All File Changes

v368_preview to v368_preview2 (2018-06-25 to 2018-07-02) v368

• src/hg/hgTracks/config.c
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    902875395d3d1adb35545e1b447aead40004935e Thu Jun 28 15:21:51 2018 -0700
    Fixing broken collapse all/expand all button on hgTracks configure page, refs #21668
• src/hg/hgc/barChartClick.c
  • lines changed 7, context: html, text, full: html, text
    e4945398e5ef0d578b54b6dd6160101492c59fba Fri Jun 29 12:20:08 2018 -0700
    Adding check to make sure barChart extraFields will fit in return array after code review feedback, refs #21657
• src/hg/hgc/hgc.c
  • lines changed 3, context: html, text, full: html, text
    bba4180a9f6831e160113325be6f1cae380f522a Tue Jun 26 11:17:34 2018 -0700
    Fixing dumb indexing mistake for decipher SNVs data, refs #21104
• src/hg/htdocs/FAQ/FAQformat.html
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    2116391b3c1571dea7f0cd00012ab4b613effe64 Tue Jun 26 11:58:03 2018 -0700
    fixed spacing and one typo
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 1, context: html, text, full: html, text
    5793423d35d99a1ea56f93a25d92e1978770c49f Tue Jun 26 13:23:29 2018 -0700
    fixed link
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    bb698611dd04e670d5f14c72df53b9cb7f185a51 Wed Jun 27 14:41:51 2018 -0700
    fixing line lengths and quotes
• src/hg/htdocs/goldenPath/help/interact.html
  • lines changed 24, context: html, text, full: html, text
    6071a4cc51990c18b5cb845c2a81bacd9e6eeaa1 Tue Jun 26 12:07:02 2018 -0700
    whitespace changes only
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    6e4c67cabd9d44e354c5fbc131c471b1f6ac1741 Tue Jun 26 13:24:50 2018 -0700
    fixing a few typos
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    ed98794c4e712996322c41398cc5a0decc969cac Wed Jun 27 14:04:37 2018 -0700
    updating link to example file for interact refs #21615
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 5, context: html, text, full: html, text
    69a650e9f302132e28030a805d6e0f71d081ad25 Wed Jun 27 14:45:58 2018 -0700
    fixing line length
• src/hg/lib/wikiLink.c
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    435de7bdfdbb9976edfa34d7d20874c7689679ba Tue Jun 26 01:48:46 2018 -0700
    Allowing non-basic-auth connections again. This reverts commit 92caf6b44d2a66bf52d2e41961355a325d9d16fb.
• src/hg/makeDb/doc/grcHhh38/grcH38P12.txt
  • lines changed 385, context: html, text, full: html, text
    1447370bc7356fcc7c9156c330c4a11e823d41c7 Fri Jun 29 15:56:23 2018 -0700
    Built a patches-only database for GRCh38.p12 (grcH38P12.txt) and added the sequences and basic annotations to grcHhh38 (patchUpdate.12.txt). refs #18853
• src/hg/makeDb/doc/grcHhh38/initialBuild.txt
  • lines changed 76, context: html, text, full: html, text
    37187ace0040e441d75f5977b7b4142ef708c6a1 Mon Jun 25 14:25:23 2018 -0700
    add ucscToINSDC, ucscToRefSeq and chromAlias procedure refs #18853
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    decd7f296eb1565ea7eed2eb7346b2a1c0b6a70a Thu Jun 28 00:20:27 2018 -0700
    import of gencode V28 for temporary grcHhh38
• src/hg/makeDb/doc/grcHhh38/patchUpdate.11.txt
  • lines changed 2, context: html, text, full: html, text
    8e2979254a2497116c9a4e58f9336918ffb2d491 Thu Jun 28 11:58:29 2018 -0700
    Added missing step to make sure p11 cumulative results are in place for adding p12 incremental results. refs #18853
  • lines changed 13, context: html, text, full: html, text
    d0f2011f6faf5aab358ef6f1852898cd9c122b2d Thu Jun 28 16:18:19 2018 -0700
    Make names more specific with patch version. refs #18553
• src/hg/makeDb/doc/grcHhh38/patchUpdate.12.txt
  • lines changed 591, context: html, text, full: html, text
    1447370bc7356fcc7c9156c330c4a11e823d41c7 Fri Jun 29 15:56:23 2018 -0700
    Built a patches-only database for GRCh38.p12 (grcH38P12.txt) and added the sequences and basic annotations to grcHhh38 (patchUpdate.12.txt). refs #18853
• src/hg/makeDb/doc/mm10.txt
  • lines changed 34, context: html, text, full: html, text
    1082bed8212e0b9ae9da9297625d7dc902a9eb3e Sun Jul 1 17:20:24 2018 -0700
    imported GENCODE VM17 (not being pushed public)
  • lines changed 4, context: html, text, full: html, text
    e91e68755708a6919f849da56fb70a9eef62fe9d Sun Jul 1 17:21:09 2018 -0700
    imported GENCODE VM17 (not being pushed public)
• src/hg/makeDb/outside/gencode/gencodeGenerateTrackDbs
  • lines changed 2, context: html, text, full: html, text
    decd7f296eb1565ea7eed2eb7346b2a1c0b6a70a Thu Jun 28 00:20:27 2018 -0700
    import of gencode V28 for temporary grcHhh38
• src/hg/makeDb/outside/gencode/gencodeLoad.mk
  • lines changed 14, context: html, text, full: html, text
    decd7f296eb1565ea7eed2eb7346b2a1c0b6a70a Thu Jun 28 00:20:27 2018 -0700
    import of gencode V28 for temporary grcHhh38
  • lines changed 17, context: html, text, full: html, text
    1082bed8212e0b9ae9da9297625d7dc902a9eb3e Sun Jul 1 17:20:24 2018 -0700
    imported GENCODE VM17 (not being pushed public)
• src/hg/makeDb/trackDb/anopheles/anoGam1/anoEstNcl.html
  • lines changed 2, context: html, text, full: html, text
    286098815f92d7ad25944601ceaaaa72355b5c48 Wed Jun 27 08:54:54 2018 -0700
    Updating redirected links found for anoGam1, uiLinks cronjob.
• src/hg/makeDb/trackDb/anopheles/anoGam1/anoEstTcl.html
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    286098815f92d7ad25944601ceaaaa72355b5c48 Wed Jun 27 08:54:54 2018 -0700
    Updating redirected links found for anoGam1, uiLinks cronjob.
• src/hg/makeDb/trackDb/anopheles/est.html
  • lines changed 2, context: html, text, full: html, text
    286098815f92d7ad25944601ceaaaa72355b5c48 Wed Jun 27 08:54:54 2018 -0700
    Updating redirected links found for anoGam1, uiLinks cronjob.
• src/hg/makeDb/trackDb/anopheles/intronEst.html
  • lines changed 2, context: html, text, full: html, text
    286098815f92d7ad25944601ceaaaa72355b5c48 Wed Jun 27 08:54:54 2018 -0700
    Updating redirected links found for anoGam1, uiLinks cronjob.
• src/hg/makeDb/trackDb/anopheles/mrna.html
  • lines changed 2, context: html, text, full: html, text
    286098815f92d7ad25944601ceaaaa72355b5c48 Wed Jun 27 08:54:54 2018 -0700
    Updating redirected links found for anoGam1, uiLinks cronjob.
• src/hg/makeDb/trackDb/anopheles/rmsk.html
  • lines changed 2, context: html, text, full: html, text
    286098815f92d7ad25944601ceaaaa72355b5c48 Wed Jun 27 08:54:54 2018 -0700
    Updating redirected links found for anoGam1, uiLinks cronjob.
• src/hg/makeDb/trackDb/anopheles/xenoMrna.html
  • lines changed 2, context: html, text, full: html, text
    286098815f92d7ad25944601ceaaaa72355b5c48 Wed Jun 27 08:54:54 2018 -0700
    Updating redirected links found for anoGam1, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/decipher.html
  • lines changed 6, context: html, text, full: html, text
    5a30bd6c5defd307f6ab7106c33c4e52fa23e7bb Mon Jun 25 14:28:01 2018 -0700
    Adding bullet points to the track description pagefor the DECIPHER Variants track, refs #21104
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    1082bed8212e0b9ae9da9297625d7dc902a9eb3e Sun Jul 1 17:20:24 2018 -0700
    imported GENCODE VM17 (not being pushed public)
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    81d112bd943afe54609ed391cc2ebd249e6ee7e8 Mon Jul 2 09:57:32 2018 -0700
    crispr10K only on beta, public refs #21575
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM17.html
  • lines changed 30, context: html, text, full: html, text
    1082bed8212e0b9ae9da9297625d7dc902a9eb3e Sun Jul 1 17:20:24 2018 -0700
    imported GENCODE VM17 (not being pushed public)
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM17.ra
  • lines changed 285, context: html, text, full: html, text
    1082bed8212e0b9ae9da9297625d7dc902a9eb3e Sun Jul 1 17:20:24 2018 -0700
    imported GENCODE VM17 (not being pushed public)
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    6422b8b95ffe6f767b6b96f645b91c8f2708e6cf Mon Jul 2 09:57:15 2018 -0700
    crispr10K only on beta, public refs #21575
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    126686eba692976cc3d92116d7e4c4f234558046 Mon Jul 2 10:01:32 2018 -0700
    crispr10K only on beta, public refs #21575
• src/hg/makeDb/trackDb/worm/ce6/algBinding.html
  • lines changed 1, context: html, text, full: html, text
    ed3133c6e8187ef2d450a967793e2dbe2a773239 Tue Jun 26 08:49:11 2018 -0700
    Updating redirected links for ce6, uiLinks cronjob
• src/hg/makeDb/trackDb/worm/ce6/gap.html
  • lines changed 1, context: html, text, full: html, text
    ed3133c6e8187ef2d450a967793e2dbe2a773239 Tue Jun 26 08:49:11 2018 -0700
    Updating redirected links for ce6, uiLinks cronjob
• src/hg/makeDb/trackDb/worm/ce6/gold.html
  • lines changed 1, context: html, text, full: html, text
    ed3133c6e8187ef2d450a967793e2dbe2a773239 Tue Jun 26 08:49:11 2018 -0700
    Updating redirected links for ce6, uiLinks cronjob
• src/hg/makeDb/trackDb/worm/ce6/multiz6way.html
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    ed3133c6e8187ef2d450a967793e2dbe2a773239 Tue Jun 26 08:49:11 2018 -0700
    Updating redirected links for ce6, uiLinks cronjob
• src/hg/makeDb/trackDb/worm/ce6/phastConsElements6way.html
  • lines changed 4, context: html, text, full: html, text
    ed3133c6e8187ef2d450a967793e2dbe2a773239 Tue Jun 26 08:49:11 2018 -0700
    Updating redirected links for ce6, uiLinks cronjob
• src/hg/makeDb/trackDb/worm/ce6/sangerGene.html
  • lines changed 1, context: html, text, full: html, text
    ed3133c6e8187ef2d450a967793e2dbe2a773239 Tue Jun 26 08:49:11 2018 -0700
    Updating redirected links for ce6, uiLinks cronjob
• src/hg/makeDb/trackDb/worm/ce6/sangerPseudoGene.html
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    ed3133c6e8187ef2d450a967793e2dbe2a773239 Tue Jun 26 08:49:11 2018 -0700
    Updating redirected links for ce6, uiLinks cronjob
• src/hg/makeDb/trackDb/worm/ce6/sangerRnaGene.html
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    ed3133c6e8187ef2d450a967793e2dbe2a773239 Tue Jun 26 08:49:11 2018 -0700
    Updating redirected links for ce6, uiLinks cronjob
• src/hg/makeDb/trackDb/worm/chainCaeJap1.html
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    ed3133c6e8187ef2d450a967793e2dbe2a773239 Tue Jun 26 08:49:11 2018 -0700
    Updating redirected links for ce6, uiLinks cronjob
• src/hg/makeDb/trackDb/worm/chainCaePb2.html
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    ed3133c6e8187ef2d450a967793e2dbe2a773239 Tue Jun 26 08:49:11 2018 -0700
    Updating redirected links for ce6, uiLinks cronjob
• src/hg/makeDb/trackDb/worm/chainCaeRem3.html
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    ed3133c6e8187ef2d450a967793e2dbe2a773239 Tue Jun 26 08:49:11 2018 -0700
    Updating redirected links for ce6, uiLinks cronjob
• src/hg/makeDb/trackDb/worm/chainSelf.html
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    ed3133c6e8187ef2d450a967793e2dbe2a773239 Tue Jun 26 08:49:11 2018 -0700
    Updating redirected links for ce6, uiLinks cronjob
• src/hg/makeDb/trackDb/worm/netCaeJap1.html
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    ed3133c6e8187ef2d450a967793e2dbe2a773239 Tue Jun 26 08:49:11 2018 -0700
    Updating redirected links for ce6, uiLinks cronjob
• src/hg/makeDb/trackDb/worm/netCaePb2.html
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    ed3133c6e8187ef2d450a967793e2dbe2a773239 Tue Jun 26 08:49:11 2018 -0700
    Updating redirected links for ce6, uiLinks cronjob
• src/hg/makeDb/trackDb/worm/netCaeRem3.html
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    ed3133c6e8187ef2d450a967793e2dbe2a773239 Tue Jun 26 08:49:11 2018 -0700
    Updating redirected links for ce6, uiLinks cronjob
• src/hg/makeDb/trackDb/worm/nucleosome.html
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    ed3133c6e8187ef2d450a967793e2dbe2a773239 Tue Jun 26 08:49:11 2018 -0700
    Updating redirected links for ce6, uiLinks cronjob
• src/hg/makeDb/trackDb/worm/nucleosomeAdjustedCoverage.html
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    ed3133c6e8187ef2d450a967793e2dbe2a773239 Tue Jun 26 08:49:11 2018 -0700
    Updating redirected links for ce6, uiLinks cronjob
• src/hg/makeDb/trackDb/worm/nucleosomeControlCoverage.html
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    ed3133c6e8187ef2d450a967793e2dbe2a773239 Tue Jun 26 08:49:11 2018 -0700
    Updating redirected links for ce6, uiLinks cronjob
• src/hg/makeDb/trackDb/worm/nucleosomeDensity.html
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    ed3133c6e8187ef2d450a967793e2dbe2a773239 Tue Jun 26 08:49:11 2018 -0700
    Updating redirected links for ce6, uiLinks cronjob
• src/hg/makeDb/trackDb/worm/nucleosomeStringency.html
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    ed3133c6e8187ef2d450a967793e2dbe2a773239 Tue Jun 26 08:49:11 2018 -0700
    Updating redirected links for ce6, uiLinks cronjob
• src/hg/utils/automation/chromAlias.pl
  • lines changed 13, context: html, text, full: html, text
    20e5049d9449bd5fab6d1b88492ed51220ae0aae Thu Jun 28 11:58:44 2018 -0700
    Removed unused chrom.sizes stuff and added error message to catch non-tab-separated input. refs #18853
• src/hg/utils/automation/makeDownloads.pl
  • lines changed 5, context: html, text, full: html, text
    5e613cffce75e0d8d9869e096ea37d51e7e39c0e Thu Jun 28 11:59:09 2018 -0700
    Added -noChromFiles to suppress per-chrom files for builds with few sequences (like just the new sequences in GRCh38.p12). refs #18853
• src/hg/utils/automation/openStack/nodeReport.sh
  • lines changed 3, context: html, text, full: html, text
    62808f3a15d9893548bb0337fde0759a477b42c9 Thu Jun 28 17:15:50 2018 -0700
    add check for valid number of CPUs refs #18874
• src/hg/utils/automation/openStack/paraHubSetup.sh
  • lines changed 74, context: html, text, full: html, text
    150d6eb8cfbfd2e2857f15ae1b6e6d3572250a27 Thu Jun 28 17:35:19 2018 -0700
    alter to work both for AWS and OpenStack instances, add timing measurement refs #18874
• src/utils/qa/weeklybld/buildEnv.csh
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    dbc531aa902ea403f67ee60a8e93a8a464d8bcfc Mon Jul 2 12:19:31 2018 -0700
    v368 preview2, refs #21564
• src/utils/userApps/fetchChromSizes
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    c36bf96149d8e5ba048a1339824a293364d6487d Thu Jun 28 10:31:28 2018 -0700
    Making temporary files used by fetchChromSizes hopefully more unique after code review feedback, refs #21657

• lines changed: 1695
• files changed: 62