All File Changes

v319_preview to v319_preview2 (2015-06-29 to 2015-07-06) v319

• src/hg/hgIntegrator/hgIntegrator.c
  • lines changed 6, context: html, text, full: html, text
    For AJAX file upload, modern browsers support the FormData API. In order to
    support older browsers (esp IE), I was instead using the JQuery plugin Bifrost
    which uses a hidden iframe to submit a form and read the result of the query.
    That worked on modern browsers too -- except IE11. So, if a browser supports
    FormData, use that; otherwise fall back on the Bifrost plugin.
    Meanwhile, I clean up UserRegionsMixin.js a bit by moving the file uploading
    code into cart.js and moving the JQuery selecting code into UserRegions.jsx.
    fixes #15609
    
• src/hg/hgTracks/hgTracks.c
  • lines changed 4, context: html, text, full: html, text
    put the database name in trackLog output
    
• src/hg/htdocs/FAQ/FAQblat.html
  • lines changed 5, context: html, text, full: html, text
    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/FAQ/FAQcite.html
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    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/FAQ/FAQcustom.html
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    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/FAQ/FAQdisplay.html
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    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/FAQ/FAQdownloads.html
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    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/FAQ/FAQformat.html
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    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/FAQ/FAQlicense.html
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    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/FAQ/FAQlink.html
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    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/FAQ/FAQmaillist.html
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    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/FAQ/FAQreleases.html
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    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/FAQ/FAQtables.html
  • lines changed 5, context: html, text, full: html, text
    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/FAQ/FAQtracks.html
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    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/FAQ/index.html
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    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/Neandertal/index.html
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    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/admin/403.html
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    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/admin/404.html
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    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/admin/500.html
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    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/admin/cvs.html
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    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/admin/git.html
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    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/admin/index.html
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    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/admin/jk-install.html
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    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/admin/mirror.html
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    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/cite.html
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    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/conditions.html
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    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/contacts.html
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    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/goldenPath/certificates/certificate_hg15.html
  • lines changed 5, context: html, text, full: html, text
    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/goldenPath/certificates/certificate_hg16.html
  • lines changed 5, context: html, text, full: html, text
    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/goldenPath/certificates/index.html
  • lines changed 5, context: html, text, full: html, text
    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 5, context: html, text, full: html, text
    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/goldenPath/datorg.html
  • lines changed 5, context: html, text, full: html, text
    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/goldenPath/gbdDescriptions.html
  • lines changed 5, context: html, text, full: html, text
    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/goldenPath/gbdDescriptionsOld.html
  • lines changed 5, context: html, text, full: html, text
    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/goldenPath/help/axt.html
  • lines changed 5, context: html, text, full: html, text
    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/goldenPath/help/bam.html
  • lines changed 5, context: html, text, full: html, text
    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/goldenPath/help/bedgraph.html
  • lines changed 5, context: html, text, full: html, text
    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/goldenPath/help/bigBed.html
  • lines changed 5, context: html, text, full: html, text
    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/goldenPath/help/bigGenePred.html
  • lines changed 5, context: html, text, full: html, text
    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/goldenPath/help/bigWig.html
  • lines changed 5, context: html, text, full: html, text
    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/goldenPath/help/blatSpec.html
  • lines changed 5, context: html, text, full: html, text
    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/goldenPath/help/chain.html
  • lines changed 5, context: html, text, full: html, text
    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/goldenPath/help/chimera.html
  • lines changed 5, context: html, text, full: html, text
    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/goldenPath/help/customColumn.html
  • lines changed 5, context: html, text, full: html, text
    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/goldenPath/help/customTrack.html
  • lines changed 5, context: html, text, full: html, text
    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/goldenPath/help/fileSearch.html
  • lines changed 5, context: html, text, full: html, text
    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/goldenPath/help/ftp.html
  • lines changed 5, context: html, text, full: html, text
    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/goldenPath/help/gbib.html
  • lines changed 5, context: html, text, full: html, text
    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/goldenPath/help/geneSearchBox.html
  • lines changed 5, context: html, text, full: html, text
    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/goldenPath/help/genomeEuro.html
  • lines changed 5, context: html, text, full: html, text
    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/goldenPath/help/haplotypes.html
  • lines changed 5, context: html, text, full: html, text
    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/goldenPath/help/hg18ToHg19LiftOver.html
  • lines changed 5, context: html, text, full: html, text
    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/goldenPath/help/hgBamTrackHelp.html
  • lines changed 5, context: html, text, full: html, text
    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/goldenPath/help/hgBaseLabel.html
  • lines changed 5, context: html, text, full: html, text
    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/goldenPath/help/hgCodonColoring.html
  • lines changed 5, context: html, text, full: html, text
    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/goldenPath/help/hgCodonColoringMrna.html
  • lines changed 5, context: html, text, full: html, text
    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/goldenPath/help/hgGenomeHelp.html
  • lines changed 5, context: html, text, full: html, text
    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/goldenPath/help/hgIndelDisplay.html
  • lines changed 5, context: html, text, full: html, text
    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/goldenPath/help/hgIntegratorHelp.html
  • lines changed 5, context: html, text, full: html, text
    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/goldenPath/help/hgNearHelp.html
  • lines changed 5, context: html, text, full: html, text
    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/goldenPath/help/hgRegMotifHelp.html
  • lines changed 5, context: html, text, full: html, text
    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/goldenPath/help/hgSessionHelp.html
  • lines changed 5, context: html, text, full: html, text
    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/goldenPath/help/hgTablesHelp.html
  • lines changed 5, context: html, text, full: html, text
    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/goldenPath/help/hgTextHelp.html
  • lines changed 5, context: html, text, full: html, text
    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 5, context: html, text, full: html, text
    Adding CGI menubar to many static pages, refs #15389
    
  • lines changed 25, context: html, text, full: html, text
    Add help doc for new Track Hub version doc and hubCheck. refs #10015
    
• src/hg/htdocs/goldenPath/help/hgTracksHelp.html
  • lines changed 5, context: html, text, full: html, text
    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/goldenPath/help/hgVcfTrackHelp.html
  • lines changed 5, context: html, text, full: html, text
    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/goldenPath/help/hgWiggleTrackHelp.html
  • lines changed 5, context: html, text, full: html, text
    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/goldenPath/help/hubQuickStart.html
  • lines changed 5, context: html, text, full: html, text
    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html
  • lines changed 5, context: html, text, full: html, text
    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/goldenPath/help/hubQuickStartGroups.html
  • lines changed 5, context: html, text, full: html, text
    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/goldenPath/help/image.html
  • lines changed 5, context: html, text, full: html, text
    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/goldenPath/help/index.html
  • lines changed 5, context: html, text, full: html, text
    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/goldenPath/help/iupac.html
  • lines changed 5, context: html, text, full: html, text
    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/goldenPath/help/liftOver.html
  • lines changed 5, context: html, text, full: html, text
    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/goldenPath/help/multiView.html
  • lines changed 5, context: html, text, full: html, text
    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/goldenPath/help/mysql.html
  • lines changed 5, context: html, text, full: html, text
    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/goldenPath/help/net.html
  • lines changed 5, context: html, text, full: html, text
    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/goldenPath/help/phastCons.html
  • lines changed 5, context: html, text, full: html, text
    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/goldenPath/help/qValue.html
  • lines changed 5, context: html, text, full: html, text
    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/goldenPath/help/query.html
  • lines changed 5, context: html, text, full: html, text
    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/goldenPath/help/sessions.html
  • lines changed 5, context: html, text, full: html, text
    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/goldenPath/help/trackDb/makefile
  • lines changed 3, context: html, text, full: html, text
    Create version 1 track hub spec (getting ready for release). refs #10015
    
  • lines changed 9, context: html, text, full: html, text
    Moving from soft link process to one more file for release of trackDb version updates
    
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.css
  • lines changed 3, context: html, text, full: html, text
    Brighten level colors a bit, prompted by WashU input. refs #10015
    
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
  • lines changed 14, context: html, text, full: html, text
    A few more hard-coded menus to fix, refs #15389
    
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.html
  • lines changed 1, context: html, text, full: html, text
    Moving from soft link process to one more file for release of trackDb version updates
    
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v0.html
  • lines changed 14, context: html, text, full: html, text
    A few more hard-coded menus to fix, refs #15389
    
  • lines changed 1, context: html, text, full: html, text
    Fix misspelling. refs #10015
    
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v1.html
  • lines changed 789, context: html, text, full: html, text
    Create version 1 track hub spec (getting ready for release). refs #10015
    
  • lines changed 1, context: html, text, full: html, text
    Fix misspelling. refs #10015
    
• src/hg/htdocs/goldenPath/help/trackDescriptions.html
  • lines changed 5, context: html, text, full: html, text
    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/goldenPath/help/trackSearch.html
  • lines changed 5, context: html, text, full: html, text
    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/goldenPath/help/trix.html
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    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/goldenPath/help/twoBit.html
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    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/goldenPath/help/vcf.html
  • lines changed 5, context: html, text, full: html, text
    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/goldenPath/help/wiggle.html
  • lines changed 5, context: html, text, full: html, text
    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/goldenPath/hgText.html
  • lines changed 5, context: html, text, full: html, text
    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/goldenPath/hgTracks.html
  • lines changed 5, context: html, text, full: html, text
    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/goldenPath/labs.html
  • lines changed 5, context: html, text, full: html, text
    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/goldenPath/mapPlots/RHguide.html
  • lines changed 5, context: html, text, full: html, text
    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 46, context: html, text, full: html, text
    added gencode announcement to archives
    
  • lines changed 56, context: html, text, full: html, text
    moved gencode announcement
    
  • lines changed 1, context: html, text, full: html, text
    changed https to http
    
  • lines changed 5, context: html, text, full: html, text
    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 5, context: html, text, full: html, text
    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/goldenPath/stats.html
  • lines changed 5, context: html, text, full: html, text
    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/index.html
  • lines changed 4, context: html, text, full: html, text
    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/indexNews.html
  • lines changed 103, context: html, text, full: html, text
    added gencode genes announcement to homepage
    
  • lines changed 1, context: html, text, full: html, text
    removed extra <hr> tag
    
  • lines changed 1, context: html, text, full: html, text
    changed https to http
    
• src/hg/htdocs/jobs.html
  • lines changed 5, context: html, text, full: html, text
    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/kc.html
  • lines changed 5, context: html, text, full: html, text
    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/knownIssues.html
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    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/license/index.html
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    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/mirror.html
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    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/staff.html
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    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/template.html
  • lines changed 5, context: html, text, full: html, text
    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/training/index.html
  • lines changed 20, context: html, text, full: html, text
    Adding CGI menubar to many static pages, refs #15389
    
  • lines changed 17, context: html, text, full: html, text
    adding a workshop. dropping completed workshop
    
  • lines changed 1, context: html, text, full: html, text
    corrected spelling
    
• src/hg/htdocs/training/vids/index.html
  • lines changed 5, context: html, text, full: html, text
    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/htdocs/util.html
  • lines changed 5, context: html, text, full: html, text
    Adding CGI menubar to many static pages, refs #15389
    
• src/hg/js/model/lib/ImModel.js
  • lines changed 16, context: html, text, full: html, text
    For AJAX file upload, modern browsers support the FormData API. In order to
    support older browsers (esp IE), I was instead using the JQuery plugin Bifrost
    which uses a hidden iframe to submit a form and read the result of the query.
    That worked on modern browsers too -- except IE11. So, if a browser supports
    FormData, use that; otherwise fall back on the Bifrost plugin.
    Meanwhile, I clean up UserRegionsMixin.js a bit by moving the file uploading
    code into cart.js and moving the JQuery selecting code into UserRegions.jsx.
    fixes #15609
    
• src/hg/js/model/lib/UserRegionsMixin.js
  • lines changed 18, context: html, text, full: html, text
    For AJAX file upload, modern browsers support the FormData API. In order to
    support older browsers (esp IE), I was instead using the JQuery plugin Bifrost
    which uses a hidden iframe to submit a form and read the result of the query.
    That worked on modern browsers too -- except IE11. So, if a browser supports
    FormData, use that; otherwise fall back on the Bifrost plugin.
    Meanwhile, I clean up UserRegionsMixin.js a bit by moving the file uploading
    code into cart.js and moving the JQuery selecting code into UserRegions.jsx.
    fixes #15609
    
• src/hg/js/model/lib/cart.js
  • lines changed 40, context: html, text, full: html, text
    For AJAX file upload, modern browsers support the FormData API. In order to
    support older browsers (esp IE), I was instead using the JQuery plugin Bifrost
    which uses a hidden iframe to submit a form and read the result of the query.
    That worked on modern browsers too -- except IE11. So, if a browser supports
    FormData, use that; otherwise fall back on the Bifrost plugin.
    Meanwhile, I clean up UserRegionsMixin.js a bit by moving the file uploading
    code into cart.js and moving the JQuery selecting code into UserRegions.jsx.
    fixes #15609
    
• src/hg/js/react/lib/UserRegions.jsx
  • lines changed 44, context: html, text, full: html, text
    For AJAX file upload, modern browsers support the FormData API. In order to
    support older browsers (esp IE), I was instead using the JQuery plugin Bifrost
    which uses a hidden iframe to submit a form and read the result of the query.
    That worked on modern browsers too -- except IE11. So, if a browser supports
    FormData, use that; otherwise fall back on the Bifrost plugin.
    Meanwhile, I clean up UserRegionsMixin.js a bit by moving the file uploading
    code into cart.js and moving the JQuery selecting code into UserRegions.jsx.
    fixes #15609
    
• src/hg/lib/mafGene.c
  • lines changed 13, context: html, text, full: html, text
    fix some problems in the mafGene library where exons that had
    non-contiguous maf blocks within them weren't be dealt with properly
    
• src/hg/lib/pubsBlat.as
  • lines changed 11, context: html, text, full: html, text
    Updating pubsBlat.as to reflect current pubsBlat table, and adding
    pubsBlat2.as to reflect Max's newer schema with more extra fields.
    refs #15610
    
• src/hg/lib/pubsBlat2.as
  • lines changed 30, context: html, text, full: html, text
    Updating pubsBlat.as to reflect current pubsBlat table, and adding
    pubsBlat2.as to reflect Max's newer schema with more extra fields.
    refs #15610
    
• src/hg/lib/userRegions.c
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    Oops, using sizeof instead of ArraySize was causing a SEGV when pasting
    bogus text with more than 5 words per line into the user regions box.
    
• src/hg/makeDb/doc/ce11/initialBuild.txt
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    correct comments on liftOver refs #15209
    
• src/hg/makeDb/doc/ce11/lastzRuns.txt
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    running up melHap1 lastz refs #15209
    
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    running up caeAng2 and melInc2 lastz refs #15209
    
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    finished with melHap1 caeAng2 melInc2 and running up panRed1 refs #15209
    
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    running up priPac3 refs #15209
    
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    running up cb4 and caePb3 refs #15209
    
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    finished up with panRed1 priPac3 cb4 caePb3 refs #15209
    
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    done with caeRem4 refs #15209
    
• src/hg/makeDb/doc/hg17.txt
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    adding haplotypeLocations table for hg17 using BLAT/Self-chain to place them. (only 2 haplotypes in hg17).
    
• src/hg/makeDb/doc/hg18.txt
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    documenting hg18.haplotypeLocationsEnsembl
    
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    adding haplotypeLocations table for hg17 using BLAT/Self-chain to place them. (only 2 haplotypes in hg17).
    
• src/hg/makeDb/doc/hg38/multiz20way.txt
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    update the CDS FASTA alignments for hg38
    
• src/hg/makeDb/doc/ucscGenes/hg38.ucscGenes16.sh
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    wrap-up of GENCODE Basic gene set
    
• src/hg/makeDb/doc/worms/caeAng2.txt
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    initial browser instructions refs #15209
    
• src/hg/makeDb/doc/worms/melInc2.txt
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    initial browser instructions refs #15209
    
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    done with masking refs #15209
    
• src/hg/makeDb/doc/worms/panRed1.txt
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    running up windowMasker refs #15209
    
• src/hg/makeDb/doc/worms/priPac3.txt
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    running up windowMasker refs #15209
    
• src/hg/makeDb/genbank/etc/genbank.conf
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    Added priPac3 - P. pacificus refs #15209
    
• src/hg/makeDb/makeGencodeKnownGene/makeGencodeKnownGene.c
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    code used to build the GENCODE Basic track
    
• src/hg/makeDb/trackDb/human/hg38/knownGene.alpha.html
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    made a few corrections per code review #15628
    
• src/hg/makeDb/trackDb/human/hg38/primateChainNet.html
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    Adding hg38-specific primate chain/net page, so hg19 values aren't being reported where they're not appropriate
    
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    A few edits suggested by Donna
    
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg.ra
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    Per Kate, reverted her previous change; refs #14353
    
• src/hg/makeDb/trackDb/makefile
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    adding melInc2 refs #15209
    
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    adding priPac3 to the build refs #15209
    
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    adding panRed1 Panagrellus redivivus to the build refs #15209
    
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    adding haeCon2 to the build refs #15209
    
• src/hg/makeDb/trackDb/worm/caeAng2/trackDb.ra
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    adding search rule for gold;
    
• src/hg/makeDb/trackDb/worm/haeCon2/description.html
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    adding haeCon2 to the build refs #15209
    
• src/hg/makeDb/trackDb/worm/haeCon2/gap.html
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    adding haeCon2 to the build refs #15209
    
• src/hg/makeDb/trackDb/worm/haeCon2/gold.html
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    adding haeCon2 to the build refs #15209
    
• src/hg/makeDb/trackDb/worm/haeCon2/trackDb.ra
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    adding haeCon2 to the build refs #15209
    
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    adding gold table search rule refs #15209
    
• src/hg/makeDb/trackDb/worm/melInc2/description.html
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    initial files from makeGenomeDb.pl refs #15209
    
• src/hg/makeDb/trackDb/worm/melInc2/gap.html
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    initial files from makeGenomeDb.pl refs #15209
    
• src/hg/makeDb/trackDb/worm/melInc2/gold.html
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    initial files from makeGenomeDb.pl refs #15209
    
• src/hg/makeDb/trackDb/worm/melInc2/trackDb.ra
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    initial files from makeGenomeDb.pl refs #15209
    
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    adding gold table search rule refs #15209
    
• src/hg/makeDb/trackDb/worm/panRed1/description.html
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    adding panRed1 Panagrellus redivivus to the build refs #15209
    
• src/hg/makeDb/trackDb/worm/panRed1/gap.html
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    adding panRed1 Panagrellus redivivus to the build refs #15209
    
• src/hg/makeDb/trackDb/worm/panRed1/gold.html
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    adding panRed1 Panagrellus redivivus to the build refs #15209
    
• src/hg/makeDb/trackDb/worm/panRed1/trackDb.ra
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    adding panRed1 Panagrellus redivivus to the build refs #15209
    
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    adding gold track search rule refs #15209
    
• src/hg/makeDb/trackDb/worm/priPac3/description.html
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    adding priPac3 to the build refs #15209
    
• src/hg/makeDb/trackDb/worm/priPac3/gap.html
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    adding priPac3 to the build refs #15209
    
• src/hg/makeDb/trackDb/worm/priPac3/gold.html
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    adding priPac3 to the build refs #15209
    
• src/hg/makeDb/trackDb/worm/priPac3/trackDb.ra
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    adding priPac3 to the build refs #15209
    
  • lines changed 5, context: html, text, full: html, text
    adding gold table search rule refs #15209
    
• src/hg/mouseStuff/netStats/netStats.c
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    removed unuseful netStats output to of chroms to stdout, seems to be spurious debug message (no redmine)
    
• src/hg/utils/automation/doRepeatMasker.pl
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    do not always have all classes to construct bigBed refs #15209
    
• src/hg/utils/checkStaticHtmlLinks/checkStaticHtmlLinks.c
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    Fixes requested by Angie in codereview
    
• src/hg/utils/hubCheck/hubCheck.c
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    Retire temporary help message. This makes version check options more visible. refs #10015
    
• src/hg/utils/paSNP/paSNP.c
  • lines changed 4, context: html, text, full: html, text
    fix some problems in the mafGene library where exons that had
    non-contiguous maf blocks within them weren't be dealt with properly
    
• src/hg/visiGene/hgVisiGene/fullTextExperiment.c
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    Fixes RM#12038. Accidentally lost the wildcard part of an SQL query in visiSearch.c which affected contributor and other searches.
    
• src/hg/visiGene/hgVisiGene/printCaption.c
  • lines changed 1, context: html, text, full: html, text
    Fixes RM#12038. Accidentally lost the wildcard part of an SQL query in visiSearch.c which affected contributor and other searches.
    
• src/hg/visiGene/hgVisiGene/visiSearch.c
  • lines changed 10, context: html, text, full: html, text
    Fixes RM#12038. Accidentally lost the wildcard part of an SQL query in visiSearch.c which affected contributor and other searches.
    
• src/inc/jsonParse.h
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    Added support for null to jsonParse, except for when we expect to find
    an int, float or boolean.
    
• src/lib/jsonParse.c
  • lines changed 97, context: html, text, full: html, text
    Added support for null to jsonParse, except for when we expect to find
    an int, float or boolean.
    
• src/test/buildTableDescriptions.pl
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    Don't expect to find autoSql for metaDb tables or big* (fileName-only) tables.
    
• src/utils/qa/weeklybld/buildEnv.csh
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    v319 preview2 refs #15624
    

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• files changed: 193