All File Changes

v418_preview to v418_preview2 (2021-07-12 to 2021-07-19) v418

• src/hg/hgPhyloPlace/phyloPlace.c
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    f97456f7cdd92737b1c2ac14a0147b0c6a30c9e1 Mon Jul 12 16:30:53 2021 -0700
    Update single-subtree button label to indicate it's a subsampled global tree.
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    3fd9e9e8d0a977ee255486e60c785aef5689cc39 Tue Jul 13 09:42:47 2021 -0700
    Add summary table for results from pasted/uploaded IDs, to show lineages & subtree numbers, requested by Russ.
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    0e66591e44d669ef83fa016069b1ceb283c01800 Thu Jul 15 12:40:43 2021 -0700
    Support more flexible ID search: accessions without dot-versions and isolate names. When loading FASTA, detect sequence names that are numeric or already in the tree and add a prefix to prevent usher from rejecting the sequences.
• src/hg/hgPhyloPlace/phyloPlace.h
  • lines changed 1, context: html, text, full: html, text
    0e66591e44d669ef83fa016069b1ceb283c01800 Thu Jul 15 12:40:43 2021 -0700
    Support more flexible ID search: accessions without dot-versions and isolate names. When loading FASTA, detect sequence names that are numeric or already in the tree and add a prefix to prevent usher from rejecting the sequences.
• src/hg/hgPhyloPlace/runUsher.c
  • lines changed 6, context: html, text, full: html, text
    82fa23eab37e677681978a8f4ffed9be2c553f8c Thu Jul 15 12:35:19 2021 -0700
    Detect missing single-subtree output (e.g. when usher rejects all sequences as already in the tree) and provide an error message with info for us to debug instead of crashing.
• src/hg/hgPhyloPlace/treeToAuspiceJson.c
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    49566dc7263cab04bca529355999e4a4e7acfa78 Tue Jul 6 10:19:05 2021 -0700
    Update to latest Nextstrain clade coloring.
• src/hg/hgPhyloPlace/vcfFromFasta.c
  • lines changed 19, context: html, text, full: html, text
    0e66591e44d669ef83fa016069b1ceb283c01800 Thu Jul 15 12:40:43 2021 -0700
    Support more flexible ID search: accessions without dot-versions and isolate names. When loading FASTA, detect sequence names that are numeric or already in the tree and add a prefix to prevent usher from rejecting the sequences.
• src/hg/hgTracks/barChartTrack.c
  • lines changed 7, context: html, text, full: html, text
    09a8f6e6a19a7dcb4adb2f51639f8e6420694f89 Thu Jul 15 20:51:22 2021 -0700
    Fixed multi-region minor problem in gtex and barchart handling the tracks ss list. fixes #27855
• src/hg/hgTracks/gtexTracks.c
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    09a8f6e6a19a7dcb4adb2f51639f8e6420694f89 Thu Jul 15 20:51:22 2021 -0700
    Fixed multi-region minor problem in gtex and barchart handling the tracks ss list. fixes #27855
• src/hg/htdocs/FAQ/FAQgenes.html
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    580478f2ae0ce19b376e7285f4d6dd5638a37e41 Tue Jul 13 10:47:31 2021 -0700
    minor language adjustments. Refs #27807
• src/hg/htdocs/goldenPath/help/gbib.html
  • lines changed 19, context: html, text, full: html, text
    87510802d69dfeccd7ae00b02cf66fe8074f0a70 Mon Jul 19 03:59:13 2021 -0700
    documenting local-only assemblies in gbib, refs #27865
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 1, context: html, text, full: html, text
    6203ae4c316893f1f8e88e8bba0ed54e704350f9 Sun Jul 18 22:04:50 2021 -0700
    Adding the word within for Code Review refs #27840
• src/hg/htdocs/goldenPath/help/wiggle.html
  • lines changed 1, context: html, text, full: html, text
    6203ae4c316893f1f8e88e8bba0ed54e704350f9 Sun Jul 18 22:04:50 2021 -0700
    Adding the word within for Code Review refs #27840
• src/hg/htdocs/license/index.html
  • lines changed 1, context: html, text, full: html, text
    c7b5b1950fe8be7b567005338703e633de5e8b1d Mon Jul 12 13:07:24 2021 -0700
    changed some wording to avoid giving impression that using liftOver and blat was ok without permission in all circumstances
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    981f85e525ffe8f34b4a96d84000cab9d158de3b Tue Jul 13 10:12:50 2021 -0700
    added a little more clarification
• src/hg/js/utils.js
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    5e3715fbe14fc37ab8ffe111c45282f10f565320 Thu Jul 15 06:05:05 2021 -0700
    changes after code review, refs #27846
• src/hg/lib/hgHgvs.c
  • lines changed 2, context: html, text, full: html, text
    9cc55e7992e4a98ef3a3336e12e78a583a7a56a1 Mon Jul 12 17:07:48 2021 -0700
    Allow lower case first letter of 3-letter amino acid code in psueudo hgvs gene searches, refs #15554
• src/hg/lib/jksql.c
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    b79f8a6f8375d675a5c7bf3b81ea7f9a9d57dad5 Mon Jul 19 03:42:14 2021 -0700
    adding local-only assemblies to GBIB/GBIC, refs #27865
• src/hg/lib/trackDbCustom.c
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    a434e74c8fe5c826a4da34050ec6b16589e0fd88 Tue Jul 13 14:56:14 2021 -0700
    Remove attempt at fixing include bigDataUrl expansion, easier to fix the data than the code for now, refs #27767
• src/hg/makeDb/genbank/etc/hgwbeta.dbs
  • lines changed 2, context: html, text, full: html, text
    b35ca4cf4b0cdb25afd1b9967dd0510085033668 Wed Jul 14 11:08:44 2021 -0700
    Turning on GenBank updates for new assembly, refs #24693
• src/hg/makeDb/hgTrackDb/hgTrackDb.c
  • lines changed 4, context: html, text, full: html, text
    4e4b1ed150e57fe0149c5e99a7d0eec0e2cddfcf Tue Jul 13 12:27:53 2021 -0700
    make sure that the settings in the cartVersion pseudo-track have the correct format (every variable must have a value)
• src/hg/makeDb/trackDb/human/hg19/refSeqComposite.html
  • lines changed 3, context: html, text, full: html, text
    428fe9cc142fcc83868271c988fdfa10f64a279d Tue Jul 13 09:12:38 2021 -0700
    Adding previous versions archives link to the Data Access section, refs #27552
• src/hg/makeDb/trackDb/human/hg38/bloodHao.ra
  • lines changed 6, context: html, text, full: html, text
    de7238c74b19ebf88401b16ac8b79dd29f6bbff4 Mon Jul 19 08:12:28 2021 -0700
    Added html setting to child stanzas. refs #26965
• src/hg/makeDb/trackDb/human/hg38/colonWang.html
  • lines changed 73, context: html, text, full: html, text
    4ac840ade74708e6c2b45f516ee0acf96bfe9bca Mon Jul 19 08:04:59 2021 -0700
    Added/deleted sentences, spruced up sections. refs #26969
• src/hg/makeDb/trackDb/human/hg38/colonWang.ra
  • lines changed 2, context: html, text, full: html, text
    e994d5fe058dae2b6aa1c2960a12b3126b7cf2ed Mon Jul 19 08:01:21 2021 -0700
    Added html setting to child stanzas. refs #26969
• src/hg/makeDb/trackDb/human/hg38/cortexVelmeshev.html
  • lines changed 81, context: html, text, full: html, text
    30e84e4bda6a7be6050bf9f24e2e0974af10bd01 Mon Jul 19 08:40:47 2021 -0700
    New details page.
• src/hg/makeDb/trackDb/human/hg38/cortexVelmeshev.ra
  • lines changed 5, context: html, text, full: html, text
    92e313ee39ceada0e1244e8065ae7e25064974d5 Mon Jul 19 08:13:17 2021 -0700
    Added html setting to child stanzas. refs #26973
• src/hg/makeDb/trackDb/human/hg38/fetalGeneAtlas.html
  • lines changed 47, context: html, text, full: html, text
    317c2212f23bb6d9172859312cfbab457a1e9046 Mon Jul 19 08:14:12 2021 -0700
    Added/deleted sentences, spruced up sections.
• src/hg/makeDb/trackDb/human/hg38/gnomad.alpha.ra
  • lines changed 4, context: html, text, full: html, text
    504acfd1a5318573c98418a3d5ebc56d93242a5d Mon Jul 12 14:35:46 2021 -0700
    Adding v3.1.1 specific information to gnomad description page, refs #27256
• src/hg/makeDb/trackDb/human/hg38/gnomadV3_1_1.html
  • lines changed 224, context: html, text, full: html, text
    504acfd1a5318573c98418a3d5ebc56d93242a5d Mon Jul 12 14:35:46 2021 -0700
    Adding v3.1.1 specific information to gnomad description page, refs #27256
• src/hg/makeDb/trackDb/human/hg38/heartCellAtlas.ra
  • lines changed 9, context: html, text, full: html, text
    c7a9d8667ccdcee98477544ce0bb412acaf69723 Mon Jul 19 08:15:55 2021 -0700
    Added html setting to child stanzas. refs #27727
• src/hg/makeDb/trackDb/human/hg38/ileumWang.html
  • lines changed 77, context: html, text, full: html, text
    4ac840ade74708e6c2b45f516ee0acf96bfe9bca Mon Jul 19 08:04:59 2021 -0700
    Added/deleted sentences, spruced up sections. refs #26969
• src/hg/makeDb/trackDb/human/hg38/ileumWang.ra
  • lines changed 2, context: html, text, full: html, text
    e994d5fe058dae2b6aa1c2960a12b3126b7cf2ed Mon Jul 19 08:01:21 2021 -0700
    Added html setting to child stanzas. refs #26969
• src/hg/makeDb/trackDb/human/hg38/kidneyStewart.ra
  • lines changed 6, context: html, text, full: html, text
    5d9de04583fe0b95cadc252c4f4060b679e39f8b Mon Jul 19 08:14:40 2021 -0700
    Added html setting to child stanzas. refs #27724
• src/hg/makeDb/trackDb/human/hg38/liverMacParland.html
  • lines changed 9, context: html, text, full: html, text
    5ecc719925bd33e25b5575c321ff64c882ac9f0b Mon Jul 19 08:15:14 2021 -0700
    Added/deleted sentences, spruced up sections.
• src/hg/makeDb/trackDb/human/hg38/muscleDeMicheli.html
  • lines changed 1, context: html, text, full: html, text
    755ca64452893270dd80da412f242f37c171d257 Fri Jun 11 16:17:36 2021 -0700
    Added back in header for display conventions. refs #26968
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    f3b7c065cbca777bc744fba24a3355ee6069af11 Mon Jul 19 08:17:04 2021 -0700
    Added/deleted sentences, spruced up sections.
• src/hg/makeDb/trackDb/human/hg38/pancreasBaron.ra
  • lines changed 4, context: html, text, full: html, text
    e3b67292fc1f410e000ba4ceebb80ccd9c271616 Mon Jul 19 08:18:05 2021 -0700
    Added html setting to child stanzas. refs #26966
• src/hg/makeDb/trackDb/human/hg38/placentaVentoTormo.ra
  • lines changed 9, context: html, text, full: html, text
    7c3e1bd75b261a590b851022cd965660a5c97b9c Mon Jul 19 08:18:44 2021 -0700
    Added html setting to child stanzas. refs #26967
• src/hg/makeDb/trackDb/human/hg38/rectumWang.html
  • lines changed 86, context: html, text, full: html, text
    4ac840ade74708e6c2b45f516ee0acf96bfe9bca Mon Jul 19 08:04:59 2021 -0700
    Added/deleted sentences, spruced up sections. refs #26969
• src/hg/makeDb/trackDb/human/hg38/rectumWang.ra
  • lines changed 2, context: html, text, full: html, text
    c5db469ab48cd0427b1654d11eb2785100fc9a12 Mon Jul 19 08:19:24 2021 -0700
    Added html setting to child stanzas. refs #26969
• src/hg/makeDb/trackDb/human/hg38/skinSoleBoldo.ra
  • lines changed 4, context: html, text, full: html, text
    82f136ff04e7d5d7c7373fc55bd63c4685b915c1 Mon Jul 19 08:27:20 2021 -0700
    Added html setting to child stanzas. refs #27726
• src/hg/makeDb/trackDb/human/trackDb.gtex.ra
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    bd9666a20cb204dfb92ea11d885d441521d46a7f Tue Jul 13 15:40:52 2021 -0700
    Restore right click config of gtexGeneV8 track, refs #27853
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.vertebrateChainNet.ra
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    4f378d9483565d6eb4e9f37b580532a18626a657 Wed Jul 14 17:54:40 2021 -0700
    Updating mm10 vertebrateChainNet track for xenTro10, refs #24693
• src/hg/makeDb/trackDb/refSeqComposite.html
  • lines changed 3, context: html, text, full: html, text
    428fe9cc142fcc83868271c988fdfa10f64a279d Tue Jul 13 09:12:38 2021 -0700
    Adding previous versions archives link to the Data Access section, refs #27552
• src/hg/makeDb/trackDb/trackDb.ra
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    cbefc3f711ab0aa3465b9cf4633266640f9cb050 Mon Jul 12 17:20:33 2021 -0700
    Updating uniprot filters refs #27756
• src/hg/utils/hubCrawl/hubCrawl.c
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    5f5b68942b3208f40494af94049234fbbb6f73b6 Tue Jul 13 09:08:17 2021 -0700
    Add hubCrawl to list of utilities managed by the build, so it stays up to date for qateam to use it every week.
• src/hg/utils/makefile
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    5f5b68942b3208f40494af94049234fbbb6f73b6 Tue Jul 13 09:08:17 2021 -0700
    Add hubCrawl to list of utilities managed by the build, so it stays up to date for qateam to use it every week.
• src/hg/utils/otto/sarscov2phylo/getNcbi.sh
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    ed0c81dda84b8a3c690fba2c78e2662c5cd6940f Mon Jul 12 16:32:14 2021 -0700
    Exclude NCBI metadata for sequences that are not (yet) in fasta.
• src/hg/utils/otto/sarscov2phylo/gisaidFromChunks.sh
  • lines changed 15, context: html, text, full: html, text
    fd68d9c62b0b68f005804457fd5934d0c10a70c8 Mon Jul 12 16:33:09 2021 -0700
    Add in country from GISAID sequence names (retaining spaces) to metadata.
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    77d911dafe3d0fefac4aa3f9e3b5982df129815f Tue Jul 13 09:43:39 2021 -0700
    join -a doesn't include placeholder columns when there is no matching line, so make output columns explicit; otherwise country can end up in clade column.
• src/hg/utils/otto/sarscov2phylo/gisaidNameToCountry.pl
  • lines changed 82, context: html, text, full: html, text
    2463467c57af3dff3d900a94ebed353bb5a749bd Mon Jul 12 16:33:25 2021 -0700
    Get GISAID country name from sequence names, correcting a few known typos and substituting Chinese cities/regions to China.
• src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh
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    ab3504a9bc0e6077a70cdcefc29264833ced8126 Mon Jul 12 16:36:23 2021 -0700
    Add in sub-UK country to match COG-UK sequence names; correct outdated lineage names in lineages.metadata.csv; make alternate lineageToName file, still need to do comparison of using it.
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    2ba814d9a2b0df7bdc2cce0bb3e52464288a61bc Tue Jul 13 09:44:37 2021 -0700
    no need to run matUtils extract -u twice.
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    873bc700cc4fbedfa5164ba912f7e69adf80b127 Thu Jul 15 12:46:17 2021 -0700
    Use matUtils annotate's new -P/--clade-paths option to assign clades using curated path files instead of -c/--clade-names. It is much faster and allows manual correction of not-quite-right paths inferred by -c. It will also require manual updates (but so did ../lineageToName.newLineages) and will fail if the tree structure changes significantly.
• src/lib/udc.c
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    82d5a7df56ab88caf3b48255b242c5b3211cc6a6 Fri Jul 16 16:47:01 2021 -0700
    Fixing UDC to use TMPDIR when defined instead of /tmp, no ticket
• src/product/ex.hg.conf
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    87510802d69dfeccd7ae00b02cf66fe8074f0a70 Mon Jul 19 03:59:13 2021 -0700
    documenting local-only assemblies in gbib, refs #27865
• src/product/installer/makefile
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    b3edd2fa97ed4d4d58af0522af8551b08e6fa6e0 Wed Jul 14 09:51:44 2021 -0700
    Adding target to gbic makefile to install to a default location so we can push the gbic script with every release
• src/utils/qa/assemblyStatsCron.py
  • lines changed 224, context: html, text, full: html, text
    3127589facd0998822593cc31527a70233c67164 Wed Jul 14 16:10:04 2021 -0700
    Moving all qateam crons to the kent src tree qa utils. They are now all called from the bin. No RM.
• src/utils/qa/assemblyStatsCronSaveStats.py
  • lines changed 214, context: html, text, full: html, text
    3127589facd0998822593cc31527a70233c67164 Wed Jul 14 16:10:04 2021 -0700
    Moving all qateam crons to the kent src tree qa utils. They are now all called from the bin. No RM.
• src/utils/qa/checkHTTPS
  • lines changed 48, context: html, text, full: html, text
    3127589facd0998822593cc31527a70233c67164 Wed Jul 14 16:10:04 2021 -0700
    Moving all qateam crons to the kent src tree qa utils. They are now all called from the bin. No RM.
• src/utils/qa/checkSyncAndMetaDataAll.py
  • lines changed 95, context: html, text, full: html, text
    3127589facd0998822593cc31527a70233c67164 Wed Jul 14 16:10:04 2021 -0700
    Moving all qateam crons to the kent src tree qa utils. They are now all called from the bin. No RM.
• src/utils/qa/hubSearchUpdate
  • lines changed 11, context: html, text, full: html, text
    3127589facd0998822593cc31527a70233c67164 Wed Jul 14 16:10:04 2021 -0700
    Moving all qateam crons to the kent src tree qa utils. They are now all called from the bin. No RM.
• src/utils/qa/makefile
  • lines changed 5, context: html, text, full: html, text
    3127589facd0998822593cc31527a70233c67164 Wed Jul 14 16:10:04 2021 -0700
    Moving all qateam crons to the kent src tree qa utils. They are now all called from the bin. No RM.
• src/utils/qa/weeklybld/buildEnv.csh
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    a7fbad70d2744eef8a7e98a88bffc6385c46a20e Mon Jul 19 10:06:56 2021 -0700
    v418 preview2, refs #27854
• src/utils/qa/weeklybld/doNewReview.csh
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    6d709bbb8e49d60bfb94a7f7ce945d238f70ab4a Mon Jul 12 10:35:11 2021 -0700
    Swapping Kate for Clay in git reports email, refs Ann email

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• files changed: 66