All File Changes

v322_base to v323_preview (2015-09-14 to 2015-09-21) v323

• confs/hgwbeta.hg.conf
  • lines changed 3, context: html, text, full: html, text
    Tracking removal of a temporary hg.conf setting on beta to enable hotkeys refs #15370
    
• src/browserbox/README.txt
  • lines changed 1, context: html, text, full: html, text
    fixing url in gbib readme
    
• src/browserbox/root/updateBrowser.sh
  • lines changed 2, context: html, text, full: html, text
    adding a link to the share data folder in gbib, refs #16022
    
  • lines changed 1, context: html, text, full: html, text
    fixing one letter typo
    
• src/browserbox/usr/local/apache/cgi-bin/hg.conf
  • lines changed 6, context: html, text, full: html, text
    allow loading of local files in gbib without the udc cache, refs #16022
    
• src/hg/hgMirror/hgMirror
  • lines changed 14, context: html, text, full: html, text
    fixing split table bug in hgMirror, refs #16033
    
  • lines changed 6, context: html, text, full: html, text
    oops, forgot the tables all_mrna and all_est. refs #16033
    
• src/hg/hgTracks/extTools.ra
  • lines changed 2, context: html, text, full: html, text
    wording change of ext tools menu
    
• src/hg/hgTracks/hgTracks.c
  • lines changed 13, context: html, text, full: html, text
    adding menu entries under genomes and genome browser, refs #16022
    
  • lines changed 20, context: html, text, full: html, text
    libifying cartGetPosition because this code is needed twice, once in
    hgTracks and also in cart.c for setting the page title. refs #16022,
    note 18
    
  • lines changed 3, context: html, text, full: html, text
    Revert "adding menu entries under genomes and genome browser, refs #16022"
    
    This reverts commit 385f6d8b1f19463d2103cee18970fa833411293f.
    
    Conflicts:
    src/hg/hgTracks/hgTracks.c
    
  • lines changed 3, context: html, text, full: html, text
    fixing merge conflict overlooked in last commit
    
• src/hg/hgTracks/makefile
  • lines changed 1, context: html, text, full: html, text
    making hgTracks copy the extTools.ra file to activate the external tools
    menu. refs #15113
    
  • lines changed 1, context: html, text, full: html, text
    adding a variable CGI-BIN_DEST that is either CGI-BIN_USER or
    CGI-BIN_BETA or CGI-BIN, depending on how make was called.
    This should avoid the triplicated rules we have everywhere.
    It doesn't work when one wants to run "make alpha beta my" but
    I think we never do that.
    Using this to copy an .ra file to the cgi-bin directory. refs #15113
    
• src/hg/hgTracks/menu.c
  • lines changed 1, context: html, text, full: html, text
    fixes after code review refs #16013
    
• src/hg/htdocs/FAQ/FAQblat.html
  • lines changed 4, context: html, text, full: html, text
    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
  • lines changed 0, context: html, text, full: html, text
    Ack. Didn't notice that I changed permissions of all those files. Reversing accidental permissions change in last commit, refs #15389
    
• src/hg/htdocs/FAQ/FAQcite.html
  • lines changed 4, context: html, text, full: html, text
    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
  • lines changed 0, context: html, text, full: html, text
    Ack. Didn't notice that I changed permissions of all those files. Reversing accidental permissions change in last commit, refs #15389
    
• src/hg/htdocs/FAQ/FAQcustom.html
  • lines changed 4, context: html, text, full: html, text
    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
  • lines changed 0, context: html, text, full: html, text
    Ack. Didn't notice that I changed permissions of all those files. Reversing accidental permissions change in last commit, refs #15389
    
• src/hg/htdocs/FAQ/FAQdisplay.html
  • lines changed 4, context: html, text, full: html, text
    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
  • lines changed 0, context: html, text, full: html, text
    Ack. Didn't notice that I changed permissions of all those files. Reversing accidental permissions change in last commit, refs #15389
    
• src/hg/htdocs/FAQ/FAQdownloads.html
  • lines changed 4, context: html, text, full: html, text
    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
  • lines changed 0, context: html, text, full: html, text
    Ack. Didn't notice that I changed permissions of all those files. Reversing accidental permissions change in last commit, refs #15389
    
• src/hg/htdocs/FAQ/FAQformat.html
  • lines changed 4, context: html, text, full: html, text
    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
  • lines changed 0, context: html, text, full: html, text
    Ack. Didn't notice that I changed permissions of all those files. Reversing accidental permissions change in last commit, refs #15389
    
• src/hg/htdocs/FAQ/FAQlicense.html
  • lines changed 4, context: html, text, full: html, text
    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
  • lines changed 0, context: html, text, full: html, text
    Ack. Didn't notice that I changed permissions of all those files. Reversing accidental permissions change in last commit, refs #15389
    
• src/hg/htdocs/FAQ/FAQlink.html
  • lines changed 4, context: html, text, full: html, text
    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
  • lines changed 0, context: html, text, full: html, text
    Ack. Didn't notice that I changed permissions of all those files. Reversing accidental permissions change in last commit, refs #15389
    
• src/hg/htdocs/FAQ/FAQmaillist.html
  • lines changed 4, context: html, text, full: html, text
    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
  • lines changed 0, context: html, text, full: html, text
    Ack. Didn't notice that I changed permissions of all those files. Reversing accidental permissions change in last commit, refs #15389
    
• src/hg/htdocs/FAQ/FAQreleases.html
  • lines changed 4, context: html, text, full: html, text
    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
  • lines changed 0, context: html, text, full: html, text
    Ack. Didn't notice that I changed permissions of all those files. Reversing accidental permissions change in last commit, refs #15389
    
• src/hg/htdocs/FAQ/FAQtables.html
  • lines changed 4, context: html, text, full: html, text
    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
  • lines changed 0, context: html, text, full: html, text
    Ack. Didn't notice that I changed permissions of all those files. Reversing accidental permissions change in last commit, refs #15389
    
• src/hg/htdocs/FAQ/FAQtracks.html
  • lines changed 4, context: html, text, full: html, text
    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
  • lines changed 0, context: html, text, full: html, text
    Ack. Didn't notice that I changed permissions of all those files. Reversing accidental permissions change in last commit, refs #15389
    
• src/hg/htdocs/FAQ/index.html
  • lines changed 4, context: html, text, full: html, text
    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
  • lines changed 0, context: html, text, full: html, text
    Ack. Didn't notice that I changed permissions of all those files. Reversing accidental permissions change in last commit, refs #15389
    
• src/hg/htdocs/Neandertal/index.html
  • lines changed 4, context: html, text, full: html, text
    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
  • lines changed 0, context: html, text, full: html, text
    Ack. Didn't notice that I changed permissions of all those files. Reversing accidental permissions change in last commit, refs #15389
    
• src/hg/htdocs/admin/403.html
  • lines changed 4, context: html, text, full: html, text
    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
  • lines changed 0, context: html, text, full: html, text
    Ack. Didn't notice that I changed permissions of all those files. Reversing accidental permissions change in last commit, refs #15389
    
• src/hg/htdocs/admin/404.html
  • lines changed 4, context: html, text, full: html, text
    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
  • lines changed 0, context: html, text, full: html, text
    Ack. Didn't notice that I changed permissions of all those files. Reversing accidental permissions change in last commit, refs #15389
    
• src/hg/htdocs/admin/500.html
  • lines changed 4, context: html, text, full: html, text
    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
  • lines changed 0, context: html, text, full: html, text
    Ack. Didn't notice that I changed permissions of all those files. Reversing accidental permissions change in last commit, refs #15389
    
• src/hg/htdocs/admin/cvs.html
  • lines changed 4, context: html, text, full: html, text
    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
  • lines changed 0, context: html, text, full: html, text
    Ack. Didn't notice that I changed permissions of all those files. Reversing accidental permissions change in last commit, refs #15389
    
• src/hg/htdocs/admin/git.html
  • lines changed 4, context: html, text, full: html, text
    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
  • lines changed 0, context: html, text, full: html, text
    Ack. Didn't notice that I changed permissions of all those files. Reversing accidental permissions change in last commit, refs #15389
    
• src/hg/htdocs/admin/index.html
  • lines changed 4, context: html, text, full: html, text
    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
  • lines changed 0, context: html, text, full: html, text
    Ack. Didn't notice that I changed permissions of all those files. Reversing accidental permissions change in last commit, refs #15389
    
• src/hg/htdocs/admin/jk-install.html
  • lines changed 4, context: html, text, full: html, text
    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
  • lines changed 0, context: html, text, full: html, text
    Ack. Didn't notice that I changed permissions of all those files. Reversing accidental permissions change in last commit, refs #15389
    
• src/hg/htdocs/admin/mirror.html
  • lines changed 4, context: html, text, full: html, text
    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
  • lines changed 0, context: html, text, full: html, text
    Ack. Didn't notice that I changed permissions of all those files. Reversing accidental permissions change in last commit, refs #15389
    
• src/hg/htdocs/cite.html
  • lines changed 4, context: html, text, full: html, text
    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
  • lines changed 0, context: html, text, full: html, text
    Ack. Didn't notice that I changed permissions of all those files. Reversing accidental permissions change in last commit, refs #15389
    
• src/hg/htdocs/conditions.html
  • lines changed 4, context: html, text, full: html, text
    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
  • lines changed 0, context: html, text, full: html, text
    Ack. Didn't notice that I changed permissions of all those files. Reversing accidental permissions change in last commit, refs #15389
    
• src/hg/htdocs/contacts.html
  • lines changed 4, context: html, text, full: html, text
    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
  • lines changed 0, context: html, text, full: html, text
    Ack. Didn't notice that I changed permissions of all those files. Reversing accidental permissions change in last commit, refs #15389
    
• src/hg/htdocs/goldenPath/certificates/certificate_hg15.html
  • lines changed 4, context: html, text, full: html, text
    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
  • lines changed 0, context: html, text, full: html, text
    Ack. Didn't notice that I changed permissions of all those files. Reversing accidental permissions change in last commit, refs #15389
    
• src/hg/htdocs/goldenPath/certificates/certificate_hg16.html
  • lines changed 4, context: html, text, full: html, text
    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
  • lines changed 0, context: html, text, full: html, text
    Ack. Didn't notice that I changed permissions of all those files. Reversing accidental permissions change in last commit, refs #15389
    
• src/hg/htdocs/goldenPath/certificates/index.html
  • lines changed 4, context: html, text, full: html, text
    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
  • lines changed 0, context: html, text, full: html, text
    Ack. Didn't notice that I changed permissions of all those files. Reversing accidental permissions change in last commit, refs #15389
    
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 4, context: html, text, full: html, text
    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
  • lines changed 0, context: html, text, full: html, text
    Ack. Didn't notice that I changed permissions of all those files. Reversing accidental permissions change in last commit, refs #15389
    
• src/hg/htdocs/goldenPath/datorg.html
  • lines changed 4, context: html, text, full: html, text
    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
  • lines changed 0, context: html, text, full: html, text
    Ack. Didn't notice that I changed permissions of all those files. Reversing accidental permissions change in last commit, refs #15389
    
• src/hg/htdocs/goldenPath/gbdDescriptions.html
  • lines changed 4, context: html, text, full: html, text
    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
  • lines changed 0, context: html, text, full: html, text
    Ack. Didn't notice that I changed permissions of all those files. Reversing accidental permissions change in last commit, refs #15389
    
• src/hg/htdocs/goldenPath/gbdDescriptionsOld.html
  • lines changed 4, context: html, text, full: html, text
    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
  • lines changed 0, context: html, text, full: html, text
    Ack. Didn't notice that I changed permissions of all those files. Reversing accidental permissions change in last commit, refs #15389
    
• src/hg/htdocs/goldenPath/help/axt.html
  • lines changed 4, context: html, text, full: html, text
    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
  • lines changed 0, context: html, text, full: html, text
    Ack. Didn't notice that I changed permissions of all those files. Reversing accidental permissions change in last commit, refs #15389
    
• src/hg/htdocs/goldenPath/help/bam.html
  • lines changed 4, context: html, text, full: html, text
    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
  • lines changed 0, context: html, text, full: html, text
    Ack. Didn't notice that I changed permissions of all those files. Reversing accidental permissions change in last commit, refs #15389
    
• src/hg/htdocs/goldenPath/help/bedgraph.html
  • lines changed 4, context: html, text, full: html, text
    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
  • lines changed 0, context: html, text, full: html, text
    Ack. Didn't notice that I changed permissions of all those files. Reversing accidental permissions change in last commit, refs #15389
    
• src/hg/htdocs/goldenPath/help/bigBed.html
  • lines changed 4, context: html, text, full: html, text
    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
  • lines changed 0, context: html, text, full: html, text
    Ack. Didn't notice that I changed permissions of all those files. Reversing accidental permissions change in last commit, refs #15389
    
• src/hg/htdocs/goldenPath/help/bigGenePred.html
  • lines changed 4, context: html, text, full: html, text
    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
  • lines changed 0, context: html, text, full: html, text
    Ack. Didn't notice that I changed permissions of all those files. Reversing accidental permissions change in last commit, refs #15389
    
• src/hg/htdocs/goldenPath/help/bigWig.html
  • lines changed 4, context: html, text, full: html, text
    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
  • lines changed 0, context: html, text, full: html, text
    Ack. Didn't notice that I changed permissions of all those files. Reversing accidental permissions change in last commit, refs #15389
    
• src/hg/htdocs/goldenPath/help/blatSpec.html
  • lines changed 4, context: html, text, full: html, text
    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
  • lines changed 0, context: html, text, full: html, text
    Ack. Didn't notice that I changed permissions of all those files. Reversing accidental permissions change in last commit, refs #15389
    
• src/hg/htdocs/goldenPath/help/chain.html
  • lines changed 4, context: html, text, full: html, text
    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
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    Ack. Didn't notice that I changed permissions of all those files. Reversing accidental permissions change in last commit, refs #15389
    
• src/hg/htdocs/goldenPath/help/chimera.html
  • lines changed 4, context: html, text, full: html, text
    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
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    Ack. Didn't notice that I changed permissions of all those files. Reversing accidental permissions change in last commit, refs #15389
    
• src/hg/htdocs/goldenPath/help/customColumn.html
  • lines changed 4, context: html, text, full: html, text
    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
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    Ack. Didn't notice that I changed permissions of all those files. Reversing accidental permissions change in last commit, refs #15389
    
• src/hg/htdocs/goldenPath/help/customTrack.html
  • lines changed 4, context: html, text, full: html, text
    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
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    Ack. Didn't notice that I changed permissions of all those files. Reversing accidental permissions change in last commit, refs #15389
    
• src/hg/htdocs/goldenPath/help/fileSearch.html
  • lines changed 4, context: html, text, full: html, text
    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
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    Ack. Didn't notice that I changed permissions of all those files. Reversing accidental permissions change in last commit, refs #15389
    
• src/hg/htdocs/goldenPath/help/ftp.html
  • lines changed 4, context: html, text, full: html, text
    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
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    Ack. Didn't notice that I changed permissions of all those files. Reversing accidental permissions change in last commit, refs #15389
    
• src/hg/htdocs/goldenPath/help/gbib.html
  • lines changed 4, context: html, text, full: html, text
    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
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    Ack. Didn't notice that I changed permissions of all those files. Reversing accidental permissions change in last commit, refs #15389
    
• src/hg/htdocs/goldenPath/help/geneSearchBox.html
  • lines changed 4, context: html, text, full: html, text
    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
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    Ack. Didn't notice that I changed permissions of all those files. Reversing accidental permissions change in last commit, refs #15389
    
• src/hg/htdocs/goldenPath/help/genomeEuro.html
  • lines changed 4, context: html, text, full: html, text
    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
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    Ack. Didn't notice that I changed permissions of all those files. Reversing accidental permissions change in last commit, refs #15389
    
• src/hg/htdocs/goldenPath/help/haplotypes.html
  • lines changed 4, context: html, text, full: html, text
    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
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    Ack. Didn't notice that I changed permissions of all those files. Reversing accidental permissions change in last commit, refs #15389
    
• src/hg/htdocs/goldenPath/help/hg18ToHg19LiftOver.html
  • lines changed 4, context: html, text, full: html, text
    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
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    Ack. Didn't notice that I changed permissions of all those files. Reversing accidental permissions change in last commit, refs #15389
    
• src/hg/htdocs/goldenPath/help/hgBamTrackHelp.html
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    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
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    Ack. Didn't notice that I changed permissions of all those files. Reversing accidental permissions change in last commit, refs #15389
    
• src/hg/htdocs/goldenPath/help/hgBaseLabel.html
  • lines changed 4, context: html, text, full: html, text
    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
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    Ack. Didn't notice that I changed permissions of all those files. Reversing accidental permissions change in last commit, refs #15389
    
• src/hg/htdocs/goldenPath/help/hgCodonColoring.html
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    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
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    Ack. Didn't notice that I changed permissions of all those files. Reversing accidental permissions change in last commit, refs #15389
    
• src/hg/htdocs/goldenPath/help/hgCodonColoringMrna.html
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    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
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    Ack. Didn't notice that I changed permissions of all those files. Reversing accidental permissions change in last commit, refs #15389
    
• src/hg/htdocs/goldenPath/help/hgGenomeHelp.html
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    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
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    Ack. Didn't notice that I changed permissions of all those files. Reversing accidental permissions change in last commit, refs #15389
    
• src/hg/htdocs/goldenPath/help/hgIndelDisplay.html
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    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
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    Ack. Didn't notice that I changed permissions of all those files. Reversing accidental permissions change in last commit, refs #15389
    
• src/hg/htdocs/goldenPath/help/hgIntegratorHelp.html
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    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
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    Ack. Didn't notice that I changed permissions of all those files. Reversing accidental permissions change in last commit, refs #15389
    
• src/hg/htdocs/goldenPath/help/hgNearHelp.html
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    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
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    Ack. Didn't notice that I changed permissions of all those files. Reversing accidental permissions change in last commit, refs #15389
    
• src/hg/htdocs/goldenPath/help/hgRegMotifHelp.html
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    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
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    Ack. Didn't notice that I changed permissions of all those files. Reversing accidental permissions change in last commit, refs #15389
    
• src/hg/htdocs/goldenPath/help/hgSessionHelp.html
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    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
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    Ack. Didn't notice that I changed permissions of all those files. Reversing accidental permissions change in last commit, refs #15389
    
• src/hg/htdocs/goldenPath/help/hgTablesHelp.html
  • lines changed 4, context: html, text, full: html, text
    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
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    Ack. Didn't notice that I changed permissions of all those files. Reversing accidental permissions change in last commit, refs #15389
    
• src/hg/htdocs/goldenPath/help/hgTextHelp.html
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    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
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    Ack. Didn't notice that I changed permissions of all those files. Reversing accidental permissions change in last commit, refs #15389
    
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
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    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
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    Ack. Didn't notice that I changed permissions of all those files. Reversing accidental permissions change in last commit, refs #15389
    
• src/hg/htdocs/goldenPath/help/hgTracksHelp.html
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    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
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• src/hg/htdocs/goldenPath/help/hgVcfTrackHelp.html
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    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
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• src/hg/htdocs/goldenPath/help/hgWiggleTrackHelp.html
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    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
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• src/hg/htdocs/goldenPath/help/hubQuickStart.html
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    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
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• src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html
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    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
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• src/hg/htdocs/goldenPath/help/hubQuickStartGroups.html
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• src/hg/htdocs/goldenPath/help/image.html
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• src/hg/htdocs/goldenPath/help/index.html
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• src/hg/htdocs/goldenPath/help/iupac.html
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    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
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• src/hg/htdocs/goldenPath/help/liftOver.html
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• src/hg/htdocs/goldenPath/help/multiView.html
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• src/hg/htdocs/goldenPath/help/mysql.html
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    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
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• src/hg/htdocs/goldenPath/help/net.html
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• src/hg/htdocs/goldenPath/help/phastCons.html
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• src/hg/htdocs/goldenPath/help/qValue.html
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• src/hg/htdocs/goldenPath/help/query.html
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• src/hg/htdocs/goldenPath/help/sessions.html
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• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
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    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
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• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v0.html
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    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
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• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v1.html
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    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
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• src/hg/htdocs/goldenPath/help/trackDescriptions.html
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• src/hg/htdocs/goldenPath/help/trackSearch.html
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• src/hg/htdocs/goldenPath/help/trix.html
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    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
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• src/hg/htdocs/goldenPath/help/twoBit.html
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• src/hg/htdocs/goldenPath/help/vcf.html
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• src/hg/htdocs/goldenPath/help/wiggle.html
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• src/hg/htdocs/goldenPath/hgText.html
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• src/hg/htdocs/goldenPath/hgTracks.html
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• src/hg/htdocs/goldenPath/labs.html
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• src/hg/htdocs/goldenPath/mapPlots/RHguide.html
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• src/hg/htdocs/goldenPath/newsarch.html
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    GRCh38 default human assembly announcement. Written by DonnaK, edited by JonathanC
    
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    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
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• src/hg/htdocs/goldenPath/pubs.html
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    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
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• src/hg/htdocs/goldenPath/stats.html
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    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
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• src/hg/htdocs/images/Apteryx_australis.jpg
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    photo courtesy of S. Moniotte, refs #16029
    
• src/hg/htdocs/images/Thamnophis_sirtalis.jpg
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    photo courtesy Copyright (C) 2011 Brian Gratwicke http://http://www.flickr.com/photos/briangratwicke/5898713669/ refs #16028
    
• src/hg/htdocs/inc/globalNavBar.inc
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    adding menu entries under genomes and genome browser, refs #16022
    
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    Revert "adding menu entries under genomes and genome browser, refs #16022"
    
    This reverts commit 385f6d8b1f19463d2103cee18970fa833411293f.
    
    Conflicts:
    src/hg/hgTracks/hgTracks.c
    
• src/hg/htdocs/index.html
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    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
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    Ack. Didn't notice that I changed permissions of all those files. Reversing accidental permissions change in last commit, refs #15389
    
• src/hg/htdocs/indexNews.html
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    GRCh38 default human assembly announcement. Written by DonnaK, edited by JonathanC
    
• src/hg/htdocs/jobs.html
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    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
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    Ack. Didn't notice that I changed permissions of all those files. Reversing accidental permissions change in last commit, refs #15389
    
• src/hg/htdocs/kc.html
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    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
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• src/hg/htdocs/knownIssues.html
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    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
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• src/hg/htdocs/license/index.html
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    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
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• src/hg/htdocs/mirror.html
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    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
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    Ack. Didn't notice that I changed permissions of all those files. Reversing accidental permissions change in last commit, refs #15389
    
• src/hg/htdocs/staff.html
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    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
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    Ack. Didn't notice that I changed permissions of all those files. Reversing accidental permissions change in last commit, refs #15389
    
• src/hg/htdocs/style/nice_menu.css
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    adding menu entries under genomes and genome browser, refs #16022
    
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    Revert "adding menu entries under genomes and genome browser, refs #16022"
    
    This reverts commit 385f6d8b1f19463d2103cee18970fa833411293f.
    
    Conflicts:
    src/hg/hgTracks/hgTracks.c
    
• src/hg/htdocs/template.html
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    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
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    Ack. Didn't notice that I changed permissions of all those files. Reversing accidental permissions change in last commit, refs #15389
    
• src/hg/htdocs/training/index.html
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    adding ULouisville workshop. dropping Max Planck, now half complete
    
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    dropping completed Munich workshop
    
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    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
• src/hg/htdocs/training/trainingMap.html
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    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
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    Ack. Didn't notice that I changed permissions of all those files. Reversing accidental permissions change in last commit, refs #15389
    
• src/hg/htdocs/training/vids/index.html
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    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
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    Ack. Didn't notice that I changed permissions of all those files. Reversing accidental permissions change in last commit, refs #15389
    
• src/hg/htdocs/util.html
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    Removing unnecessary includes now that hgMenuBar exists, refs #15389
    
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    Ack. Didn't notice that I changed permissions of all those files. Reversing accidental permissions change in last commit, refs #15389
    
• src/hg/inc/cart.h
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    libifying cartGetPosition because this code is needed twice, once in
    hgTracks and also in cart.c for setting the page title. refs #16022,
    note 18
    
• src/hg/js/jquery.plugins.js
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    adding menu entries under genomes and genome browser, refs #16022
    
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    Revert "adding menu entries under genomes and genome browser, refs #16022"
    
    This reverts commit 385f6d8b1f19463d2103cee18970fa833411293f.
    
    Conflicts:
    src/hg/hgTracks/hgTracks.c
    
• src/hg/lib/cart.c
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    libifying cartGetPosition because this code is needed twice, once in
    hgTracks and also in cart.c for setting the page title. refs #16022,
    note 18
    
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    make the "genome" keyword result in the web code setting the position to the default position # no redmine
    
• src/hg/lib/customPp.c
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    allowing auto-creating of track line from local files, refs #16011
    
• src/hg/lib/hAnno.c
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    Oops, was forgetting to use the right database for wiggle custom tracks (thanks Matt!). fixes #16037
    
• src/hg/lib/hgFind.c
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    Fixed hgsid issue in hgGateway, refs #16031
    
• src/hg/makeDb/doc/ce11/initialBuild.txt
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    done with browser and in the pushQ refs #15209
    
• src/hg/makeDb/doc/ce11/lastzRuns.txt
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    run up self lastz refs refs #15209
    
• src/hg/makeDb/schema/all.joiner
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    Adding tablesIgnored entries for cnvDevDelay track, refs #9391
    
• src/hg/makeDb/trackDb/anopheles/anoGam1/anoEstNcl.html
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    Updating links on A gambiae track description pages
    
• src/hg/makeDb/trackDb/anopheles/anoGam1/anoEstTcl.html
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    Updating links on A gambiae track description pages
    
• src/hg/makeDb/trackDb/contrastGene.html
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    Updating links on rat (rn4) track description pages
    
• src/hg/makeDb/trackDb/ferret/musFur1/description.html
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    Updates to various assembly gateway description pages
    
• src/hg/makeDb/trackDb/human/hg38/defaultPriority.ra
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    Turning off some hg38 default tracks
    
• src/hg/makeDb/trackDb/human/hg38/trackDb.20way.ra
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    reorder slightly to match phylo tree image, the distances are essentially identically in this reorder so it is not different, just more convenient refs #14560
    
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
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    Turning off some hg38 default tracks
    
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    Turning off stsMap by default
    
• src/hg/makeDb/trackDb/human/trackDb.ra
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    Added search rules for CNV Developmental Delay track; refs #9391
    
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    Added shortCircuit values to CNV Developmental Delay search stanzas; refs #9391
    
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    Changed shortCircuit to semiShortCircuit for CNV Developmental Delay search rules; refs #9391
    
• src/hg/makeDb/trackDb/makefile
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    order DBS in alpha order, keep them that way refs #16028
    
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    Adding thaSir1 entry to trackDb makefile, refs #16028
    
• src/hg/makeDb/trackDb/marmoset/calJac3/bacEnds.html
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    Updating links on marmoset (calJac3) track description page
    
• src/hg/makeDb/trackDb/mgcFullMrna.html
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    Updating links on rat (rn4) track description pages
    
• src/hg/makeDb/trackDb/mouse/trackDb.ra
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    Updating hgc links for mouse IKMC Genes track
    
• src/hg/makeDb/trackDb/pubs.html
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    Updating links on rat (rn4) track description pages
    
• src/hg/makeDb/trackDb/reptiles/thaSir1/description.html
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    Adding trackDb.ra files for thaSir1, refs #16028
    
• src/hg/makeDb/trackDb/reptiles/thaSir1/gap.html
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    Adding trackDb.ra files for thaSir1, refs #16028
    
• src/hg/makeDb/trackDb/reptiles/thaSir1/gold.html
  • lines changed 33, context: html, text, full: html, text
    Adding trackDb.ra files for thaSir1, refs #16028
    
• src/hg/makeDb/trackDb/reptiles/thaSir1/trackDb.ra
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    Adding trackDb.ra files for thaSir1, refs #16028
    
• src/hg/makeDb/trackDb/shrew/sorAra2/description.html
  • lines changed 1, context: html, text, full: html, text
    Updates to various assembly gateway description pages
    
• src/hg/makeDb/trackDb/wallaby/macEug2/description.html
  • lines changed 1, context: html, text, full: html, text
    Updates to various assembly gateway description pages
    
• src/hg/makeDb/trackDb/worm/ce11/trackDb.ra
  • lines changed 12, context: html, text, full: html, text
    adding chainSelf refs #15209
    
• src/hg/makeDb/trackDb/zebrafish/UMassChIP-Seq.html
  • lines changed 1, context: html, text, full: html, text
    Changing link on zebrafish (danRer5) track description page
    
• src/hg/mouseStuff/chainMergeSort/chainMergeSort.c
  • lines changed 18, context: html, text, full: html, text
    switch from using makeTempName to rTempName for creating temporary
    files. If a -tempDir options was specified, makeTempName would stick a
    `./' in front of the tempDir, resulting in a directory that doesn't
    exist. Also change file path arrays to use define rather than fixed
    number. (no redmine)
    
• src/hg/utils/otto/decipher/buildDecipher
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    a few changes to the decipher otto scripts to make them less verbose
    
• src/hg/utils/otto/decipher/checkDecipher.sh
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    a few changes to the decipher otto scripts to make them less verbose
    
• src/hg/utils/otto/decipher/validateDecipher.sh
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    a few changes to the decipher otto scripts to make them less verbose
    
• src/hg/utils/otto/geneReviews/buildGeneReviews.sh
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    update to the genereview otto scripts # no redmine
    
• src/hg/utils/otto/geneReviews/checkGeneReviews.sh
  • lines changed 2, context: html, text, full: html, text
    update to the genereview otto scripts # no redmine
    
• src/hg/utils/otto/geneReviews/geneReviewsWrapper.sh
  • lines changed 1, context: html, text, full: html, text
    update to the genereview otto scripts # no redmine
    
• src/hg/utils/otto/geneReviews/makefile
  • lines changed 20, context: html, text, full: html, text
    update to the genereview otto scripts # no redmine
    
• src/hg/utils/otto/geneReviews/validateGeneReviews.sh
  • lines changed 1, context: html, text, full: html, text
    update to the genereview otto scripts # no redmine
    
• src/hg/utils/otto/gwas/checkGwas.sh
  • lines changed 12, context: html, text, full: html, text
    updates to the GWAS otto download files # no redmine
    
• src/hg/utils/otto/gwas/expectedColumns.txt
  • lines changed 32, context: html, text, full: html, text
    updates to the GWAS otto download files # no redmine
    
• src/hg/utils/otto/gwas/makefile
  • lines changed 2, context: html, text, full: html, text
    updates to the GWAS otto download files # no redmine
    
• src/hg/utils/otto/gwas/perlParser.pl
  • lines changed 18, context: html, text, full: html, text
    updates to the GWAS otto download files # no redmine
    
• src/hg/utils/otto/gwas/validateGwas.sh
  • lines changed 3, context: html, text, full: html, text
    updates to the GWAS otto download files # no redmine
    
• src/hg/utils/otto/isca/buildISCA.csh
  • lines changed 43, context: html, text, full: html, text
    new ISCA (ClinGen) process #no redmine
    
• src/hg/utils/otto/isca/checkISCA.sh
  • lines changed 18, context: html, text, full: html, text
    new ISCA (ClinGen) process #no redmine
    
• src/hg/utils/otto/isca/gvfToBed8Attrs.pl
  • lines changed 39, context: html, text, full: html, text
    new ISCA (ClinGen) process #no redmine
    
• src/hg/utils/otto/isca/iscaWrapper.sh
  • lines changed 1, context: html, text, full: html, text
    new ISCA (ClinGen) process #no redmine
    
• src/hg/utils/otto/isca/makefile
  • lines changed 1, context: html, text, full: html, text
    new ISCA (ClinGen) process #no redmine
    
• src/hg/utils/otto/isca/validateISCA.sh
  • lines changed 12, context: html, text, full: html, text
    new ISCA (ClinGen) process #no redmine
    
• src/hg/utils/otto/omim/buildOmimTracks.csh
  • lines changed 4, context: html, text, full: html, text
    added hg38 support to OMIM otto scripts. This has actually been
    happening for a while, but I hadn't checked in the code. no redmine
    
• src/hg/utils/otto/omim/checkOmim.sh
  • lines changed 18, context: html, text, full: html, text
    added hg38 support to OMIM otto scripts. This has actually been
    happening for a while, but I hadn't checked in the code. no redmine
    
• src/hg/utils/otto/omim/checkOmimUpload.sh
  • lines changed 1, context: html, text, full: html, text
    added hg38 support to OMIM otto scripts. This has actually been
    happening for a while, but I hadn't checked in the code. no redmine
    
  • lines changed 17, context: html, text, full: html, text
    update OMIM upload script # no redmine
    
• src/hg/utils/otto/omim/doOmimAv/makefile
  • lines changed 2, context: html, text, full: html, text
    added hg38 support to OMIM otto scripts. This has actually been
    happening for a while, but I hadn't checked in the code. no redmine
    
• src/hg/utils/otto/omim/doOmimGene2/makefile
  • lines changed 2, context: html, text, full: html, text
    added hg38 support to OMIM otto scripts. This has actually been
    happening for a while, but I hadn't checked in the code. no redmine
    
• src/hg/utils/otto/omim/doOmimGeneSymbols/makefile
  • lines changed 2, context: html, text, full: html, text
    added hg38 support to OMIM otto scripts. This has actually been
    happening for a while, but I hadn't checked in the code. no redmine
    
• src/hg/utils/otto/omim/doOmimLocation/makefile
  • lines changed 2, context: html, text, full: html, text
    added hg38 support to OMIM otto scripts. This has actually been
    happening for a while, but I hadn't checked in the code. no redmine
    
• src/inc/cgi_build_rules.mk
  • lines changed 15, context: html, text, full: html, text
    adding a variable CGI-BIN_DEST that is either CGI-BIN_USER or
    CGI-BIN_BETA or CGI-BIN, depending on how make was called.
    This should avoid the triplicated rules we have everywhere.
    It doesn't work when one wants to run "make alpha beta my" but
    I think we never do that.
    Using this to copy an .ra file to the cgi-bin directory. refs #15113
    
• src/inc/net.h
  • lines changed 3, context: html, text, full: html, text
    fixed so that redir does not store params like password and byterange. Instead, I made a function in net.c to do it and now call it to apply those extra params later at runtime. This is both more secure and correct.
    
• src/lib/annoStreamBigWig.c
  • lines changed 3, context: html, text, full: html, text
    Oops, forgot to check whether a region search had no results - thx Matt! fixes #16038
    
• src/lib/net.c
  • lines changed 44, context: html, text, full: html, text
    fixed so that redir does not store params like password and byterange. Instead, I made a function in net.c to do it and now call it to apply those extra params later at runtime. This is both more secure and correct.
    
  • lines changed 1, context: html, text, full: html, text
    This extra condition has been missing since 2011-10-21.
    
• src/lib/udc.c
  • lines changed 63, context: html, text, full: html, text
    Initial checkin of changes for cached udc redirect support.
    
  • lines changed 40, context: html, text, full: html, text
    Using more efficient redirect method. Because the net functions do not make it easy to use HEAD instead of GET and save the header lines in a hash, without some major reworking of net.c, this is the best we can do.
    
  • lines changed 28, context: html, text, full: html, text
    fixed so that redir does not store params like password and byterange. Instead, I made a function in net.c to do it and now call it to apply those extra params later at runtime. This is both more secure and correct.
    
  • lines changed 67, context: html, text, full: html, text
    optimize code to check the old value and see if there is any change, before just writing the new redir value. Also moved the code into a new subroutine
    
  • lines changed 2, context: html, text, full: html, text
    Fixes mayOpen for transparent case when the file does not exist. Do not errAbort, return NULL instead. Hiram ran into this with his wiggle utilities.
    
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v323 preview1 refs #15948
    
• src/utils/qa/weeklybld/doNewBranch.csh
  • lines changed 1, context: html, text, full: html, text
    correct email address to local users refs #15948
    

• lines changed: 1712
• files changed: 316