All File Changes

v419_base to v420_preview (2021-08-16 to 2021-08-23) v420

• confs/hgwdev.hg.conf
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    0bbbda18bc0468214c8f571fffd79df03c4cb4ba Sun Aug 22 01:11:47 2021 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/hgGene/hgGeneData/Mouse/mm39/links.ra
  • lines changed 9, context: html, text, full: html, text
    d0aad7f66c2fee0fa9366c3b3caf4d761750c055 Tue Aug 17 10:27:07 2021 -0700
    first version of Gencode genes (knownGene version) for mm39
• src/hg/hgGene/hgGeneData/Mouse/mm39/otherOrgs.ra
  • lines changed 36, context: html, text, full: html, text
    d0aad7f66c2fee0fa9366c3b3caf4d761750c055 Tue Aug 17 10:27:07 2021 -0700
    first version of Gencode genes (knownGene version) for mm39
• src/hg/hgPhyloPlace/phyloPlace.c
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    54ca6218fe814ea456902835cc107d50dec93f80 Thu Aug 19 17:06:39 2021 -0700
    Instead of complaining when a protobuf has mutations that appear in the problematic sites file, just remove those sites from the set of sites to mask because they were not masked (yet) when the protobuf was created. It's better to be consistent, and not spam the user with warnings caused by the Problematic Sites track being newer than the selected tree.
• src/hg/hgPhyloPlace/runUsher.c
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    81d541d9b6147b2a699ca84b2f450825fb489802 Mon Aug 16 15:23:18 2021 -0700
    Removing -l (--retain-input-branch-lengths) option from usher because it causes all-0 lengths in subtrees (& wasn't necessary in the first place) -- reported to Russ by user.
• src/hg/hgPhyloPlace/treeToAuspiceJson.c
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    6aef35d07511c6edd9f656fd2d9d0cf95212d3e5 Wed Aug 18 17:13:49 2021 -0700
    Reverse child order in Auspice JSON output so that root of tree usually won't collide with the legend.
• src/hg/hgc/hgc.c
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    2b6c6b0a93928d762a71612a7b2be14aba56c436 Thu Aug 19 14:53:02 2021 -0700
    we need to replace /gbdb with hgdownload: addresses on gBiB. refs #28109
• src/hg/hgc/rnaFoldClick.c
  • lines changed 1, context: html, text, full: html, text
    99956f21187562fe5f789185a150b9b9dbde7b01 Mon Aug 16 14:46:03 2021 -0700
    make sure a stack variable is initialized. #27801
• src/hg/htdocs/admin/404.html
  • lines changed 2, context: html, text, full: html, text
    7da9b908054e075d9a03a1204f143083ca0d0772 Thu Aug 19 02:45:36 2021 -0700
    encouraging users to contact us in error messages, refs #28013
• src/hg/htdocs/admin/500.html
  • lines changed 6, context: html, text, full: html, text
    7da9b908054e075d9a03a1204f143083ca0d0772 Thu Aug 19 02:45:36 2021 -0700
    encouraging users to contact us in error messages, refs #28013
  • lines changed 1, context: html, text, full: html, text
    56b7b15ecc9c0d756662207337498669aaa66f30 Fri Aug 20 15:24:18 2021 -0700
    Clarifying message for error page, refs #28013
• src/hg/htdocs/admin/cvs.html
  • lines changed 43, context: html, text, full: html, text
    7da9b908054e075d9a03a1204f143083ca0d0772 Thu Aug 19 02:45:36 2021 -0700
    encouraging users to contact us in error messages, refs #28013
• src/hg/htdocs/admin/jk-install.html
  • lines changed 2, context: html, text, full: html, text
    7da9b908054e075d9a03a1204f143083ca0d0772 Thu Aug 19 02:45:36 2021 -0700
    encouraging users to contact us in error messages, refs #28013
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    ccb6dc94178bd4d574601bdbb22f2d455d67b98e Fri Aug 20 15:33:03 2021 -0700
    Fixing link in page, refs #28013
• src/hg/htdocs/goldenPath/newsarch.html
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    43624b8ec9e2b51e76d6213d2428c6411fe5dcb6 Tue Jul 27 13:54:41 2021 -0700
    Code review minor edits refs #27904
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    4d1cbe4059ce40d0de6f2904d507fa913d6b05aa Thu Aug 19 10:49:28 2021 -0700
    Fixing merge conflixt No RM
• src/hg/htdocs/indexNews.html
  • lines changed 1, context: html, text, full: html, text
    43624b8ec9e2b51e76d6213d2428c6411fe5dcb6 Tue Jul 27 13:54:41 2021 -0700
    Code review minor edits refs #27904
• src/hg/js/autocomplete.js
  • lines changed 36, context: html, text, full: html, text
    4ddbd4de63bff1948c81c6b84aa9334cdadeeb8c Fri Aug 20 17:48:25 2021 -0700
    restore the watermark in the position box if we update the hgTracks image. refs #27728
• src/hg/js/hgTracks.js
  • lines changed 3, context: html, text, full: html, text
    4ddbd4de63bff1948c81c6b84aa9334cdadeeb8c Fri Aug 20 17:48:25 2021 -0700
    restore the watermark in the position box if we update the hgTracks image. refs #27728
• src/hg/js/utils.js
  • lines changed 9, context: html, text, full: html, text
    9ae3838a15f502274e50073853baeeed95be6173 Thu Aug 19 05:47:52 2021 -0700
    fixing GA button tracking not working on FF <= 78 (at least), refs
• src/hg/lib/hAnno.c
  • lines changed 3, context: html, text, full: html, text
    2b6c6b0a93928d762a71612a7b2be14aba56c436 Thu Aug 19 14:53:02 2021 -0700
    we need to replace /gbdb with hgdownload: addresses on gBiB. refs #28109
• src/hg/lib/hgFind.c
  • lines changed 1, context: html, text, full: html, text
    776afaa6ba708aed97b79ceccb2a445e129b2f4c Thu Aug 19 12:44:36 2021 -0700
    add a hReplaceGbdb() for knownGene fast search
• src/hg/lib/hgHgvs.c
  • lines changed 1, context: html, text, full: html, text
    c2204b34508ac64160836ae01a16fe3f2baa3fd8 Thu Aug 19 13:25:45 2021 -0700
    don't assume LRG bigBed is local cuz that will fail on GBiB
• src/hg/makeDb/doc/hg19.txt
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    c5138b8f09d285273c15ad132516fbc4613a86a9 Fri Aug 20 15:18:42 2021 -0700
    First commit for JASAPR tracks refs #27061
• src/hg/makeDb/doc/hg38/hg38.txt
  • lines changed 11, context: html, text, full: html, text
    c5138b8f09d285273c15ad132516fbc4613a86a9 Fri Aug 20 15:18:42 2021 -0700
    First commit for JASAPR tracks refs #27061
  • lines changed 11, context: html, text, full: html, text
    73b463410df5d0e73fa068c2eb66df33cfceb6ee Fri Aug 20 15:57:37 2021 -0700
    Fixing makeDoc location as requested and short html edit refs #27061
• src/hg/makeDb/doc/hg38/jaspar.txt
  • lines changed 10, context: html, text, full: html, text
    73b463410df5d0e73fa068c2eb66df33cfceb6ee Fri Aug 20 15:57:37 2021 -0700
    Fixing makeDoc location as requested and short html edit refs #27061
• src/hg/makeDb/doc/vgpAsmHub/vgp.legacy.orderList.tsv
  • lines changed 6, context: html, text, full: html, text
    a5d57dd607d091f0d80c64ec20245aafd8e13d25 Fri Aug 20 12:16:33 2021 -0700
    update adding 8 new assemblies and 5 updated assemblies refs #23891
• src/hg/makeDb/doc/vgpAsmHub/vgp.primary.orderList.tsv
  • lines changed 14, context: html, text, full: html, text
    a5d57dd607d091f0d80c64ec20245aafd8e13d25 Fri Aug 20 12:16:33 2021 -0700
    update adding 8 new assemblies and 5 updated assemblies refs #23891
• src/hg/makeDb/doc/wuhCor1/phylogenetics.txt
  • lines changed 2, context: html, text, full: html, text
    e1e82df47c6536c27af380103fd0bdcb87fcbe4d Mon Aug 16 15:24:37 2021 -0700
    Updated Problematic Sites track.
• src/hg/makeDb/trackDb/human/cadd.ra
  • lines changed 12, context: html, text, full: html, text
    bc1b5ba86e1748595027762a35c8f9a05d769a08 Tue Aug 17 11:41:33 2021 -0700
    Changing default CADD scores and adding a note to the desc page refs #28010
• src/hg/makeDb/trackDb/human/caddSuper.html
  • lines changed 7, context: html, text, full: html, text
    bc1b5ba86e1748595027762a35c8f9a05d769a08 Tue Aug 17 11:41:33 2021 -0700
    Changing default CADD scores and adding a note to the desc page refs #28010
  • lines changed 2, context: html, text, full: html, text
    378e3494ee2068332b2ce41f45122ce76e464167 Wed Aug 18 20:33:18 2021 -0700
    changed a break to a paragraph
• src/hg/makeDb/trackDb/human/exomeProbesets.html
  • lines changed 7, context: html, text, full: html, text
    3abfa2a7125a73d5acd489f728e6328bddbe8e2c Tue Aug 17 14:37:25 2021 -0700
    a few rewordings and punc tweaks I noticed
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    ca25e18e5199ca30a5dcdd8611b8e8e22ac45fdf Tue Aug 17 14:41:07 2021 -0700
    missed a missing comma
• src/hg/makeDb/trackDb/human/hg38/trackDb.241way.ra
  • lines changed 1, context: html, text, full: html, text
    f9067264c2fad18b676e12996ffc071d1fb4df8c Fri Aug 20 10:07:27 2021 -0700
    Setting the long label to 75 characters and keep the project name in the title, refs #27519
• src/hg/makeDb/trackDb/human/jaspar.html
  • lines changed 165, context: html, text, full: html, text
    c5138b8f09d285273c15ad132516fbc4613a86a9 Fri Aug 20 15:18:42 2021 -0700
    First commit for JASAPR tracks refs #27061
  • lines changed 1, context: html, text, full: html, text
    73b463410df5d0e73fa068c2eb66df33cfceb6ee Fri Aug 20 15:57:37 2021 -0700
    Fixing makeDoc location as requested and short html edit refs #27061
• src/hg/makeDb/trackDb/human/jaspar.ra
  • lines changed 45, context: html, text, full: html, text
    c5138b8f09d285273c15ad132516fbc4613a86a9 Fri Aug 20 15:18:42 2021 -0700
    First commit for JASAPR tracks refs #27061
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    c5138b8f09d285273c15ad132516fbc4613a86a9 Fri Aug 20 15:18:42 2021 -0700
    First commit for JASAPR tracks refs #27061
• src/hg/makeDb/trackDb/mouse/mm39/knownGene.html
  • lines changed 142, context: html, text, full: html, text
    0d7eae2999eedc95d9205d915feec3575e783849 Wed Aug 18 12:42:35 2021 -0700
    html for mm39 knownGene
• src/hg/makeDb/trackDb/mouse/mm39/knownGene.ra
  • lines changed 1, context: html, text, full: html, text
    d0aad7f66c2fee0fa9366c3b3caf4d761750c055 Tue Aug 17 10:27:07 2021 -0700
    first version of Gencode genes (knownGene version) for mm39
• src/hg/makeDb/trackDb/relatedTracks.ra
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    1f9979f9019875b9b35349a29a74e651dfbc6ea4 Thu Aug 19 10:04:04 2021 -0700
    updating related tracks, refs #27965
• src/hg/utils/automation/doHgNearBlastp.pl
  • lines changed 3, context: html, text, full: html, text
    d0aad7f66c2fee0fa9366c3b3caf4d761750c055 Tue Aug 17 10:27:07 2021 -0700
    first version of Gencode genes (knownGene version) for mm39
• src/hg/utils/cartEditSuperTrack/cartEditSuperTrack.c
  • lines changed 1, context: html, text, full: html, text
    2f81eb835c8cffd5ba9937cec91b3a0f1c64541d Wed Aug 18 14:47:31 2021 -0700
    fixed a usage message and added a makefile for the tests in cartEditSuperTrack.c
• src/hg/utils/cartEditSuperTrack/tests/makefile
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    2f81eb835c8cffd5ba9937cec91b3a0f1c64541d Wed Aug 18 14:47:31 2021 -0700
    fixed a usage message and added a makefile for the tests in cartEditSuperTrack.c
• src/hg/utils/hubPublicCheck/hubPublicCheck.c
  • lines changed 10, context: html, text, full: html, text
    767f6d5f100faf63370d0a0c317db0311c055d64 Thu Aug 19 16:20:12 2021 -0700
    update dbCount when updating dbList in the hubPublic table
• src/hg/utils/otto/knownGene/buildBioCyc.sh
  • lines changed 17, context: html, text, full: html, text
    d0aad7f66c2fee0fa9366c3b3caf4d761750c055 Tue Aug 17 10:27:07 2021 -0700
    first version of Gencode genes (knownGene version) for mm39
• src/hg/utils/otto/knownGene/buildBlast.sh
  • lines changed 123, context: html, text, full: html, text
    d0aad7f66c2fee0fa9366c3b3caf4d761750c055 Tue Aug 17 10:27:07 2021 -0700
    first version of Gencode genes (knownGene version) for mm39
• src/hg/utils/otto/knownGene/buildCgap.sh
  • lines changed 17, context: html, text, full: html, text
    d0aad7f66c2fee0fa9366c3b3caf4d761750c055 Tue Aug 17 10:27:07 2021 -0700
    first version of Gencode genes (knownGene version) for mm39
• src/hg/utils/otto/knownGene/buildCore.sh
  • lines changed 56, context: html, text, full: html, text
    d0aad7f66c2fee0fa9366c3b3caf4d761750c055 Tue Aug 17 10:27:07 2021 -0700
    first version of Gencode genes (knownGene version) for mm39
• src/hg/utils/otto/knownGene/buildCore.sh.safe
  • lines changed 208, context: html, text, full: html, text
    d0aad7f66c2fee0fa9366c3b3caf4d761750c055 Tue Aug 17 10:27:07 2021 -0700
    first version of Gencode genes (knownGene version) for mm39
• src/hg/utils/otto/knownGene/buildEnv.sh
  • lines changed 49, context: html, text, full: html, text
    d0aad7f66c2fee0fa9366c3b3caf4d761750c055 Tue Aug 17 10:27:07 2021 -0700
    first version of Gencode genes (knownGene version) for mm39
• src/hg/utils/otto/knownGene/buildFoldUtr.sh
  • lines changed 52, context: html, text, full: html, text
    d0aad7f66c2fee0fa9366c3b3caf4d761750c055 Tue Aug 17 10:27:07 2021 -0700
    first version of Gencode genes (knownGene version) for mm39
• src/hg/utils/otto/knownGene/buildKegg.sh
  • lines changed 35, context: html, text, full: html, text
    d0aad7f66c2fee0fa9366c3b3caf4d761750c055 Tue Aug 17 10:27:07 2021 -0700
    first version of Gencode genes (knownGene version) for mm39
• src/hg/utils/otto/knownGene/buildKnown.sh
  • lines changed 16, context: html, text, full: html, text
    d0aad7f66c2fee0fa9366c3b3caf4d761750c055 Tue Aug 17 10:27:07 2021 -0700
    first version of Gencode genes (knownGene version) for mm39
• src/hg/utils/otto/knownGene/buildMafGene.sh
  • lines changed 96, context: html, text, full: html, text
    7c5f089c583b6a7ff0439109000eb121e6ff5d8b Tue Aug 17 14:50:36 2021 -0700
    build the knownGene and knownCanonical mafGene downloads
• src/hg/utils/otto/knownGene/buildPfamScop.sh
  • lines changed 101, context: html, text, full: html, text
    d0aad7f66c2fee0fa9366c3b3caf4d761750c055 Tue Aug 17 10:27:07 2021 -0700
    first version of Gencode genes (knownGene version) for mm39
• src/hg/utils/otto/knownGene/buildTo.sh
  • lines changed 48, context: html, text, full: html, text
    d0aad7f66c2fee0fa9366c3b3caf4d761750c055 Tue Aug 17 10:27:07 2021 -0700
    first version of Gencode genes (knownGene version) for mm39
• src/hg/utils/otto/sarscov2phylo/extractPublicTree.sh
  • lines changed 54, context: html, text, full: html, text
    95c99e66b78b8b8c4e26bb1ea91a0113d64caf04 Thu Aug 19 11:54:39 2021 -0700
    matUtils annotate -P fails too often because of little changes in the tree that affect which mutations are collapsed into the same code (or not). More sophisticated path-finding logic in matUtils could help with that, but until then, use the previous day's clade assignments as input for matUtils annotate -c for the big tree, and use the big tree's clade assignments as input for -c for the public-only tree.
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    60cefbcaddbd1627848c16242aa8145a5186e6a4 Thu Aug 19 20:28:13 2021 -0700
    Use matUtils extract's new option to write protobuf for the awesome Taxodium viewer (cov2tree.org); add it to public downloads.
• src/hg/utils/otto/sarscov2phylo/getCogUk.sh
  • lines changed 20, context: html, text, full: html, text
    3d8092305bf17c5c01713c6ed9b6ba3c289dd8ef Thu Aug 19 11:40:27 2021 -0700
    Add retries for NCBI and COG-UK fetches to get around sporadic network errors.
• src/hg/utils/otto/sarscov2phylo/getNcbi.sh
  • lines changed 1, context: html, text, full: html, text
    acc58669e6546b8705ab44c76add237111279610 Mon Aug 16 15:30:22 2021 -0700
    Use unzip -o (overwrite) so reruns don't get hung up on a prompt.
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    3d8092305bf17c5c01713c6ed9b6ba3c289dd8ef Thu Aug 19 11:40:27 2021 -0700
    Add retries for NCBI and COG-UK fetches to get around sporadic network errors.
• src/hg/utils/otto/sarscov2phylo/searchAllSarsCov2BioSample.sh
  • lines changed 1, context: html, text, full: html, text
    67217b614063c0bf07f4b5b69f0705d0125e32b4 Mon Aug 16 15:31:07 2021 -0700
    Wow, 1 million seemed like such a high ceiling once... but GenBank has more than that number of SARS-CoV-2 genomes now\!
• src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh
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    95c99e66b78b8b8c4e26bb1ea91a0113d64caf04 Thu Aug 19 11:54:39 2021 -0700
    matUtils annotate -P fails too often because of little changes in the tree that affect which mutations are collapsed into the same code (or not). More sophisticated path-finding logic in matUtils could help with that, but until then, use the previous day's clade assignments as input for matUtils annotate -c for the big tree, and use the big tree's clade assignments as input for -c for the public-only tree.
  • lines changed 11, context: html, text, full: html, text
    60cefbcaddbd1627848c16242aa8145a5186e6a4 Thu Aug 19 20:28:13 2021 -0700
    Use matUtils extract's new option to write protobuf for the awesome Taxodium viewer (cov2tree.org); add it to public downloads.
• src/product/installer/browserSetup.sh
  • lines changed 37, context: html, text, full: html, text
    e33c2417fd2222c625b62ab604c02d6e82ce3938 Fri Aug 20 04:51:37 2021 -0700
    making GBIC script work on centos8 again, refs #27795
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    d8ac5e07aaace709a641bf14affbcd9d179c4096 Fri Aug 20 06:35:28 2021 -0700
    making GBIC work on Fedora 34, refs #27795
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    528252c5b46cd55f8eab447434db29d8ac2c7518 Fri Aug 20 06:57:10 2021 -0700
    making GBIC script work on centos7 again, refs #27795
• src/utils/qa/weeklybld/buildEnv.csh
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    20a2c9be900bc80472c918e9fe199ff97eb8f0bd Mon Aug 23 10:04:46 2021 -0700
    v420 preview1, refs #27946

• lines changed: 1806
• files changed: 71