All File Changes

v423_preview2 to v423_base (2021-11-01 to 2021-11-09) v423

• confs/hgwdev.hg.conf
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    2abdb9fc1bd7a8c28a51dd11e6959983b9730981 Sun Nov 7 01:11:43 2021 -0700
    Installing updated hg.conf files from UCSC servers
• src/browserbox/home/browser/downloadTools
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    fd1f371bb63ecef5e29dd770f52043f6eec3d719 Mon Nov 8 06:15:14 2021 -0800
    fixing gbibAddTools on GBIB to make blat-related tools available, refs #28423
• src/browserbox/home/browser/gbibAddTools
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    a9aec4b359d86fc7d9662b8bdcb7e61828093e9b Tue Nov 2 06:18:18 2021 -0700
    moving BLAT tools into main bin directory in GBIB and GBIC, refs #28435
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    fd1f371bb63ecef5e29dd770f52043f6eec3d719 Mon Nov 8 06:15:14 2021 -0800
    fixing gbibAddTools on GBIB to make blat-related tools available, refs #28423
• src/hg/hgHubConnect/hgHubConnect.c
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    534cd7320709280f4a579731e2638d039a6cffd9 Tue Nov 2 16:00:03 2021 -0700
    Joining sentence and paragraph related to linking as feedback from Dan, refs #28324
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    0df2065b4bf9f313234bd65b1fd23e53f79be4c0 Wed Nov 3 08:36:06 2021 -0700
    fixing OFF/OFF bug and revising wording a little for hgHubConnect, refs #28324
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    ab47b1a355db4af04610515c1dab0371108f4fc1 Fri Nov 5 17:31:10 2021 -0700
    fixing ON/OFF thing again, wording and make window closable, refs #28324
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    8153d228aaa147e117f599f7bf96702515abee46 Tue Nov 9 05:41:55 2021 -0800
    fixing stray measureTiming messages in hgHubConnect, refs #28324
• src/hg/hgc/barChartClick.c
  • lines changed 33, context: html, text, full: html, text
    8e5ea49d44db7a5d17dd310d1cc1a73d3140ed8a Wed Nov 3 11:28:21 2021 -0700
    Get barChartCategoryUrl working on hgc pages, refs #28442
• src/hg/htdocs/goldenPath/help/hgTablesHelp.html
  • lines changed 59, context: html, text, full: html, text
    7f7928d7115d32d6018254b9f8f241cc6e6c7716 Tue Nov 2 16:03:21 2021 -0700
    Adding doc about Batch Queries using positions refs #28436
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
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    f0e3124182a84a61e850b3db8954dc120b04c82d Fri Nov 5 20:24:10 2021 -0700
    added link to Definition Document at top of page to make it more obvious
• src/hg/htdocs/goldenPath/pubs.html
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    cbe663c386edabed801fcf0f7eac97a21b9383c9 Mon Nov 1 15:11:29 2021 -0700
    Adding 2022 NAR paper, ahead of print
• src/hg/inc/barChartCategory.h
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    8e5ea49d44db7a5d17dd310d1cc1a73d3140ed8a Wed Nov 3 11:28:21 2021 -0700
    Get barChartCategoryUrl working on hgc pages, refs #28442
• src/hg/inc/versionInfo.h
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    db9dbdd0aaa3a906a54b9a0a8ae0a516efdcfdbc Tue Nov 9 08:30:47 2021 -0800
    New version number v423
• src/hg/lib/barChartCategory.c
  • lines changed 12, context: html, text, full: html, text
    8e5ea49d44db7a5d17dd310d1cc1a73d3140ed8a Wed Nov 3 11:28:21 2021 -0700
    Get barChartCategoryUrl working on hgc pages, refs #28442
• src/hg/lib/customFactory.c
  • lines changed 6, context: html, text, full: html, text
    26e50fc73b51156c02e07d431aca5f0c2621108b Wed Nov 3 13:48:27 2021 -0700
    Allow barChartCategoryUrl in custom tracks and track hubs instead of barChartBars, refs #28442
• src/hg/lib/makefile
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    8e5ea49d44db7a5d17dd310d1cc1a73d3140ed8a Wed Nov 3 11:28:21 2021 -0700
    Get barChartCategoryUrl working on hgc pages, refs #28442
• src/hg/lib/trackHub.c
  • lines changed 2, context: html, text, full: html, text
    26e50fc73b51156c02e07d431aca5f0c2621108b Wed Nov 3 13:48:27 2021 -0700
    Allow barChartCategoryUrl in custom tracks and track hubs instead of barChartBars, refs #28442
• src/hg/makeDb/doc/asmHubs/master.run.list
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    e6e7f4271023cbd1bf9521e1b9dd0548c65773aa Mon Nov 8 12:05:41 2021 -0800
    adding in 97 Lepidoptera assemblies for David Thybert alignment project no redmine
• src/hg/makeDb/doc/hg19.txt
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    f9c9ff4d1f24831e1957d6cbf4214072abfb4001 Tue Nov 2 11:07:02 2021 -0700
    staging jaspar 2022 track and mouse tracks refs #28322
• src/hg/makeDb/doc/hg38/jaspar.txt
  • lines changed 10, context: html, text, full: html, text
    f9c9ff4d1f24831e1957d6cbf4214072abfb4001 Tue Nov 2 11:07:02 2021 -0700
    staging jaspar 2022 track and mouse tracks refs #28322
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
  • lines changed 96, context: html, text, full: html, text
    47a79f098982f6f7b6511f1e2ea8435eb3b21778 Mon Nov 8 12:14:16 2021 -0800
    adding in 97 Lepidoptera assemblies for David Thybert alignment project no redmine
• src/hg/makeDb/doc/mm10.txt
  • lines changed 20, context: html, text, full: html, text
    f9c9ff4d1f24831e1957d6cbf4214072abfb4001 Tue Nov 2 11:07:02 2021 -0700
    staging jaspar 2022 track and mouse tracks refs #28322
• src/hg/makeDb/doc/mm39/jaspar.txt
  • lines changed 11, context: html, text, full: html, text
    f9c9ff4d1f24831e1957d6cbf4214072abfb4001 Tue Nov 2 11:07:02 2021 -0700
    staging jaspar 2022 track and mouse tracks refs #28322
• src/hg/makeDb/doc/wuhCor1/phylogenetics.txt
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    999310144add887891307673ea81cadc756fdac8 Tue Nov 2 13:08:38 2021 -0700
    Updated Problematic Sites track.
• src/hg/makeDb/trackDb/human/dbSnp153Composite.html
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    10a26eb6cecb17fd722e6f9bad1656329f733c28 Tue Nov 2 16:11:00 2021 -0700
    Adding note about defined regions refs#28436
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
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    df146a6c5a52e0fad4c93d9d3613ae36a8427c27 Tue Nov 2 07:14:39 2021 -0700
    improving docs for rmsk track refs #28410 on hg38 and tiny changes to liftover tracks, no redmine
• src/hg/makeDb/trackDb/human/hg38/defaultPriority.ra
  • lines changed 1, context: html, text, full: html, text
    df146a6c5a52e0fad4c93d9d3613ae36a8427c27 Tue Nov 2 07:14:39 2021 -0700
    improving docs for rmsk track refs #28410 on hg38 and tiny changes to liftover tracks, no redmine
• src/hg/makeDb/trackDb/human/hg38/liftOver.ra
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    df146a6c5a52e0fad4c93d9d3613ae36a8427c27 Tue Nov 2 07:14:39 2021 -0700
    improving docs for rmsk track refs #28410 on hg38 and tiny changes to liftover tracks, no redmine
• src/hg/makeDb/trackDb/human/hg38/liverMacParland.ra
  • lines changed 4, context: html, text, full: html, text
    e9b2523bf46514da918bf48d1c565bb723b86ee7 Tue Nov 2 11:53:29 2021 -0700
    Removing release tags refs #26970
• src/hg/makeDb/trackDb/human/hg38/rmsk.html
  • lines changed 123, context: html, text, full: html, text
    df146a6c5a52e0fad4c93d9d3613ae36a8427c27 Tue Nov 2 07:14:39 2021 -0700
    improving docs for rmsk track refs #28410 on hg38 and tiny changes to liftover tracks, no redmine
• src/hg/makeDb/trackDb/human/hg38/t2tChain.html
  • lines changed 15, context: html, text, full: html, text
    614acd9998d8bf93388baa79c1fcf68c897872bc Sun Nov 7 13:24:36 2021 -0800
    updated t2tChain doc
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    9f8ad4b0b4fe771c02fff97fbc27922664af8658 Mon Nov 8 05:58:45 2021 -0800
    removed metion of netClass from T2T page
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    42301e0e8aab86c86ed78d77a416e3ecd02f0f25 Mon Nov 8 06:14:09 2021 -0800
    updating t2t track docs a little, refs #28380
• src/hg/makeDb/trackDb/human/jaspar.html
  • lines changed 34, context: html, text, full: html, text
    f9c9ff4d1f24831e1957d6cbf4214072abfb4001 Tue Nov 2 11:07:02 2021 -0700
    staging jaspar 2022 track and mouse tracks refs #28322
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    19870454d7c3d8f29a5800477bcaa36babee5a98 Tue Nov 2 17:10:33 2021 -0700
    Finishing Development for jaspar update refs #28322
• src/hg/makeDb/trackDb/human/jaspar.ra
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    f9c9ff4d1f24831e1957d6cbf4214072abfb4001 Tue Nov 2 11:07:02 2021 -0700
    staging jaspar 2022 track and mouse tracks refs #28322
• src/hg/makeDb/trackDb/human/orphadata.html
  • lines changed 22, context: html, text, full: html, text
    95e81239e580138a18d7ffccce94bf8ba53e0c64 Thu Nov 4 11:28:23 2021 -0700
    Edits to orphanet before release refs #14319
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    95e81239e580138a18d7ffccce94bf8ba53e0c64 Thu Nov 4 11:28:23 2021 -0700
    Edits to orphanet before release refs #14319
• src/hg/makeDb/trackDb/mouse/jaspar.html
  • lines changed 224, context: html, text, full: html, text
    19870454d7c3d8f29a5800477bcaa36babee5a98 Tue Nov 2 17:10:33 2021 -0700
    Finishing Development for jaspar update refs #28322
• src/hg/makeDb/trackDb/mouse/jaspar.ra
  • lines changed 38, context: html, text, full: html, text
    f9c9ff4d1f24831e1957d6cbf4214072abfb4001 Tue Nov 2 11:07:02 2021 -0700
    staging jaspar 2022 track and mouse tracks refs #28322
• src/hg/makeDb/trackDb/mouse/trackDb.ra
  • lines changed 4, context: html, text, full: html, text
    f9c9ff4d1f24831e1957d6cbf4214072abfb4001 Tue Nov 2 11:07:02 2021 -0700
    staging jaspar 2022 track and mouse tracks refs #28322
• src/hg/makeDb/trackDb/trackDb.chainNet.asmHub.ra
  • lines changed 43, context: html, text, full: html, text
    7b52d31632f9b473eba9939d2d30ce703e401553 Fri Oct 29 15:58:44 2021 -0700
    lastz chainNet on GCF_002742125.1 Ramboullet sheep refs #28409
• src/hg/utils/automation/doWindowMasker.pl
  • lines changed 35, context: html, text, full: html, text
    bcf35aa04eb90031bdf817fec6e4262481e77fd8 Mon Nov 1 10:31:15 2021 -0700
    no need to run WM without the sdust option that other result is never used no redmin
• src/hg/utils/hubCheck/hubCheck.c
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    d1ae0e8ccdaca655a17c804ff1aac8b47ef59f31 Thu Nov 4 14:30:59 2021 -0700
    fixed spelling error
• src/hg/utils/hubCheck/tests/expected/supertrackChild.txt
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    d1ae0e8ccdaca655a17c804ff1aac8b47ef59f31 Thu Nov 4 14:30:59 2021 -0700
    fixed spelling error
• src/hg/utils/otto/dbVar/dbVarWrapper.sh
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    5bf9bb6115274226f4dd5795e56e2172e1c4869c Tue Nov 2 09:05:50 2021 -0700
    Changing recipient to ottomeister, no RM
• src/hg/utils/otto/grcIncident/grcUpdate.sh
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    509ca92e669051a902cfbd411962c2859cfe53c6 Wed Nov 3 10:36:51 2021 -0700
    Adding myself to sent mail. No RM
• src/hg/utils/otto/orphanet/orphadata.as
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    a905febc7c2e8c3d7fc32228620f3e728e4da97e Thu Nov 4 11:51:15 2021 -0700
    Changing autoSql description of orphanet track, refs #14319
• src/hg/utils/otto/otto.crontab
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    fbb9b8d0b9cdf28c0dff2a4fd552e538dd2f4b8d Fri Nov 5 13:50:09 2021 -0700
    Removing the ISCA cron. It was deprecated about a year ago and we had not turned off the otto.
• src/hg/utils/otto/sarscov2phylo/combineMetadata.sh
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    2c3a1d65d38fbd4b75eb55b3f8e854a452254459 Tue Nov 2 12:58:07 2021 -0700
    Crank down on duplicate lines of metadata (reported by Theo Sanderson IIRC).
• src/hg/utils/otto/sarscov2phylo/extractPublicTree.sh
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    75d8863314800ba0199291f101308dc2e52435be Tue Nov 2 12:53:58 2021 -0700
    Add the new -M (--clade-mutations) option to matUtils annotate for precise (yet hopefully more stable than --clade-paths) identification of lineage root nodes.
• src/hg/utils/otto/sarscov2phylo/kuRunMatOptimize.sh
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    dab60a7ef0dc81b9ef5992d26cced0a5b7fa1435 Tue Nov 2 12:59:25 2021 -0700
    Helper script for running matOptimize on the cluster
• src/hg/utils/otto/sarscov2phylo/nextstrain.clade-mutations.tsv
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    07cbdefa64e387ad41f07f6c900a058cfbbe118c Tue Nov 2 12:50:50 2021 -0700
    Adding mutation sets for Nextstrain Clades and selected Pango lineages (mostly VoCs) for use with matUtils annotate --clade-mutations. These are based on paths in the current tree, but with forward & back-mutations removed or changed to N. AY.* path ends checked vs. table in https://www.pango.network/summary-of-designated-ay-lineages/ .
• src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv
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    07cbdefa64e387ad41f07f6c900a058cfbbe118c Tue Nov 2 12:50:50 2021 -0700
    Adding mutation sets for Nextstrain Clades and selected Pango lineages (mostly VoCs) for use with matUtils annotate --clade-mutations. These are based on paths in the current tree, but with forward & back-mutations removed or changed to N. AY.* path ends checked vs. table in https://www.pango.network/summary-of-designated-ay-lineages/ .
• src/hg/utils/otto/sarscov2phylo/runPangolin.sh
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    b2702356792837c28408c0dc239c42f066f02e06 Tue Nov 2 13:03:26 2021 -0700
    Helper script for running Pangolin on the cluster.
• src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh
  • lines changed 4, context: html, text, full: html, text
    543b4946d460da38fd7dae2c3bfb3ece9af03218 Tue Nov 2 12:53:34 2021 -0700
    Add the new -M (--clade-mutations) option to matUtils annotate for precise (yet hopefully more stable than --clade-paths) identification of lineage root nodes. Also clip input columns when tacking on clade & lineage from tree at end, so we can run multiple times without gaining extra columns.
• src/hg/utils/otto/sarscov2phylo/updateLineageTreePb.sh
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    921f73e5adb3b42171efedb00a795fa4651655a7 Tue Nov 2 13:07:42 2021 -0700
    Use the new --clade-mutations option for matUtils annotate (but adjust mutations to be rooted in lineage A instead of B). The simplified trees always win, so don't bother testing unsimplified trees, saves ~1.5 hours.
• src/hg/utils/otto/sarscov2phylo/usherClusterRun.sh
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    0b7dfc66c9f922d96a37066655a01299a3c70de0 Tue Nov 2 12:56:59 2021 -0700
    Run matOptimize on the cluster. It uses MPI for job management; reserve cluster nodes with a fake parasol job and specify those nodes for MPI.
• src/inc/srcVersion.h
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    db9dbdd0aaa3a906a54b9a0a8ae0a516efdcfdbc Tue Nov 9 08:30:47 2021 -0800
    New version number v423
• src/lib/https.c
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    6967882140acccb8707ce3972428f012e468b678 Fri Nov 5 16:48:28 2021 -0700
    Fixing https to report output errors correctly in CGI GUI especially hgCustom and hgHubConnect. Errors appear in the log. Including bad ssl certificates which are explicitly logged to stderr.
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    4aea274afe01d6d6bf2c444b6cc1d8e03370d5f9 Sat Nov 6 10:27:53 2021 -0700
    Revert "Fixing https to report output errors correctly in CGI GUI especially hgCustom and hgHubConnect. Errors appear in the log. Including bad ssl certificates which are explicitly logged to stderr." This reverts commit 6967882140acccb8707ce3972428f012e468b678. These improvements will be delayed until the next release cycle so that we have more time for testing.
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    50f971f315c432f4d11d090e3ccc180d1ad3c421 Sat Nov 6 10:32:01 2021 -0700
    Revert "Add trust_first flag to https.c for verify makes openssl 1.0 compatible with LetsEncrypt flags. fixes #28332" This reverts commit ea0ea7155718c9acacc21f07b2d8cd247a2e9707. This cert verify functionality will return in a future release with more features and testing.
• src/product/installer/browserSetup.sh
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    a9aec4b359d86fc7d9662b8bdcb7e61828093e9b Tue Nov 2 06:18:18 2021 -0700
    moving BLAT tools into main bin directory in GBIB and GBIC, refs #28435
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    62c9a2b425dd3b7f0ce1c37044a085ef31702375 Wed Nov 3 00:23:57 2021 -0700
    fix blat directory rename problem, refs #28432
• src/utils/cpgIslandExt/cpg_lh.c
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    50367dd2101774592c5367431d32a7b9ef5c17ab Fri Nov 5 14:53:51 2021 -0700
    fixup integer overflow error which eliminated CpG detection in high GC content regions refs #26707
• src/utils/qa/weeklybld/buildEnv.csh
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    e85bdc343dee113035e7c1107225a2c9e8ba7887 Tue Nov 9 08:27:02 2021 -0800
    v423 final build, refs #28404

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• files changed: 67