All File Changes

v376_preview2 to v376_base (2019-01-07 to 2019-01-14) v376

• README
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    2c859d0371fa0f86a651058ed61b61eca0bbf939 Thu Jan 10 04:19:01 2019 -0800
    changes after code review, refs #22726
• src/hg/cirm/cdw/cdwWebBrowse/cdwHelp.h
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    1618f943df5d435b2ec6b1fa6738b0d50f90a19a Fri Jan 11 15:47:11 2019 -0800
    Revamp of CIRM CGI look to match static pages, refs #22765
• src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c
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    3db8d858b4b080f39716860736c0d4241e61cb45 Fri Jan 11 12:16:45 2019 -0800
    Fixing redmine #22664 - where clear search and urls setting filters interacted badly.
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    1618f943df5d435b2ec6b1fa6738b0d50f90a19a Fri Jan 11 15:47:11 2019 -0800
    Revamp of CIRM CGI look to match static pages, refs #22765
• src/hg/cirm/cdw/cdwWebBrowse/cirm-motd.html
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    1618f943df5d435b2ec6b1fa6738b0d50f90a19a Fri Jan 11 15:47:11 2019 -0800
    Revamp of CIRM CGI look to match static pages, refs #22765
• src/hg/cirm/cdw/cdwWebBrowse/version.doc
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    d5f406f657703095abba3b5a0d01022feca8678e Fri Jan 11 12:18:57 2019 -0800
    Documenting version upgrade.
• src/hg/cirm/cdw/inc/cdwLib.h
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    1618f943df5d435b2ec6b1fa6738b0d50f90a19a Fri Jan 11 15:47:11 2019 -0800
    Revamp of CIRM CGI look to match static pages, refs #22765
• src/hg/cirm/cdw/lib/cdwLib.c
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    1618f943df5d435b2ec6b1fa6738b0d50f90a19a Fri Jan 11 15:47:11 2019 -0800
    Revamp of CIRM CGI look to match static pages, refs #22765
• src/hg/cirm/cdw/lib/cdwNavBar.h
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    1618f943df5d435b2ec6b1fa6738b0d50f90a19a Fri Jan 11 15:47:11 2019 -0800
    Revamp of CIRM CGI look to match static pages, refs #22765
• src/hg/cirm/cdw/lib/cdwPageFooter.h
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    1618f943df5d435b2ec6b1fa6738b0d50f90a19a Fri Jan 11 15:47:11 2019 -0800
    Revamp of CIRM CGI look to match static pages, refs #22765
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    d171d52f067be7ae8160593a1f5d942e082292e7 Fri Jan 11 16:12:49 2019 -0800
    Slight update to CIRM CGI footer, refs #22765
• src/hg/cirm/cdw/lib/cdwPageHeader.h
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    1618f943df5d435b2ec6b1fa6738b0d50f90a19a Fri Jan 11 15:47:11 2019 -0800
    Revamp of CIRM CGI look to match static pages, refs #22765
• src/hg/cirm/gateway/htdocs/images/magnify.png
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    8c78a3333c784d0f809b508de26822b34a8459ae Fri Jan 11 16:28:29 2019 -0800
    Adding magnify icon to CIRM image set, refs #22765
• src/hg/cirm/gateway/htdocs/js/cirmStuff.js
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    1618f943df5d435b2ec6b1fa6738b0d50f90a19a Fri Jan 11 15:47:11 2019 -0800
    Revamp of CIRM CGI look to match static pages, refs #22765
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    a2e333ffe410c9ce6930582b7e899a4fabce68ef Fri Jan 11 16:49:46 2019 -0800
    Forgot to make some Javascript methods available, refs #22765
• src/hg/cirm/gateway/htdocs/makefile
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    1618f943df5d435b2ec6b1fa6738b0d50f90a19a Fri Jan 11 15:47:11 2019 -0800
    Revamp of CIRM CGI look to match static pages, refs #22765
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    bca8478c545266e36e3baf6b390b71541f93fd87 Fri Jan 11 16:19:39 2019 -0800
    Fixing small development leftover in CIRM gateway makefile, refs #22765
• src/hg/cirm/gateway/htdocs/style/cirmStyle.css
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    1618f943df5d435b2ec6b1fa6738b0d50f90a19a Fri Jan 11 15:47:11 2019 -0800
    Revamp of CIRM CGI look to match static pages, refs #22765
• src/hg/hgGene/domains.c
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    8ff444aede0ee3714ac58c90273665de428b6258 Mon Jan 7 22:58:47 2019 -0800
    fixup warnings from gcc-7 compiler refs #22738
• src/hg/hgSession/hgSession.c
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    143d61e0e74ac86bb4590ef26671f586b310ac27 Tue Jan 8 09:56:19 2019 -0800
    Fixing indentation that caused gcc-7 to complain, no ticket
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    4a5d2dbd54249e247fb49728e5fc9c598cb37efb Fri Jan 11 11:29:12 2019 -0800
    If it appears that the user tried to upload custom track data as a session, then give them a link to hgCustom. refs #22638
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    38eb8f2928026c01ab5b442fb964b6486dbf02ef Fri Jan 11 11:59:18 2019 -0800
    Daniel found that the compress (.Z) and zip options were failing. Turns out hgSession was the only user of textOutCompressMenuContents. Follow suit with other CGIs and offer only gzip for compression. refs #22638
• src/hg/hgTables/correlatePlot.c
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    8ff444aede0ee3714ac58c90273665de428b6258 Mon Jan 7 22:58:47 2019 -0800
    fixup warnings from gcc-7 compiler refs #22738
• src/hg/hgTracks/barChartTrack.c
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    8ff444aede0ee3714ac58c90273665de428b6258 Mon Jan 7 22:58:47 2019 -0800
    fixup warnings from gcc-7 compiler refs #22738
• src/hg/hgTracks/gvfTrack.c
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    2e3ff81c51e4a9ae5fa3ec8725406aa22ac63625 Thu Jan 10 12:22:27 2019 -0800
    Fixing display of origin 'not provided' in some tracks, refs #22757
• src/hg/hgTracks/pubsTracks.c
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    5a4323ed4e7fc1bf46bd2448cecf498cf6585783 Tue Jan 8 07:18:19 2019 -0800
    fixing gcc7 warn as per Hiram email, no redmine
• src/hg/hgc/hgc.c
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    8ff444aede0ee3714ac58c90273665de428b6258 Mon Jan 7 22:58:47 2019 -0800
    fixup warnings from gcc-7 compiler refs #22738
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    75220726105e48416a3cfe931ec0b12e0378d71c Wed Jan 9 09:48:17 2019 -0800
    Fix gcc-7 compiler warning reported by Hiram that was actually a bug, although never triggered by real data. refs #22738
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    f9a0e9c65aad6d8e3be3002a1be9f6aac341f459 Thu Jan 10 10:32:23 2019 -0800
    Adding bottleneck delay to all of hgc, refs #22693
• src/hg/hgc/interactClick.c
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    78fd91be04dff4959bde5bf8b404677576c11603 Wed Jan 9 10:25:06 2019 -0800
    Fix computation on interact cluster mode region coordinates on details page. refs #22750
• src/hg/hgc/lowelab.c
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    8ff444aede0ee3714ac58c90273665de428b6258 Mon Jan 7 22:58:47 2019 -0800
    fixup warnings from gcc-7 compiler refs #22738
• src/hg/htdocs/FAQ/FAQdownloads.html
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    53d8ad75dc5029d8e99d506a1a324ecc822eff85 Wed Jan 9 09:51:43 2019 -0800
    Adding statements about making utilities executable after download, refs #22684
• src/hg/htdocs/FAQ/FAQgenes.html
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    7741fe1408a9f85d10075e1e70c5039f83494cf3 Thu Jan 10 09:52:35 2019 -0800
    Fixed 404, removed sentence linking to ensembl release history
• src/hg/htdocs/goldenPath/help/customTrackText.html
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    3d1c3923c9f089f7a87b6e34bb5e1e7a34b8708b Mon Jan 7 16:03:48 2019 -0800
    Fixing some minor html styling ref#22730
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    5033739c9c18fe5bb2326a8c2efe9208b3f6f317 Mon Jan 7 16:22:44 2019 -0800
    Adding 'type bigBed # +' into track hub documentation, refs #21572
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    a9797d7cc14b1280fa6dec7dae65a7227f94a013 Fri Jan 11 15:51:50 2019 -0800
    Minor changes mentioned in code review #22732
• src/hg/htdocs/goldenPath/help/cutters.html
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    88a0712380829528b6d40aad3b9c05f057df35eb Thu Jan 10 10:46:17 2019 -0800
    404 staticLinks, correcting a bad path
• src/hg/htdocs/goldenPath/help/gbib.html
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    a75d14e3125b7b2b8ecbc8814e84f2549615b9bf Thu Jan 10 11:35:04 2019 -0800
    Fixed 404, statickLinks cronJob hardcoded genome store path
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
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    5033739c9c18fe5bb2326a8c2efe9208b3f6f317 Mon Jan 7 16:22:44 2019 -0800
    Adding 'type bigBed # +' into track hub documentation, refs #21572
• src/hg/htdocs/goldenPath/help/hubQuickStart.html
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    5033739c9c18fe5bb2326a8c2efe9208b3f6f317 Mon Jan 7 16:22:44 2019 -0800
    Adding 'type bigBed # +' into track hub documentation, refs #21572
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    a6ea28b73ccd3cead1fd51bd826fe666fa69059c Fri Jan 11 09:47:15 2019 -0800
    adding proper relative linkOut for standard BED columns, refs #21572
• src/hg/htdocs/goldenPath/help/mirrorManual.html
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    a805621e787ad8bb93448cb4ea93372c7b1e7f5e Wed Jan 9 12:50:30 2019 -0800
    adding line break to line that is longer than 100 characters, refs #22728
• src/hg/htdocs/history.html
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    4254ba712021ab98d54becf01ef41aa404f90aba Fri Jan 11 12:44:42 2019 -0800
    Creating a new HTML page to capture Genome Browser history, refs #20314
• src/hg/inc/tablesTables.h
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    1618f943df5d435b2ec6b1fa6738b0d50f90a19a Fri Jan 11 15:47:11 2019 -0800
    Revamp of CIRM CGI look to match static pages, refs #22765
• src/hg/inc/versionInfo.h
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    6ef40810240496b20cdd47ce1656d8d6d179aa24 Mon Jan 14 10:04:55 2019 -0800
    New version number v376
• src/hg/inc/web.h
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    1618f943df5d435b2ec6b1fa6738b0d50f90a19a Fri Jan 11 15:47:11 2019 -0800
    Revamp of CIRM CGI look to match static pages, refs #22765
• src/hg/js/hgTracks.js
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    07e89aebd40aced0b9f8f0eec0dae892e48dcda9 Wed Jan 9 14:29:51 2019 -0800
    Adding missing copyright statement to hgTracks.js
• src/hg/lib/botDelay.c
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    8a8f9698cc723ee0651d4cfa474f0b3a0abbf701 Thu Jan 10 04:17:19 2019 -0800
    changes after code review, refs #22726
• src/hg/lib/cart.c
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    3b42c8080b54ad87a6c37efbb3a78a0781b7e8ac Fri Jan 11 10:35:21 2019 -0800
    Fixing unencoded HTML characters caught by Daniel's testing. Also, when we quit, there might be thousands of errors left in the file, so say 'At least N errors...'. refs #22638
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    4825356e637c9de04de21505c471e2fe1361c6bc Fri Jan 11 11:01:19 2019 -0800
    Daniel pointed out that we were accepting short files with 0 valid settings but a not-too-high number of errors -- reject those files. refs #22638
• src/hg/lib/gbLoaded.sql
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    cd4b5b043806f6b09c8a3136d90f6565eee8ba12 Fri Jan 11 09:55:07 2019 -0800
    add SQL file that describes gbLoaded table
• src/hg/lib/hui.c
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    a231d814e4831153d26f2ed270ab8e0b5880f51a Tue Jan 8 15:22:36 2019 -0800
    don't forget to close UI boxes if necessary
• src/hg/lib/tablesTables.c
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    1618f943df5d435b2ec6b1fa6738b0d50f90a19a Fri Jan 11 15:47:11 2019 -0800
    Revamp of CIRM CGI look to match static pages, refs #22765
• src/hg/lib/web.c
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    1618f943df5d435b2ec6b1fa6738b0d50f90a19a Fri Jan 11 15:47:11 2019 -0800
    Revamp of CIRM CGI look to match static pages, refs #22765
• src/hg/makeDb/genbank/etc/hgwdev.dbs
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    94967843fea177b6204a94048b625835f4492347 Thu Jan 10 11:34:32 2019 -0800
    take out grcHhh38 since testing is done
• src/hg/makeDb/hgKgMrna/hgKgMrna.c
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    92e11163659de6cc7ec35fc41d299f29ff8c9952 Mon Jan 7 23:37:29 2019 -0800
    fixup warnings from gcc-7 compiler refs #22738
• src/hg/makeDb/tfbsConsLoc/seq.c
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    92e11163659de6cc7ec35fc41d299f29ff8c9952 Mon Jan 7 23:37:29 2019 -0800
    fixup warnings from gcc-7 compiler refs #22738
• src/hg/makeDb/trackDb/affyRatio.html
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    e8bb9347513c5f45e33907cbbeeb42a0beab5eb1 Mon Jan 7 15:30:52 2019 -0800
    Updating redirected links for hg17, uiLinks cronjob.
• src/hg/makeDb/trackDb/bacteria/staAur2/aaCounts.ra
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    19dfd38645e4055c0927d59547dbb511852d544c Wed Jan 9 16:27:48 2019 -0800
    turn on labelOnFeature refs #19937
• src/hg/makeDb/trackDb/cat/felCat4/cons6way.html
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    1ea0984a23e3591edc364d51abbb0969f5985905 Mon Jan 14 09:43:44 2019 -0800
    Updating http to https for felCat4, uiLinks cronjob.
• src/hg/makeDb/trackDb/chicken/galGal6/cons77way.html
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    10382206878b477cafd8ffa2e510d07bdab2a60b Fri Jan 11 16:21:57 2019 -0800
    Fixed incorrect reference species line in table 1 #22687
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    19e9e888cd4298b690ba0bf5878d897f757dc921 Fri Jan 11 16:24:19 2019 -0800
    Removed redundant chicken line in table #22687
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    d0e295a3a1ba5cfd24b577e1fa4178609ae7c2be Fri Jan 11 16:53:46 2019 -0800
    Removed extra comma #22687
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    27dc82b112115c9cbc1ee98b905191264a562616 Fri Jan 11 16:56:44 2019 -0800
    Removed redundant the #22687
• src/hg/makeDb/trackDb/drosophila/dm6/cons124way.html
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    33a50687933b048d0bc77263ac467e9e280b7606 Wed Jan 9 11:11:42 2019 -0800
    add genomewiki out links refs #18874
• src/hg/makeDb/trackDb/drosophila/droSim1/gold.html
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    fd013da8dd77c29c8674d43ee9257724da9f5f42 Mon Jan 7 14:00:20 2019 -0800
    Updating http to https for droSim1, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/HInvGeneMrna.html
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    e8bb9347513c5f45e33907cbbeeb42a0beab5eb1 Mon Jan 7 15:30:52 2019 -0800
    Updating redirected links for hg17, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/affyGnf1h.html
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    e8bb9347513c5f45e33907cbbeeb42a0beab5eb1 Mon Jan 7 15:30:52 2019 -0800
    Updating redirected links for hg17, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/affyTxnPhase2.html
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    e8bb9347513c5f45e33907cbbeeb42a0beab5eb1 Mon Jan 7 15:30:52 2019 -0800
    Updating redirected links for hg17, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/altGraphX.html
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    e8bb9347513c5f45e33907cbbeeb42a0beab5eb1 Mon Jan 7 15:30:52 2019 -0800
    Updating redirected links for hg17, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/augustus.html
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    e8bb9347513c5f45e33907cbbeeb42a0beab5eb1 Mon Jan 7 15:30:52 2019 -0800
    Updating redirected links for hg17, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/chainSelf.html
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    e8bb9347513c5f45e33907cbbeeb42a0beab5eb1 Mon Jan 7 15:30:52 2019 -0800
    Updating redirected links for hg17, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/encodeBuFirstExon.html
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    e8bb9347513c5f45e33907cbbeeb42a0beab5eb1 Mon Jan 7 15:30:52 2019 -0800
    Updating redirected links for hg17, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/encodeBu_ORChID1.html
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    e8bb9347513c5f45e33907cbbeeb42a0beab5eb1 Mon Jan 7 15:30:52 2019 -0800
    Updating redirected links for hg17, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/encodeEgaspSuper.html
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    e8bb9347513c5f45e33907cbbeeb42a0beab5eb1 Mon Jan 7 15:30:52 2019 -0800
    Updating redirected links for hg17, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/encodeEgaspUpdate.html
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    e8bb9347513c5f45e33907cbbeeb42a0beab5eb1 Mon Jan 7 15:30:52 2019 -0800
    Updating redirected links for hg17, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/encodeGencodeGeneOct05.html
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    e8bb9347513c5f45e33907cbbeeb42a0beab5eb1 Mon Jan 7 15:30:52 2019 -0800
    Updating redirected links for hg17, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/encodeGencodeIntronOct05.html
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    e8bb9347513c5f45e33907cbbeeb42a0beab5eb1 Mon Jan 7 15:30:52 2019 -0800
    Updating redirected links for hg17, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/encodePseudogene.html
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    e8bb9347513c5f45e33907cbbeeb42a0beab5eb1 Mon Jan 7 15:30:52 2019 -0800
    Updating redirected links for hg17, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/encodeRikenCage.html
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    e8bb9347513c5f45e33907cbbeeb42a0beab5eb1 Mon Jan 7 15:30:52 2019 -0800
    Updating redirected links for hg17, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/encodeUcsdNgChip.html
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    e8bb9347513c5f45e33907cbbeeb42a0beab5eb1 Mon Jan 7 15:30:52 2019 -0800
    Updating redirected links for hg17, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/encodeUcsdNgValChip.html
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    e8bb9347513c5f45e33907cbbeeb42a0beab5eb1 Mon Jan 7 15:30:52 2019 -0800
    Updating redirected links for hg17, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/encodeUncFaire.html
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    e8bb9347513c5f45e33907cbbeeb42a0beab5eb1 Mon Jan 7 15:30:52 2019 -0800
    Updating redirected links for hg17, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/encodeYaleChIPSTAT1Pval.html
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    e8bb9347513c5f45e33907cbbeeb42a0beab5eb1 Mon Jan 7 15:30:52 2019 -0800
    Updating redirected links for hg17, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/encodeYaleChIPSTAT1Sig.html
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    e8bb9347513c5f45e33907cbbeeb42a0beab5eb1 Mon Jan 7 15:30:52 2019 -0800
    Updating redirected links for hg17, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/encodeYaleChIPSTAT1Sites.html
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    e8bb9347513c5f45e33907cbbeeb42a0beab5eb1 Mon Jan 7 15:30:52 2019 -0800
    Updating redirected links for hg17, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/encodeYaleMASPlacRNATransMap.html
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    e8bb9347513c5f45e33907cbbeeb42a0beab5eb1 Mon Jan 7 15:30:52 2019 -0800
    Updating redirected links for hg17, uiLinks cronjob.
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• src/hg/makeDb/trackDb/human/hg17/encodeNhgriDukeDnaseHs.html
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• src/hg/makeDb/trackDb/human/hg17/encodeTbaCons.html
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• src/hg/makeDb/trackDb/human/hg17/encodeTbaElements.html
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• src/hg/makeDb/trackDb/human/hg17/encodeUCDavisChip.html
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• src/hg/makeDb/trackDb/human/hg17/encodeUViennaRnaz.html
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• src/hg/makeDb/trackDb/human/hg17/encodeUWRegulomeBase.html
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• src/hg/makeDb/trackDb/human/hg17/encodeUcDavisChipHits.html
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• src/hg/makeDb/trackDb/human/hg17/encodeUcsdNgGif.html
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• src/hg/makeDb/trackDb/human/hg17/encodeUppsalaChip.html
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• src/hg/makeDb/trackDb/human/hg17/encodeUppsalaChipBut.html
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• src/hg/makeDb/trackDb/human/hg17/encodeYaleAffyRNATars.html
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• src/hg/makeDb/trackDb/human/hg17/encodeYaleAffyRNATransMap.html
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• src/hg/makeDb/trackDb/human/hg17/encodeYaleChipPval.html
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• src/hg/makeDb/trackDb/human/hg17/encodeYaleChipRfbr.html
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• src/hg/makeDb/trackDb/human/hg17/encodeYaleChipSig.html
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• src/hg/makeDb/trackDb/human/hg17/encodeYaleChipSites.html
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• src/hg/makeDb/trackDb/human/hg17/exoniphy.html
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• src/hg/makeDb/trackDb/human/hg17/hapmapSnps.html
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• src/hg/makeDb/trackDb/human/hg17/knownGene.html
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• src/hg/makeDb/trackDb/human/hg17/multiz17way.html
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• src/hg/makeDb/trackDb/human/hg17/nscan.html
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• src/hg/makeDb/trackDb/human/hg17/phastConsElements17way.html
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• src/hg/makeDb/trackDb/human/hg17/picTar.html
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• src/hg/makeDb/trackDb/human/hg17/regPotential5X.html
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• src/hg/makeDb/trackDb/human/hg17/retroposons.html
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• src/hg/makeDb/trackDb/human/hg17/rgdQtl.html
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• src/hg/makeDb/trackDb/human/hg17/sangamoDnaseHs.html
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• src/hg/makeDb/trackDb/human/hg17/tfbsConsSites.html
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• src/hg/makeDb/trackDb/human/syntenyCow.html
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• src/hg/makeDb/trackDb/human/trackDb.geneHancer.ra
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    2b1ccb78facf79d39c4396eb6e1a2b9f987da60f Wed Jan 9 10:26:52 2019 -0800
    URL changed to reflect fieldname change in update from Simon F. May be reverted before track release to original (to match GB standards of lower case initial char).
• src/hg/makeDb/trackDb/human/vegaGene.html
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• src/hg/makeDb/trackDb/human/vegaPseudoGene.html
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• src/hg/makeDb/trackDb/human/wgRna.html
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    Updating redirected links for hg17, uiLinks cronjob.
• src/hg/makeDb/trackDb/mouse/mm10/TabulaMurisFacsDataset.html
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    45186c3fd8eefc0ceab4c0489a0ff0054754451e Mon Jan 14 02:25:41 2019 -0800
    adding single cell track, refs #21811
• src/hg/makeDb/trackDb/mouse/mm10/TabulaMurisFacsDatasetCov.html
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    45186c3fd8eefc0ceab4c0489a0ff0054754451e Mon Jan 14 02:25:41 2019 -0800
    adding single cell track, refs #21811
• src/hg/makeDb/trackDb/mouse/mm10/TabulaMurisFacsDatasetJunc.html
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    45186c3fd8eefc0ceab4c0489a0ff0054754451e Mon Jan 14 02:25:41 2019 -0800
    adding single cell track, refs #21811
• src/hg/makeDb/trackDb/mouse/mm10/TabulaMurisFacsDatasetReads.html
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    45186c3fd8eefc0ceab4c0489a0ff0054754451e Mon Jan 14 02:25:41 2019 -0800
    adding single cell track, refs #21811
• src/hg/makeDb/trackDb/mouse/mm10/singleCell.html
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    45186c3fd8eefc0ceab4c0489a0ff0054754451e Mon Jan 14 02:25:41 2019 -0800
    adding single cell track, refs #21811
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
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    45186c3fd8eefc0ceab4c0489a0ff0054754451e Mon Jan 14 02:25:41 2019 -0800
    adding single cell track, refs #21811
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.tabulamuris.ra
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    45186c3fd8eefc0ceab4c0489a0ff0054754451e Mon Jan 14 02:25:41 2019 -0800
    adding single cell track, refs #21811
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    42ac9f8b1bba1eca3c564b8e3e52fc526b2d925d Mon Jan 14 02:27:00 2019 -0800
    adding single cell expression track, refs #21811
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    8c534c739bf0b88e2f663f316ba810d7500efdd7 Mon Jan 14 02:29:11 2019 -0800
    moving single cell to expression group, refs #21811
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    bf842d4366c5623f492e45e2b828bae3ac72c138 Mon Jan 14 02:30:03 2019 -0800
    got the wrong group, refs #21811
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    2c71e5a9c36410edd94ac431631797ee167b7650 Mon Jan 14 02:37:22 2019 -0800
    title of single cell expression track, refs #21811
• src/hg/makeDb/trackDb/snp125.html
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    e8bb9347513c5f45e33907cbbeeb42a0beab5eb1 Mon Jan 7 15:30:52 2019 -0800
    Updating redirected links for hg17, uiLinks cronjob.
• src/hg/makeDb/trackDb/worm/caeRem3/ctgPos2.html
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    3ae110c22a027ab53b415bc53e03f86bcb6cc427 Mon Jan 7 15:33:53 2019 -0800
    Updating redirected links for caeRem3, uiLinks cronjob.
• src/hg/makeDb/trackDb/worm/caeRem3/gold.html
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    3ae110c22a027ab53b415bc53e03f86bcb6cc427 Mon Jan 7 15:33:53 2019 -0800
    Updating redirected links for caeRem3, uiLinks cronjob.
• src/hg/makeDb/trackDb/worm/ce11/cons135way.html
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    d350603f0c4c4a2abd12d1815e5ffc279edca810 Wed Jan 9 09:21:00 2019 -0800
    Fixing description page for nematode 135way cons track ref#22599
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    99ba856cebad15c443f1fd899cb508f713ecb997 Thu Jan 10 13:51:46 2019 -0800
    adding links to genomewiki pages for alignment parameters refs #22599
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    9e6ae71131883d5ca15621277b71fc1a6dc3026b Thu Jan 10 14:02:01 2019 -0800
    Adding a missing space ref#22599
• src/hg/makeDb/trackDb/worm/ce11/trackDb.135way.ra
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    043eee2ef6e515e19d73e5f5e9ddc9430d5055ea Mon Jan 7 10:23:31 2019 -0800
    Adding pennantIcon to 135way cons track ref#22599
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    f24ab57716bdde7ccc5aae31de99745a5a34ac4f Mon Jan 7 14:17:32 2019 -0800
    Adding release tags to stage track on beta ref#22599
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    42a6a74219888452fe15f3411006cc09c31944a1 Tue Jan 8 09:20:27 2019 -0800
    Fixed release tags for composite track and made previous ce11 cons track hide by default ref#22599
• src/hg/makeDb/trackDb/worm/ce11/trackDb.26way.ra
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    42a6a74219888452fe15f3411006cc09c31944a1 Tue Jan 8 09:20:27 2019 -0800
    Fixed release tags for composite track and made previous ce11 cons track hide by default ref#22599
• src/hg/makeDb/trackDb/worm/ce11/trackDb.ra
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    42a6a74219888452fe15f3411006cc09c31944a1 Tue Jan 8 09:20:27 2019 -0800
    Fixed release tags for composite track and made previous ce11 cons track hide by default ref#22599
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    7bce38fb065e2532d193edb744197be904b98ab0 Thu Jan 10 14:45:23 2019 -0800
    Removing release tags for rr release ref#22599
• src/hg/makefile
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    5100482eae1129e7908b391ff0d34ad0ff329558 Wed Jan 9 13:02:56 2019 -0800
    Removing an unused old utility that doesn't compile with the new compiler.
• src/hg/nci60/findStanAlignments.c
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    92e11163659de6cc7ec35fc41d299f29ff8c9952 Mon Jan 7 23:37:29 2019 -0800
    fixup warnings from gcc-7 compiler refs #22738
• src/hg/near/hgExpDistance/makefile
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    6c50a71565d1acb5ef2a32506841630cb96c8b44 Mon Jan 7 22:06:12 2019 -0800
    fix broken link on ubuntu with gcc-7 refs #22738
• src/hg/oneShot/freen/freen.c
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    a81c32df01d71beeaba0322068ee6ec7c0b7234e Wed Jan 9 13:12:30 2019 -0800
    Adding minor comment change just to test out git commit cycle going into redmine.
• src/hg/reviewSanity/makefile
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    5100482eae1129e7908b391ff0d34ad0ff329558 Wed Jan 9 13:02:56 2019 -0800
    Removing an unused old utility that doesn't compile with the new compiler.
• src/hg/reviewSanity/reviewSanity.c
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    5100482eae1129e7908b391ff0d34ad0ff329558 Wed Jan 9 13:02:56 2019 -0800
    Removing an unused old utility that doesn't compile with the new compiler.
• src/hg/rnaStructure/hgLoadRnaFold/hgLoadRnaFold.c
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    a034b848fd11772864bbf24d42d75c4ae407f698 Wed Jan 9 13:07:37 2019 -0800
    Fixing a logic error that the new compiler (gcc 7) caught.
• src/hg/utils/automation/EnsGeneAutomate.pm
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    00d83bed7a21f4cc479ceb8c0edddad0beb8e575 Fri Jan 11 15:00:01 2019 -0800
    adding v95 definitions refs #22761
• src/hg/utils/hubCheck/hubCheck.c
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    85096f9fd3a7c7565dac3d1e462228cb31c3df66 Mon Jan 7 18:28:40 2019 -0800
    Skip and warn if empty setting (file format err) is encountered. refs #22714
• src/hg/utils/otto/gwas/checkGwas.sh
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    9b20d4965dd3254ead33943b4a40184b67d7e688 Wed Jan 9 11:59:25 2019 -0800
    Update otto omim and gwas scripts to use newest released dbsnp version, refs #18151
• src/hg/utils/otto/gwas/makefile
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    9b20d4965dd3254ead33943b4a40184b67d7e688 Wed Jan 9 11:59:25 2019 -0800
    Update otto omim and gwas scripts to use newest released dbsnp version, refs #18151
• src/hg/utils/otto/omim/buildOmimTracks.sh
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    9b20d4965dd3254ead33943b4a40184b67d7e688 Wed Jan 9 11:59:25 2019 -0800
    Update otto omim and gwas scripts to use newest released dbsnp version, refs #18151
• src/htslib/vcf.c
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    b8eb25b7e9f20be978dc8f0ef6e4199582baa686 Wed Jan 9 11:10:19 2019 -0800
    fix a problem that Hiram introduced in code that is never called. #22736
• src/inc/srcVersion.h
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    6ef40810240496b20cdd47ce1656d8d6d179aa24 Mon Jan 14 10:04:55 2019 -0800
    New version number v376
• src/lib/htmshell.c
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    1618f943df5d435b2ec6b1fa6738b0d50f90a19a Fri Jan 11 15:47:11 2019 -0800
    Revamp of CIRM CGI look to match static pages, refs #22765
• src/product/installer/browserSetup.sh
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    acf98a6a45505727ce08a8e1d083db7dd85c339b Tue Jan 8 13:36:24 2019 -0800
    removing extras repo force as it leads to problems with JnJ
• src/utils/qa/linkCheckExclude
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    97ef5606a3edc776157ecce3566aa06e2e6928db Fri Jan 11 15:02:18 2019 -0800
    Adding new static docs, syncing with /cluster/bin/scripts/ version
• src/utils/qa/weeklybld/buildEnv.csh
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    150f978c44ab986bf27d7459d47e76a106e8ad69 Mon Jan 14 10:03:54 2019 -0800
    v376 final build, refs #22686

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• files changed: 187