
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    0813750f49dca93bbbf1166426f948b4c088853f Fri Aug 26 11:40:22 2022 -0700
    better table order by clade and now with DNA zoo links refs #29898
• src/hg/makeDb/trackDb/human/hg38/genotypeArrays.html
  • lines changed 2, context: html, text, full: html, text
    9b5a8fa766c7dece7b119d39ab9c75b2280797bc Thu Aug 25 15:41:10 2022 -0700
    Minor edit and fixing the downloads site link for the hg38 description page, refs #29309
• src/hg/makeDb/trackDb/human/hg38/knownGene.ra
  • lines changed 1, context: html, text, full: html, text
    940598740bcd29eb7c1dc8e5de037b8ffce92eea Wed Aug 24 16:07:08 2022 -0700
    add extra arguments to knowGene type to get hgTables to offer mRNA sequence and protein sequence
• src/hg/makeDb/trackDb/human/hg38/trackDb.241way.ra
  • lines changed 1, context: html, text, full: html, text
    5d340f2b9087dd0506f9c8eee44069560958511f Tue Aug 23 18:32:32 2022 -0700
    the cactus241way needed a summary maf file refs #29859
• src/hg/makeDb/trackDb/human/hg38/trackDb.470way.ra
  • lines changed 76, context: html, text, full: html, text
    9fa0ffc55381e5c333341f8ce7faf3818f62b1bf Mon Aug 22 13:13:59 2022 -0700
    working on getting the 470way track showing refs #29898
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    c99321c88364e2260c65b45f783be4d85fc7e4c1 Mon Aug 22 14:14:50 2022 -0700
    beginning to show 470way track refs #29898
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    cd5445acd87062d87ac842ef7c0304a7e1b10ff0 Mon Aug 22 20:29:08 2022 -0700
    now with speciesLabels for common names refs #29898
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    6907673bc86172b4135b8d3cfabf42c9fe0d7283 Tue Aug 23 14:11:29 2022 -0700
    moved the bigMaf file to hgdownload refs #29898
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    47c7cfedbc9527543b09f70125831deec08def62 Thu Aug 25 14:04:31 2022 -0700
    fix sGroup lists to include everything and in order by percent matching NTs to reference hg38 refs #29898
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    8f969d54541b267aa3dc20dedeb5431866ec3433 Fri Aug 26 11:41:45 2022 -0700
    adding frames an iRows to the 470-way refs #29898
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
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    064ae6d621e4823cd0ae6f2dd9a620df34d6b9ca Mon Aug 22 14:25:25 2022 -0700
    beginning to show 470way track refs #29898
  • lines changed 1, context: html, text, full: html, text
    5d340f2b9087dd0506f9c8eee44069560958511f Tue Aug 23 18:32:32 2022 -0700
    the cactus241way needed a summary maf file refs #29859
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    032d0580bf423295d14153703b029f1c52c57651 Fri Aug 26 13:46:07 2022 -0700
    Adding priority settings and updating pennantIcons, refs #29309 #29492
  • lines changed 1, context: html, text, full: html, text
    17c777a5dd54e65d04e3abb852e0c4ee8aa652da Fri Aug 26 14:44:53 2022 -0700
    Removing the score filter due to scores being 0 in hg38, refs #29492
• src/hg/makeDb/trackDb/human/trackDb.ra
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    6f40c544e077ac2a21a887075ed2b109e3a09746 Mon Aug 22 14:15:38 2022 -0700
    Updating the dbSNP 155 priority and updating dbSNP 153 visibility, refs #27751
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    e7df267b56264aa28ff7da011e77f79dd99350d3 Fri Aug 26 13:09:55 2022 -0700
    reduce label options and add mouseOver
• src/hg/makeDb/trackDb/tagTypes.tab
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    c99321c88364e2260c65b45f783be4d85fc7e4c1 Mon Aug 22 14:14:50 2022 -0700
    beginning to show 470way track refs #29898
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    8f969d54541b267aa3dc20dedeb5431866ec3433 Fri Aug 26 11:41:45 2022 -0700
    adding frames an iRows to the 470-way refs #29898
• src/hg/makeDb/trackDb/trackDb.chainNet.asmHub.ra
  • lines changed 119, context: html, text, full: html, text
    3148a2ad3b931f8f9b8412b698ee20a48dd4c391 Tue Aug 23 14:10:38 2022 -0700
    adding lastz/chain/net Asiatic elephant GCF_024166365.1 to hg38 per user request refs #29905
• src/hg/utils/hubClone/hubClone.c
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    4528d923d5f2496c93fcd8c53f9134912448bd42 Thu Aug 25 14:21:02 2022 -0700
    Support multiple include files in a trackDb file.
• src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv
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    7bf716f89e4ee2e32bc34e5c0e196d3363b35f69 Fri Jul 1 14:57:42 2022 -0700
    Added new lineages BC.2, BG.3-4, BA.2.74-75, BA.4.1.3-4, BA.4.2-5, BA.5.1.1-3, BF.1.1, BF.2-5, BA.5.2.2-4, BE.1.1, BE.2-3, BA.5.3.3-4, BA.5.6. Also tweaked miscBA1BA2Post17k back a node to keep XM from including things it shouldn't, and added a couple proposed lineages.
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    e3539f8a3105f813200f7f21928d9813a3f81b24 Tue Jul 5 11:53:29 2022 -0700
    Corrected path to BA.2.43. Added BA.2.76, BA.2.77, BA.4.6, BA.5.1.4. Removed proposed570 -- it was BC.2.
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    fb7e6a7f3484531a39976a131c38662623adf824 Wed Jul 6 14:46:59 2022 -0700
    Corrected path for BA.2.53.
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    be3ecf652180e0b491d02e4dc4fd1a8309a829b6 Wed Jul 6 18:13:18 2022 -0700
    Yikes, never added AY.5.7 (missing from Chris's spreadsheet but in pango-designation/lineages.csv since April 1; p-d#387). Also added B.1.1.28 since it wasn't annotated for some reason.
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    8f10afb2f9cfde2ddfa5a1982fe4f7de0ce720de Mon Aug 1 14:15:19 2022 -0700
    Added BA.2.3.19, BA.2.9.5, BG.5, BA.2.13.1, BA.2.36.1 (may change to BA.2.X), BA.2.38.1-2, BA.2.78-81, BA.2.79.1, BA.4.7, BA.5.1.5-8, BF.6-12, BA.5.2.5, BA.5.6.1, BA.5.7-9, recombinants XAJ-XAP -- pango-designation v1.12 and v1.13. Also added proposed885; removed proposed757, 759, 789 since they were designated. Removed BA.2.3.9_rev241 because I started masking 241 in BA.2. Changed BA.2.13 path: removed G24368N, not needed. Changed BA.3.1 path after fixing tree: unmasked C28311T, removed C27874N and A28461N. Added BA.3.1_revs to catch split branch with reversions. Changed BA.4.3. path: removed C203T because it is now masked in BA.2 (would be pango-masked anyway). Changed BA.5.1: added T27438C to BA.5.1 path, added BA.5.1_no27438 split branch. Changed BA.5.2.1: unmask A28330G. Added BA.5.2_no28330 split branch.
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    1909321bc89456da06cb8793a9dbe7541563420e Fri Aug 19 12:10:42 2022 -0700
    BA.2.36.1 renamed to BA.2.82. Added BA.2.9.6, BA.2.10.4, BA.2.38.3, BA.2.75.1-2, BA.2.76.1-2, BG.6, BH.1, BJ.1, BA.5.1.9-11, BA.5.5.1, BA.5.6.2, BA.5.10, BE.1.2, BF.13, BF.14, BK.1. Renamed proposed 798 to XAQ, addded XAR. -- pango-designation v1.14 Also added proposed882, proposed911, BA.5.2.1_no28330; tweaked BA.5.2_no28330 to be more explicit about 28330.
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    7e4f3ed58a9c5632b6e65a8eb13447a84b9b5b5f Tue Aug 23 10:50:51 2022 -0700
    Added label BA.2_21765_no22792 for persistent problematic branch that resulted in misdesignation of BA.2.36.1 (corrected to BA.2.82). Tweaked path of BA.2.75.2 to handle a couple sites with reversions, ugh.
• src/hg/utils/vcfToHgvs/tests/expected/stopLoss.tab
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    0b8e4c09fe3a2cb3ab8a05807cebba50cbe1e94c Wed Aug 24 16:59:30 2022 -0700
    vcfToHgvs: Exclude XM_ and XR_ transcripts -- they're not 'real' HGVS and also very unstable from one version to the next.
• src/hg/utils/vcfToHgvs/vcfToHgvs.c
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    0b8e4c09fe3a2cb3ab8a05807cebba50cbe1e94c Wed Aug 24 16:59:30 2022 -0700
    vcfToHgvs: Exclude XM_ and XR_ transcripts -- they're not 'real' HGVS and also very unstable from one version to the next.
• src/inc/srcVersion.h
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    03120dc602a76d48ada675d28511ec53a1ecb756 Mon Aug 29 10:10:23 2022 -0700
    New version number v436
• src/lib/vcf.c
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    d517d7563a1e14f913bf2d21893daada5e35134d Wed Aug 24 14:15:31 2022 -0700
    Use chopTabs not chopLine for VCF header parsing. refs #29923
• src/utils/qa/weeklybld/buildEnv.csh
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    5a112e2d1730041b47cf56a3311792bf7dfe22b5 Mon Aug 29 10:08:33 2022 -0700
    v436 final build, refs #29878

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