All File Changes

v369_base to v370_preview (2018-07-30 to 2018-08-06) v370

• src/hg/hgCollection/hgCollection.c
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    9be895864ea582e182ee6bd0d9f1f72b873ef43b Wed Aug 1 14:39:04 2018 -0700
    deal with single quotes in hub names in hgCollection. #21837
• src/hg/hgGeneGraph/hgGeneGraph
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    e035146f3dc0ce0eaac009b1a37b416b31b068ea Wed Aug 1 13:37:07 2018 -0700
    refs #21729. Added CSP and nonce and javascript-separation routines to the Python library hgLib in PyLib. Changed hgGeneGraph to use those functions and stop XSS attacks. Modified commit for demonstration.
• src/hg/hgMirror/hgMirror
  • lines changed 2, context: html, text, full: html, text
    61473b62bd8eb79eba17ec6db437c6cafeb71e20 Thu Aug 2 00:23:53 2018 -0700
    fixing mm6 on hgMirror, refs #21768
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    9e14ec0edafe9e5e6adb8ffd81ecad25e7864114 Thu Aug 2 17:21:09 2018 -0700
    fixes #21842. Adds CSP anti-XSS protection to hgMirror.
• src/hg/hgTracks/bigBedFilter.h
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    ff297774c7e9cb7056b780ea5554dc1ad2e22c10 Wed Aug 1 12:57:43 2018 -0700
    add regular expression filtering on bigBeds.
• src/hg/hgTracks/bigBedTrack.c
  • lines changed 28, context: html, text, full: html, text
    ff297774c7e9cb7056b780ea5554dc1ad2e22c10 Wed Aug 1 12:57:43 2018 -0700
    add regular expression filtering on bigBeds.
• src/hg/hgTracks/simpleTracks.c
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    a39c1560e7478da85f06f632c5a31cd911fe538d Thu Aug 2 17:10:12 2018 -0700
    make subtracks in composites actually sort by floating point priority
• src/hg/htdocs/goldenPath/help/bigBed.html
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    0fea9e58da32e82f7467d7f6a9d642ef1fdd0750 Tue Jul 31 14:00:06 2018 -0700
    Adding bedSort to bigBed.html and TrackHub search per user input MLQ refs #21824
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 3, context: html, text, full: html, text
    0fea9e58da32e82f7467d7f6a9d642ef1fdd0750 Tue Jul 31 14:00:06 2018 -0700
    Adding bedSort to bigBed.html and TrackHub search per user input MLQ refs #21824
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 143, context: html, text, full: html, text
    1f000c7ca9336f8f25b35068e03ec744e744b28a Tue Jul 31 14:40:43 2018 -0700
    Announcing the Ensembl v92 track release, refs #21421
• src/hg/htdocs/images/GIlogo.png
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    a07565d2804e8dd84abec39fc436a908deb331d4 Wed Aug 1 17:05:35 2018 -0700
    New logo for homepage and gateway page that includes Genomics Institute, refs #21788
• src/hg/htdocs/index.html
  • lines changed 1, context: html, text, full: html, text
    a07565d2804e8dd84abec39fc436a908deb331d4 Wed Aug 1 17:05:35 2018 -0700
    New logo for homepage and gateway page that includes Genomics Institute, refs #21788
• src/hg/htdocs/indexNews.html
  • lines changed 13, context: html, text, full: html, text
    1f000c7ca9336f8f25b35068e03ec744e744b28a Tue Jul 31 14:40:43 2018 -0700
    Announcing the Ensembl v92 track release, refs #21421
• src/hg/htdocs/style/jWest.css
  • lines changed 2, context: html, text, full: html, text
    a07565d2804e8dd84abec39fc436a908deb331d4 Wed Aug 1 17:05:35 2018 -0700
    New logo for homepage and gateway page that includes Genomics Institute, refs #21788
• src/hg/htdocs/training/index.html
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    c32b931830babbe7c5fb17f8fb9b62e0b6c0f4ef Tue Jul 31 12:16:04 2018 -0700
    added link to Newcastle Med Malaysia
• src/hg/inc/customFactory.h
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    bdae0cc6b4f696ae636298e5dad17050abaed42b Fri Aug 3 12:07:39 2018 -0700
    Don't load big* tracks when copying custom tracks at session load.
• src/hg/lib/annoStreamDbPslPlus.c
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    ceee920e8cd7b510dce7101d1338cc76287ba96e Mon Jul 30 09:38:22 2018 -0700
    Just in case we someday have additional subset(s) of ncbiRefSeq such as ncbiRefSeqClinVar, instead of hardcoding Curated and Predicted, support any ncbiRefSeq* table.
• src/hg/lib/cart.c
  • lines changed 1, context: html, text, full: html, text
    bdae0cc6b4f696ae636298e5dad17050abaed42b Fri Aug 3 12:07:39 2018 -0700
    Don't load big* tracks when copying custom tracks at session load.
• src/hg/lib/customFactory.c
  • lines changed 4, context: html, text, full: html, text
    0fb492400a83b9d96c96ccf6e02a43bd3e54b08a Thu Jul 26 12:20:54 2018 -0700
    A little refinement to pgSnp recognizer errors.
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    9a28fb2c91a89916b38621fb81410edf2855948f Thu Jul 26 12:36:38 2018 -0700
    Hardcoded 'Error line 1' is often not correct -- use lineFileAbort to get the correct line number.
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    1aa790ffdd6b8846d8aaddee3d3cfb60be1d05c8 Mon Jul 30 10:00:28 2018 -0700
    If type=bed is asserted, then show detailed error messages instead of just failing to detect BED when there's a problem. refs #21793
  • lines changed 13, context: html, text, full: html, text
    bdae0cc6b4f696ae636298e5dad17050abaed42b Fri Aug 3 12:07:39 2018 -0700
    Don't load big* tracks when copying custom tracks at session load.
• src/hg/lib/customTrack.c
  • lines changed 1, context: html, text, full: html, text
    5a8eb01f550f3e1460d17e3f71ce4f240a3bb81d Fri Jul 27 15:10:18 2018 -0700
    linefile.c supports .zip files, so customTrack.c should too.
• src/hg/lib/hui.c
  • lines changed 3, context: html, text, full: html, text
    5de1619cb074256503643e45baaddb640eb1d426 Mon Jul 30 14:57:44 2018 -0700
    fix numeric filters on assembly hubs
  • lines changed 26, context: html, text, full: html, text
    ff297774c7e9cb7056b780ea5554dc1ad2e22c10 Wed Aug 1 12:57:43 2018 -0700
    add regular expression filtering on bigBeds.
  • lines changed 1, context: html, text, full: html, text
    bb11fa1509720944e955a22d75d16c64efa348d1 Fri Aug 3 12:42:09 2018 -0700
    take out commented-out line
• src/hg/lib/jWestBanner.html
  • lines changed 3, context: html, text, full: html, text
    a07565d2804e8dd84abec39fc436a908deb331d4 Wed Aug 1 17:05:35 2018 -0700
    New logo for homepage and gateway page that includes Genomics Institute, refs #21788
• src/hg/lib/pgSnp.c
  • lines changed 3, context: html, text, full: html, text
    0fb492400a83b9d96c96ccf6e02a43bd3e54b08a Thu Jul 26 12:20:54 2018 -0700
    A little refinement to pgSnp recognizer errors.
• src/hg/makeDb/doc/mm10.txt
  • lines changed 36, context: html, text, full: html, text
    d3518198671cc06c098d20f5ac35735d7b3ecbed Fri Aug 3 11:45:55 2018 -0700
    import of gencode VM18
• src/hg/makeDb/outside/gencode/gencodeLoad.mk
  • lines changed 3, context: html, text, full: html, text
    d3518198671cc06c098d20f5ac35735d7b3ecbed Fri Aug 3 11:45:55 2018 -0700
    import of gencode VM18
• src/hg/makeDb/schema/all.joiner
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    d3518198671cc06c098d20f5ac35735d7b3ecbed Fri Aug 3 11:45:55 2018 -0700
    import of gencode VM18
• src/hg/makeDb/trackDb/drosophila/chainAnoGam1.html
  • lines changed 1, context: html, text, full: html, text
    43b16127594aa23ad9bda0e7c85ac7a5dfda3b2c Fri Aug 3 08:31:14 2018 -0700
    Updating redirected links for dm2, uiLinks cronjob.
• src/hg/makeDb/trackDb/drosophila/chainApiMel2.html
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    43b16127594aa23ad9bda0e7c85ac7a5dfda3b2c Fri Aug 3 08:31:14 2018 -0700
    Updating redirected links for dm2, uiLinks cronjob.
• src/hg/makeDb/trackDb/drosophila/chainDp3.html
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    43b16127594aa23ad9bda0e7c85ac7a5dfda3b2c Fri Aug 3 08:31:14 2018 -0700
    Updating redirected links for dm2, uiLinks cronjob.
• src/hg/makeDb/trackDb/drosophila/chainDroAna1.html
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    43b16127594aa23ad9bda0e7c85ac7a5dfda3b2c Fri Aug 3 08:31:14 2018 -0700
    Updating redirected links for dm2, uiLinks cronjob.
• src/hg/makeDb/trackDb/drosophila/chainDroMoj1.html
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    43b16127594aa23ad9bda0e7c85ac7a5dfda3b2c Fri Aug 3 08:31:14 2018 -0700
    Updating redirected links for dm2, uiLinks cronjob.
• src/hg/makeDb/trackDb/drosophila/chainDroPer1.html
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    43b16127594aa23ad9bda0e7c85ac7a5dfda3b2c Fri Aug 3 08:31:14 2018 -0700
    Updating redirected links for dm2, uiLinks cronjob.
• src/hg/makeDb/trackDb/drosophila/chainDroSec1.html
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    43b16127594aa23ad9bda0e7c85ac7a5dfda3b2c Fri Aug 3 08:31:14 2018 -0700
    Updating redirected links for dm2, uiLinks cronjob.
• src/hg/makeDb/trackDb/drosophila/chainDroSim1.html
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    43b16127594aa23ad9bda0e7c85ac7a5dfda3b2c Fri Aug 3 08:31:14 2018 -0700
    Updating redirected links for dm2, uiLinks cronjob.
• src/hg/makeDb/trackDb/drosophila/chainDroVir1.html
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    43b16127594aa23ad9bda0e7c85ac7a5dfda3b2c Fri Aug 3 08:31:14 2018 -0700
    Updating redirected links for dm2, uiLinks cronjob.
• src/hg/makeDb/trackDb/drosophila/chainDroYak1.html
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    43b16127594aa23ad9bda0e7c85ac7a5dfda3b2c Fri Aug 3 08:31:14 2018 -0700
    Updating redirected links for dm2, uiLinks cronjob.
• src/hg/makeDb/trackDb/drosophila/dm2/affyDrosDevSignal.html
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    43b16127594aa23ad9bda0e7c85ac7a5dfda3b2c Fri Aug 3 08:31:14 2018 -0700
    Updating redirected links for dm2, uiLinks cronjob.
• src/hg/makeDb/trackDb/drosophila/dm2/affyDrosDevTransfrags.html
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    43b16127594aa23ad9bda0e7c85ac7a5dfda3b2c Fri Aug 3 08:31:14 2018 -0700
    Updating redirected links for dm2, uiLinks cronjob.
• src/hg/makeDb/trackDb/drosophila/dm2/bacEndPairs.html
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    43b16127594aa23ad9bda0e7c85ac7a5dfda3b2c Fri Aug 3 08:31:14 2018 -0700
    Updating redirected links for dm2, uiLinks cronjob.
• src/hg/makeDb/trackDb/drosophila/dm2/multiz15way.html
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    43b16127594aa23ad9bda0e7c85ac7a5dfda3b2c Fri Aug 3 08:31:14 2018 -0700
    Updating redirected links for dm2, uiLinks cronjob.
• src/hg/makeDb/trackDb/drosophila/dm2/picTar.html
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    43b16127594aa23ad9bda0e7c85ac7a5dfda3b2c Fri Aug 3 08:31:14 2018 -0700
    Updating redirected links for dm2, uiLinks cronjob.
• src/hg/makeDb/trackDb/drosophila/netAnoGam1.html
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    43b16127594aa23ad9bda0e7c85ac7a5dfda3b2c Fri Aug 3 08:31:14 2018 -0700
    Updating redirected links for dm2, uiLinks cronjob.
• src/hg/makeDb/trackDb/drosophila/netApiMel2.html
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    43b16127594aa23ad9bda0e7c85ac7a5dfda3b2c Fri Aug 3 08:31:14 2018 -0700
    Updating redirected links for dm2, uiLinks cronjob.
• src/hg/makeDb/trackDb/drosophila/netDp3.html
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    43b16127594aa23ad9bda0e7c85ac7a5dfda3b2c Fri Aug 3 08:31:14 2018 -0700
    Updating redirected links for dm2, uiLinks cronjob.
• src/hg/makeDb/trackDb/drosophila/netDroAna1.html
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    43b16127594aa23ad9bda0e7c85ac7a5dfda3b2c Fri Aug 3 08:31:14 2018 -0700
    Updating redirected links for dm2, uiLinks cronjob.
• src/hg/makeDb/trackDb/drosophila/netDroMoj1.html
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    43b16127594aa23ad9bda0e7c85ac7a5dfda3b2c Fri Aug 3 08:31:14 2018 -0700
    Updating redirected links for dm2, uiLinks cronjob.
• src/hg/makeDb/trackDb/drosophila/netDroPer1.html
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    43b16127594aa23ad9bda0e7c85ac7a5dfda3b2c Fri Aug 3 08:31:14 2018 -0700
    Updating redirected links for dm2, uiLinks cronjob.
• src/hg/makeDb/trackDb/drosophila/netDroSec1.html
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    43b16127594aa23ad9bda0e7c85ac7a5dfda3b2c Fri Aug 3 08:31:14 2018 -0700
    Updating redirected links for dm2, uiLinks cronjob.
• src/hg/makeDb/trackDb/drosophila/netDroSim1.html
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    43b16127594aa23ad9bda0e7c85ac7a5dfda3b2c Fri Aug 3 08:31:14 2018 -0700
    Updating redirected links for dm2, uiLinks cronjob.
• src/hg/makeDb/trackDb/drosophila/netDroVir1.html
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    43b16127594aa23ad9bda0e7c85ac7a5dfda3b2c Fri Aug 3 08:31:14 2018 -0700
    Updating redirected links for dm2, uiLinks cronjob.
• src/hg/makeDb/trackDb/drosophila/netDroYak1.html
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    43b16127594aa23ad9bda0e7c85ac7a5dfda3b2c Fri Aug 3 08:31:14 2018 -0700
    Updating redirected links for dm2, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/clinvar.html
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    85100484574838acc699603309b382553bf054a9 Tue Jul 31 08:35:45 2018 -0700
    updating track docs after clinvar color changes, refs #21810
• src/hg/makeDb/trackDb/human/decipher.html
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    9939d8816d82d781df85dcd3b246f3f81594715d Mon Jul 30 16:43:09 2018 -0700
    Editing the DECIPHER track description page to make the SNVs color settings a bit easier to read, no Redmine.
• src/hg/makeDb/trackDb/human/hg19/hg19Patch13.ra
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    76ed76400e74c4d68169da61f775ae2db4b13d96 Thu Aug 2 11:28:46 2018 -0700
    Moving the GRC Patch track to the second item in the Mapping and Sequencing section for mm10, hg19, and hg38. The GRC Patch track is now on by default on these tracks. refs #19187
• src/hg/makeDb/trackDb/human/hg38/hg38Patch11.ra
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    76ed76400e74c4d68169da61f775ae2db4b13d96 Thu Aug 2 11:28:46 2018 -0700
    Moving the GRC Patch track to the second item in the Mapping and Sequencing section for mm10, hg19, and hg38. The GRC Patch track is now on by default on these tracks. refs #19187
• src/hg/makeDb/trackDb/mouse/mm10/mm10Patch4.ra
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    76ed76400e74c4d68169da61f775ae2db4b13d96 Thu Aug 2 11:28:46 2018 -0700
    Moving the GRC Patch track to the second item in the Mapping and Sequencing section for mm10, hg19, and hg38. The GRC Patch track is now on by default on these tracks. refs #19187
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.gencode.ra
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    d3518198671cc06c098d20f5ac35735d7b3ecbed Fri Aug 3 11:45:55 2018 -0700
    import of gencode VM18
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeSuper.html
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    d3518198671cc06c098d20f5ac35735d7b3ecbed Fri Aug 3 11:45:55 2018 -0700
    import of gencode VM18
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM18.html
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    d3518198671cc06c098d20f5ac35735d7b3ecbed Fri Aug 3 11:45:55 2018 -0700
    import of gencode VM18
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM18.ra
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    d3518198671cc06c098d20f5ac35735d7b3ecbed Fri Aug 3 11:45:55 2018 -0700
    import of gencode VM18
• src/hg/makeDb/trackDb/mouse/mm7/defaultPriority.ra
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    a9fe0e2fe29801c840928891b4ef0fb41f0f1ec0 Thu Aug 2 11:50:40 2018 -0700
    Moving the RefSeq genes track before the Other RefSeq genes track for mm7 and mm8, refs #19187
• src/hg/makeDb/trackDb/mouse/mm8/defaultPriority.ra
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    a9fe0e2fe29801c840928891b4ef0fb41f0f1ec0 Thu Aug 2 11:50:40 2018 -0700
    Moving the RefSeq genes track before the Other RefSeq genes track for mm7 and mm8, refs #19187
• src/hg/makeDb/trackDb/mouse/mm9/defaultPriority.ra
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    8d8478a216fa893bc968ff5932f152b508e869b9 Thu Aug 2 11:44:48 2018 -0700
    Moving the RefSeq genes track to come before the Other RefSeq genes track for mm9, refs #19187
• src/hg/pyLib/hgLib.py
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    e035146f3dc0ce0eaac009b1a37b416b31b068ea Wed Aug 1 13:37:07 2018 -0700
    refs #21729. Added CSP and nonce and javascript-separation routines to the Python library hgLib in PyLib. Changed hgGeneGraph to use those functions and stop XSS attacks. Modified commit for demonstration.
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    9e14ec0edafe9e5e6adb8ffd81ecad25e7864114 Thu Aug 2 17:21:09 2018 -0700
    fixes #21842. Adds CSP anti-XSS protection to hgMirror.
• src/hg/utils/genePredToBigGenePred/genePredToBigGenePred.c
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    44a3dfeeefb052ca3805064b6eb4f13e4670244c Tue Jul 31 09:33:46 2018 -0700
    adding link to .as file to bigGenePred usage, no redmine
• src/hg/utils/otto/decipher/decipherWrapper.sh
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    88fdba717f564f098e1694c8349fd8c92bc728c6 Fri Aug 3 07:56:18 2018 -0700
    Adding myself to otto emails, no refs
• src/hg/utils/otto/geneReviews/geneReviewsWrapper.sh
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    88fdba717f564f098e1694c8349fd8c92bc728c6 Fri Aug 3 07:56:18 2018 -0700
    Adding myself to otto emails, no refs
• src/hg/utils/otto/gwas/gwasWrapper.sh
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    88fdba717f564f098e1694c8349fd8c92bc728c6 Fri Aug 3 07:56:18 2018 -0700
    Adding myself to otto emails, no refs
• src/hg/utils/otto/isca/iscaWrapper.sh
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    88fdba717f564f098e1694c8349fd8c92bc728c6 Fri Aug 3 07:56:18 2018 -0700
    Adding myself to otto emails, no refs
• src/hg/utils/otto/omim/omimUploadWrapper.sh
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    88fdba717f564f098e1694c8349fd8c92bc728c6 Fri Aug 3 07:56:18 2018 -0700
    Adding myself to otto emails, no refs
• src/hg/utils/otto/omim/omimWrapper.sh
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    88fdba717f564f098e1694c8349fd8c92bc728c6 Fri Aug 3 07:56:18 2018 -0700
    Adding myself to otto emails, no refs
• src/utils/qa/weeklybld/buildEnv.csh
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    7a38ed9a2b9a746236c8b177d736ef58105ffb39 Mon Aug 6 10:10:32 2018 -0700
    v370 preview1, refs #21768

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• files changed: 78