All File Changes

v327_base to v328_preview (2016-01-11 to 2016-01-18) v328

• src/browserbox/root/updateBrowser.sh
  • lines changed 33, context: html, text, full: html, text
    fixing virtualbox auto-detect and skipping inno-db to save RAM, refs #16616
    
  • lines changed 8, context: html, text, full: html, text
    adding innodb support again, refs #16616
    
  • lines changed 1, context: html, text, full: html, text
    adding target=_blank for the gbib data folder link in the menu, refs #16616
    
  • lines changed 7, context: html, text, full: html, text
    reducing R's footprint a bit in the GBiB, refs #16616
    
  • lines changed 7, context: html, text, full: html, text
    not cleaning ~/bin anymore because Hiram. refs #16616
    
• src/hg/cirm/cdw/lib/cdwLib.c
  • lines changed 11, context: html, text, full: html, text
    get cdwLib to use htslib
    
• src/hg/cirm/cdw/wrangle/addMetaDataToJson/addMetaDataToJson
  • lines changed 53, context: html, text, full: html, text
    Refactoring this code, it no longer touches the .html files, refs# 16216
    
• src/hg/cirm/cdw/wrangle/addMetaDataToJson/tests/makefile
  • lines changed 5, context: html, text, full: html, text
    Adding test cases for a program in the visualization pipeline. refs #16216
    
  • lines changed 1, context: html, text, full: html, text
    Test files for the addMetaDataToJson script, refs# 16182
    
• src/hg/cirm/cdw/wrangle/addMetaDataToJson/tests/meta.tab
  • lines changed 9, context: html, text, full: html, text
    Adding test cases for a program in the visualization pipeline. refs #16216
    
• src/hg/cirm/cdw/wrangle/addMetaDataToJson/tests/testClusters.html
  • lines changed 209, context: html, text, full: html, text
    Adding test cases for a program in the visualization pipeline. refs #16216
    
  • lines changed 217, context: html, text, full: html, text
    Test files for the addMetaDataToJson script, refs# 16182
    
• src/hg/cirm/cdw/wrangle/addMetaDataToJson/tests/testClusters.json
  • lines changed 36, context: html, text, full: html, text
    Adding test cases for a program in the visualization pipeline. refs #16216
    
  • lines changed 15, context: html, text, full: html, text
    Test files for the addMetaDataToJson script, refs# 16182
    
• src/hg/expMatrixToJson/expMatrixToJson.c
  • lines changed 255, context: html, text, full: html, text
    fixing up the javascript that is printed, added some options to the visualization. refs #16216
    
  • lines changed 245, context: html, text, full: html, text
    Heavy refactoring to the .html output, now all javascript is in the file d3.dendrograms.js, refs# 16216
    
• src/hg/expMatrixToJson/tests/makefile
  • lines changed 3, context: html, text, full: html, text
    Added a makefile and testing conditions for the matrix to visualization. Also a file to explain the expected cluster values. refs #16216
    
  • lines changed 8, context: html, text, full: html, text
    Added some makefile options to make testing easier, refs #16216
    
• src/hg/expMatrixToJson/tests/matrix.mx
  • lines changed 2, context: html, text, full: html, text
    Added a makefile and testing conditions for the matrix to visualization. Also a file to explain the expected cluster values. refs #16216
    
• src/hg/expMatrixToJson/tests/matrixResults.txt
  • lines changed 7, context: html, text, full: html, text
    Added a makefile and testing conditions for the matrix to visualization. Also a file to explain the expected cluster values. refs #16216
    
• src/hg/hgTables/bam.c
  • lines changed 6, context: html, text, full: html, text
    yet more work on support CRAM under htslib
    
• src/hg/hgTracks/bamTrack.c
  • lines changed 6, context: html, text, full: html, text
    yet more work on support CRAM under htslib
    
• src/hg/hgTracks/hgTracks.c
  • lines changed 2, context: html, text, full: html, text
    commenting out for production
    
• src/hg/hgVai/hgVai.c
  • lines changed 1, context: html, text, full: html, text
    Added the capability to substitute $hgsid from the cart in a help file
    included by webIncludeHelpFileSubst, for internal links.
    Improved the description of hgVai Transcript Status options.
    refs #16502
    
• src/hg/hgc/bamClick.c
  • lines changed 6, context: html, text, full: html, text
    yet more work on support CRAM under htslib
    
• src/hg/hgc/hgc.c
  • lines changed 1, context: html, text, full: html, text
    Fixes problem with link. The variable had gotten renamed from singleHaplo which is confusing, to singleAltHaplo which is clearer.
    
• src/hg/htdocs/goldenPath/help/hgVaiHelpText.html
  • lines changed 17, context: html, text, full: html, text
    Adding description of dbNSFP v3.1a for hg38, including new scores from VEST.
    refs #16503
    
  • lines changed 25, context: html, text, full: html, text
    Adding minimal explanation of transcript status options.
    refs #16502
    
  • lines changed 15, context: html, text, full: html, text
    Added the capability to substitute $hgsid from the cart in a help file
    included by webIncludeHelpFileSubst, for internal links.
    Improved the description of hgVai Transcript Status options.
    refs #16502
    
• src/hg/htdocs/goldenPath/help/multiRegionHelp.html
  • lines changed 105, context: html, text, full: html, text
    Replacing image with non highlight and fix of doc suggestions, refs #16565
    
  • lines changed 18, context: html, text, full: html, text
    Replaced two more pictures and more edits, refs #16565
    
  • lines changed 1, context: html, text, full: html, text
    Typo correction, refs #16565
    
  • lines changed 12, context: html, text, full: html, text
    More small edits, refs #16565
    
  • lines changed 90, context: html, text, full: html, text
    Incorporating changes from Luvinas code review, refs #16565
    
• src/hg/htdocs/goldenPath/help/net.html
  • lines changed 100, context: html, text, full: html, text
    Corrected net help page, refs #14581
    
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 1, context: html, text, full: html, text
    Minor correction based on CR, refs #16640
    
• src/hg/htdocs/images/MultiRegionBED12Example.png
  • lines changed 0, context: html, text, full: html, text
    Committing multi-region pictures to kent src, refs #16565
    
• src/hg/htdocs/images/MultiRegionBEDFileInOrder.png
  • lines changed 0, context: html, text, full: html, text
    Committing multi-region pictures to kent src, refs #16565
    
• src/hg/htdocs/images/MultiRegionBEDFileOutOrder.png
  • lines changed 0, context: html, text, full: html, text
    Committing multi-region pictures to kent src, refs #16565
    
• src/hg/htdocs/images/MultiRegionBEDSearchRedirectMessage.png
  • lines changed 0, context: html, text, full: html, text
    Committing multi-region pictures to kent src, refs #16565
    
• src/hg/htdocs/images/MultiRegionButton.png
  • lines changed 0, context: html, text, full: html, text
    Committing multi-region pictures to kent src, refs #16565
    
• src/hg/htdocs/images/MultiRegionConfigurationWindow.png
  • lines changed 0, context: html, text, full: html, text
    Committing multi-region pictures to kent src, refs #16565
    
• src/hg/htdocs/images/MultiRegionExonPadding.png
  • lines changed 0, context: html, text, full: html, text
    Committing multi-region pictures to kent src, refs #16565
    
  • lines changed 0, context: html, text, full: html, text
    Updating an image in the doc, test, refs #16565
    
• src/hg/htdocs/images/MultiRegionHaplotypeView.png
  • lines changed 0, context: html, text, full: html, text
    Committing multi-region pictures to kent src, refs #16565
    
  • lines changed 0, context: html, text, full: html, text
    Replacing image with non highlight and fix of doc suggestions, refs #16565
    
• src/hg/htdocs/images/MultiRegionHighlighted.png
  • lines changed 0, context: html, text, full: html, text
    Committing multi-region pictures to kent src, refs #16565
    
• src/hg/htdocs/images/MultiRegionMitochondrialPacked.png
  • lines changed 0, context: html, text, full: html, text
    Committing multi-region pictures to kent src, refs #16565
    
• src/hg/htdocs/images/MultiRegionMitochondrialUnpacked.png
  • lines changed 0, context: html, text, full: html, text
    Committing multi-region pictures to kent src, refs #16565
    
• src/hg/htdocs/images/MultiRegionMouseHighlighted.png
  • lines changed 0, context: html, text, full: html, text
    Committing multi-region pictures to kent src, refs #16565
    
• src/hg/htdocs/images/MultiRegionSOD1.png
  • lines changed 0, context: html, text, full: html, text
    Committing multi-region pictures to kent src, refs #16565
    
• src/hg/htdocs/images/MultiRegionXDefault.png
  • lines changed 0, context: html, text, full: html, text
    Replaced two more pictures and more edits, refs #16565
    
• src/hg/htdocs/images/MultiRegionXGeneOnly.png
  • lines changed 0, context: html, text, full: html, text
    Replaced two more pictures and more edits, refs #16565
    
• src/hg/inc/hVarSubst.h
  • lines changed 8, context: html, text, full: html, text
    Added the capability to substitute $hgsid from the cart in a help file
    included by webIncludeHelpFileSubst, for internal links.
    Improved the description of hgVai Transcript Status options.
    refs #16502
    
• src/hg/inc/hgBam.h
  • lines changed 8, context: html, text, full: html, text
    yet more work on support CRAM under htslib
    
• src/hg/inc/web.h
  • lines changed 5, context: html, text, full: html, text
    Added the capability to substitute $hgsid from the cart in a help file
    included by webIncludeHelpFileSubst, for internal links.
    Improved the description of hgVai Transcript Status options.
    refs #16502
    
• src/hg/js/d3.dendrograms.js
  • lines changed 578, context: html, text, full: html, text
    The new home for the visuzlization javascript code, refs# 16468, 16216,16341
    
• src/hg/lib/customTrack.c
  • lines changed 9, context: html, text, full: html, text
    removing a check for 2002-era internet browsers after
    confirmation from Angie. This will allow pasting of local file paths in GBiB or
    mirrors into the custom track box. No redmine.
    
  • lines changed 2, context: html, text, full: html, text
    fixing stupid mistake in previous commit
    
• src/hg/lib/hVarSubst.c
  • lines changed 35, context: html, text, full: html, text
    Added the capability to substitute $hgsid from the cart in a help file
    included by webIncludeHelpFileSubst, for internal links.
    Improved the description of hgVai Transcript Status options.
    refs #16502
    
• src/hg/lib/hgBam.c
  • lines changed 26, context: html, text, full: html, text
    yet more work on support CRAM under htslib
    
• src/hg/lib/web.c
  • lines changed 30, context: html, text, full: html, text
    Added the capability to substitute $hgsid from the cart in a help file
    included by webIncludeHelpFileSubst, for internal links.
    Improved the description of hgVai Transcript Status options.
    refs #16502
    
• src/hg/makeDb/doc/augustusGene.txt
  • lines changed 16, context: html, text, full: html, text
    Commit of files related to gorGor4 assembly release, refs #16220
    
• src/hg/makeDb/doc/gorGor4/initialBuild.txt
  • lines changed 890, context: html, text, full: html, text
    Commit of files related to gorGor4 assembly release, refs #16220
    
• src/hg/makeDb/doc/gorGor4/lastzRuns.txt
  • lines changed 71, context: html, text, full: html, text
    Commit of files related to gorGor4 assembly release, refs #16220
    
• src/hg/makeDb/doc/hg38/hg38.txt
  • lines changed 45, context: html, text, full: html, text
    corrected altSeqLiftOverPsl table contents refs #11681
    
• src/hg/makeDb/doc/hg38/hg38Patch5.txt
  • lines changed 1, context: html, text, full: html, text
    Cleaned up priority settings
    
• src/hg/makeDb/doc/hg38/hg38Patch6.txt
  • lines changed 733, context: html, text, full: html, text
    Files and docs for hg38Patch6, refs #16648
    
  • lines changed 1, context: html, text, full: html, text
    Cleaned up priority settings
    
  • lines changed 1, context: html, text, full: html, text
    Fixed typo in hg38p6 docs, refs #16648
    
• src/hg/makeDb/doc/hg38/patchDescr.pl
  • lines changed 6, context: html, text, full: html, text
    Files and docs for hg38Patch6, refs #16648
    
  • lines changed 1, context: html, text, full: html, text
    Fixed NCBI ftp link in description page script, refs #16648
    
• src/hg/makeDb/schema/all.joiner
  • lines changed 1, context: html, text, full: html, text
    Commit of files related to gorGor4 assembly release, refs #16220
    
  • lines changed 2, context: html, text, full: html, text
    using altLocations in more places than just hg38 now.
    
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 1, context: html, text, full: html, text
    Updating vendor cv.ra vendor link, no redmine
    
• src/hg/makeDb/trackDb/cv/beta/cv.ra
  • lines changed 1, context: html, text, full: html, text
    Updating vendor cv.ra vendor link, no redmine
    
• src/hg/makeDb/trackDb/cv/public/cv.ra
  • lines changed 1, context: html, text, full: html, text
    Updating vendor cv.ra vendor link, no redmine
    
• src/hg/makeDb/trackDb/drosophila/droEre1/description.html
  • lines changed 1, context: html, text, full: html, text
    Minor CR edit, refs #16642
    
• src/hg/makeDb/trackDb/human/chainNetPrimate.ra
  • lines changed 18, context: html, text, full: html, text
    Commit of files related to gorGor4 assembly release, refs #16220
    
• src/hg/makeDb/trackDb/human/hg38/hg38Patch5.html
  • lines changed 351, context: html, text, full: html, text
    Files and docs for hg38Patch6, refs #16648
    
• src/hg/makeDb/trackDb/human/hg38/hg38Patch6.html
  • lines changed 371, context: html, text, full: html, text
    Files and docs for hg38Patch6, refs #16648
    
  • lines changed 2, context: html, text, full: html, text
    Fixed bad link URL, refs #16648
    
• src/hg/makeDb/trackDb/human/hg38/hg38Patch6.ra
  • lines changed 118, context: html, text, full: html, text
    Files and docs for hg38Patch6, refs #16648
    
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Files and docs for hg38Patch6, refs #16648
    
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV24.html
  • lines changed 32, context: html, text, full: html, text
    added APPRIS documentation
    
• src/hg/makeDb/trackDb/mouse/snp142.html
  • lines changed 2, context: html, text, full: html, text
    Minor changes to snp142 track description page, refs #15934
    
• src/hg/makeDb/trackDb/mouse/trackDb.ra
  • lines changed 32, context: html, text, full: html, text
    add search rules for mm10.snp142 #15934
    
• src/inc/bamFile.h
  • lines changed 10, context: html, text, full: html, text
    yet more work on support CRAM under htslib
    
• src/lib/bamFile.c
  • lines changed 51, context: html, text, full: html, text
    yet more work on support CRAM under htslib
    
  • lines changed 2, context: html, text, full: html, text
    a little more tweaking of CRAM support
    
• src/utils/bedCollapse.pl
  • lines changed 12, context: html, text, full: html, text
    fixup usage message to clearly explain what this does and allow stdin as an input argument no redmine
    
• src/utils/bedSingleCover.pl
  • lines changed 55, context: html, text, full: html, text
    similar to bedCollapse.pl but even more condensing of any overlapping items no redmine
    
  • lines changed 4, context: html, text, full: html, text
    add usage note of how to use awk to run up a featureBits measurement no redmine
    
• src/utils/makefile
  • lines changed 1, context: html, text, full: html, text
    adding bedSingleCover.pl to the utils list no redmine
    
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v328 preview1 refs #16513
    
• src/utils/qa/weeklybld/sendLogEmail.pl
  • lines changed 2, context: html, text, full: html, text
    out of test mode send mail to all refs #16513
    
  • lines changed 2, context: html, text, full: html, text
    eliminate duplicates in the list of victims refs #16513
    

• lines changed: 5079
• files changed: 97