All File Changes

v304_preview2 to v304_base (2014-08-04 to 2014-08-11) v304

• src/hg/genePredToGtf/genePredToGtf.c
  • lines changed 1, context: html, text, full: html, text
    fixing typo in help message.
• src/hg/hgSession/hgSession.c
  • lines changed 2, context: html, text, full: html, text
    Fixes #12559. GenomeSpace support added to hgTables.
• src/hg/hgTables/genomeSpace.c
  • lines changed 692, context: html, text, full: html, text
    Fixes #12559. GenomeSpace support added to hgTables.
  • lines changed 10, context: html, text, full: html, text
    Adding more flexibility so that if genomeSpace is not configured in hg.conf (or set to blank values), then it will be ignored, and GS will not appear in hgTables pages: mainPage, usage, etc.
  • lines changed 2, context: html, text, full: html, text
    oops. We tolerate missing genomeSpace settings now -- that will simply make GS features disappear.
• src/hg/hgTables/hgTables.c
  • lines changed 72, context: html, text, full: html, text
    Fixes #12559. GenomeSpace support added to hgTables.
  • lines changed 4, context: html, text, full: html, text
    in hgTables, don't look for bigDataUrl in composite headers regardlessof their type #13769
    
  • lines changed 1, context: html, text, full: html, text
    oops, forgot to initialize a variable
• src/hg/hgTables/hgTables.h
  • lines changed 24, context: html, text, full: html, text
    Fixes #12559. GenomeSpace support added to hgTables.
  • lines changed 3, context: html, text, full: html, text
    Adding more flexibility so that if genomeSpace is not configured in hg.conf (or set to blank values), then it will be ignored, and GS will not appear in hgTables pages: mainPage, usage, etc.
• src/hg/hgTables/mainPage.c
  • lines changed 13, context: html, text, full: html, text
    Fixes #12559. GenomeSpace support added to hgTables.
  • lines changed 34, context: html, text, full: html, text
    Adding more flexibility so that if genomeSpace is not configured in hg.conf (or set to blank values), then it will be ignored, and GS will not appear in hgTables pages: mainPage, usage, etc.
  • lines changed 1, context: html, text, full: html, text
    oops, extra quote not needed in javascript statement.
• src/hg/hgTables/makefile
  • lines changed 1, context: html, text, full: html, text
    Fixes #12559. GenomeSpace support added to hgTables.
• src/hg/hgTables/usage.c
  • lines changed 3, context: html, text, full: html, text
    Fixes #12559. GenomeSpace support added to hgTables.
  • lines changed 22, context: html, text, full: html, text
    Adding more flexibility so that if genomeSpace is not configured in hg.conf (or set to blank values), then it will be ignored, and GS will not appear in hgTables pages: mainPage, usage, etc.
• src/hg/hgTracks/hgTracks.c
  • lines changed 6, context: html, text, full: html, text
    temporarily checking in a message to warn that udcTimeout is set inhgTracks
    
  • lines changed 4, context: html, text, full: html, text
    make a link in the warning about udcTimout being set to clear theudcTimeout variable #13675
    
• src/hg/hgTracks/simpleTracks.c
  • lines changed 2, context: html, text, full: html, text
    Restoring the default values for lfColors after the changes in a4adfa326b and 936b5b531.Otherwise we have use of uninitialized variable when linkedFeaturesNameColor calls lfColors
    for a track that just sets a color (not shades, itemRgb or itemColor method), e.g. ensGene.
    refs #13746, #13704
    
• src/hg/hgVai/hgVai.c
  • lines changed 2, context: html, text, full: html, text
    Fixes #12559. GenomeSpace support added to hgTables.
• src/hg/htdocs/FAQ/FAQreleases.html
  • lines changed 1, context: html, text, full: html, text
    Changes based on CR, refs #13751
• src/hg/htdocs/FB-f-Logo__blue_22.jpg
  • lines changed 0, context: html, text, full: html, text
    adding facebook logo for homepage link to GB FB page
  • lines changed 0, context: html, text, full: html, text
    oops should be in images directory
• src/hg/htdocs/goldenPath/help/customTrackText.html
  • lines changed 1, context: html, text, full: html, text
    Correcting typo, CR #13749
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 3, context: html, text, full: html, text
    Appending note about debugging hubs, will push out once v304 is released refs #13675
• src/hg/htdocs/images/FB-f-Logo__blue_22.jpg
  • lines changed 0, context: html, text, full: html, text
    oops should be in images directory
• src/hg/htdocs/indexIntro.html
  • lines changed 2, context: html, text, full: html, text
    fixing tooltip on the DONATE button
• src/hg/htdocs/indexNews.html
  • lines changed 7, context: html, text, full: html, text
    adding link to GB Facebook page and fixing tooltip for Twitter link by changing 'alt' to 'title'
  • lines changed 1, context: html, text, full: html, text
    removing extra '</TD>' that I accidentally added, thanks Hiram
  • lines changed 1, context: html, text, full: html, text
    Adding href without visible link to google+ page. refs#13739
• src/hg/htdocs/staff.html
  • lines changed 16, context: html, text, full: html, text
    udpating some staff titles
  • lines changed 2, context: html, text, full: html, text
    adding CIRM Stem Cell DMC to Jim's title
• src/hg/inc/gtexData.h
  • lines changed 64, context: html, text, full: html, text
    Tool to load GTEx (NIH Common Fund Gene Tissue Expression). Quite similar to microarray table organization.
• src/hg/inc/gtexSample.h
  • lines changed 69, context: html, text, full: html, text
    Tool to load GTEx (NIH Common Fund Gene Tissue Expression). Quite similar to microarray table organization.
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    New version number v304
• src/hg/lib/bed5SourceVals.as
  • lines changed 12, context: html, text, full: html, text
    Generalize sourceScores, per Angie's suggestion
• src/hg/lib/cart.c
  • lines changed 1, context: html, text, full: html, text
    Fixes #12559. GenomeSpace support added to hgTables.
• src/hg/lib/gtexData.as
  • lines changed 7, context: html, text, full: html, text
    Tool to load GTEx (NIH Common Fund Gene Tissue Expression). Quite similar to microarray table organization.
• src/hg/lib/gtexData.c
  • lines changed 156, context: html, text, full: html, text
    Tool to load GTEx (NIH Common Fund Gene Tissue Expression). Quite similar to microarray table organization.
• src/hg/lib/gtexSample.as
  • lines changed 8, context: html, text, full: html, text
    Tool to load GTEx (NIH Common Fund Gene Tissue Expression). Quite similar to microarray table organization.
• src/hg/lib/gtexSample.c
  • lines changed 155, context: html, text, full: html, text
    Tool to load GTEx (NIH Common Fund Gene Tissue Expression). Quite similar to microarray table organization.
• src/hg/lib/trackHub.c
  • lines changed 1, context: html, text, full: html, text
    fix problem in hgc with '.'s in table names in superTracks in trackHubs.
• src/hg/lib/web.c
  • lines changed 4, context: html, text, full: html, text
    Fixes #12559. GenomeSpace support added to hgTables.
• src/hg/lib/wgEncodeRegDnaseClusteredSources.as
  • lines changed 6, context: html, text, full: html, text
    Renaming cells table to sources and adding .as. refs #13490
  • lines changed 1, context: html, text, full: html, text
    Correct tablename mismatch
• src/hg/makeDb/doc/encodeRegHg19.txt
  • lines changed 12, context: html, text, full: html, text
    Adding source table that describes sourceIds in main bed table. Not currently used by hgc (which still uses inputTrackTable). It is there for VAI. refs 13490
  • lines changed 8, context: html, text, full: html, text
    Rename Cells table to Sources. refs #13490
  • lines changed 1, context: html, text, full: html, text
    Renaming cells table to sources and adding .as. refs #13490
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 1, context: html, text, full: html, text
    CCDS is now available on hg38
• src/hg/makeDb/genbank/etc/hgwbeta.dbs
  • lines changed 2, context: html, text, full: html, text
    Moving rn6 up to urget databases for genbank updates, refs #13578
• src/hg/makeDb/genbank/etc/rr.dbs
  • lines changed 2, context: html, text, full: html, text
    Moving rn6 up to urget databases for genbank updates, refs #13578
• src/hg/makeDb/outside/hgGtex/expected/gtexTest.tab
  • lines changed 3, context: html, text, full: html, text
    Add trivial test to Gtex loader
• src/hg/makeDb/outside/hgGtex/expected/gtexTestSamples.tab
  • lines changed 2921, context: html, text, full: html, text
    Add trivial test to Gtex loader
• src/hg/makeDb/outside/hgGtex/hgGtex.c
  • lines changed 231, context: html, text, full: html, text
    Tool to load GTEx (NIH Common Fund Gene Tissue Expression). Quite similar to microarray table organization.
  • lines changed 68, context: html, text, full: html, text
    Minor cleanup
  • lines changed 70, context: html, text, full: html, text
    Add sample grouping of Gtex data
  • lines changed 59, context: html, text, full: html, text
    Medians basically works
  • lines changed 4, context: html, text, full: html, text
    Add debug
  • lines changed 4, context: html, text, full: html, text
    Fix problem with median compute (lost last sample in set)
  • lines changed 2, context: html, text, full: html, text
    Fix another off by one err
• src/hg/makeDb/outside/hgGtex/input/samples.txt
  • lines changed 4502, context: html, text, full: html, text
    Add trivial test to Gtex loader
  • lines changed 4502, context: html, text, full: html, text
    Aim GTex tests at real data
• src/hg/makeDb/outside/hgGtex/input/small.gct
  • lines changed 6, context: html, text, full: html, text
    Add trivial test to Gtex loader
  • lines changed 6, context: html, text, full: html, text
    Aim GTex tests at real data
• src/hg/makeDb/outside/hgGtex/makefile
  • lines changed 3, context: html, text, full: html, text
    Tool to load GTEx (NIH Common Fund Gene Tissue Expression). Quite similar to microarray table organization.
  • lines changed 9, context: html, text, full: html, text
    Add trivial test to Gtex loader
  • lines changed 5, context: html, text, full: html, text
    Aim GTex tests at real data
• src/hg/makeDb/outside/hgGtex/samples.txt
  • lines changed 4502, context: html, text, full: html, text
    Tool to load GTEx (NIH Common Fund Gene Tissue Expression). Quite similar to microarray table organization.
  • lines changed 4502, context: html, text, full: html, text
    Add trivial test to Gtex loader
• src/hg/makeDb/outside/hgGtex/test.gct
  • lines changed 6, context: html, text, full: html, text
    Tool to load GTEx (NIH Common Fund Gene Tissue Expression). Quite similar to microarray table organization.
  • lines changed 6, context: html, text, full: html, text
    Add trivial test to Gtex loader
• src/hg/makeDb/trackDb/human/cloneEnd.trackDb.ra
  • lines changed 95, context: html, text, full: html, text
    after cleaning bad mappings and adding badEnds table refs #13713
  • lines changed 25, context: html, text, full: html, text
    filter only 3X median length filter refs #13713
  • lines changed 128, context: html, text, full: html, text
    now as a composite track instead of a supertrack refs #13713
  • lines changed 24, context: html, text, full: html, text
    updated clone end description page with table of stats refs #13713
  • lines changed 145, context: html, text, full: html, text
    adding search definitions for all tables refs #13713
  • lines changed 2, context: html, text, full: html, text
    fixup COR search rules refs #13713
  • lines changed 4, context: html, text, full: html, text
    fixup rules for WI2 RP11 multipleMaps badEnds refs #13713
  • lines changed 1, context: html, text, full: html, text
    correct badEnds search refs #13713
• src/hg/makeDb/trackDb/human/cloneEndSuper.html
  • lines changed 41, context: html, text, full: html, text
    updated clone end description page with table of stats refs #13713
• src/hg/makeDb/trackDb/human/cytoBand.html
  • lines changed 18, context: html, text, full: html, text
    Changing links and references on cytoband track description page, refs #13379
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRegDnaseClustered.ra
  • lines changed 12, context: html, text, full: html, text
    Adding cell table/file to V3 DNase Clusters. refs #13490
  • lines changed 9, context: html, text, full: html, text
    Renaming cells table to sources and adding .as. refs #13490
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeHaibTfbs.ra
  • lines changed 3, context: html, text, full: html, text
    Staging correction of controlId metaData for ENCODE HAIB TFBS refs #13476
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeHaibTfbs.ra
  • lines changed 3, context: html, text, full: html, text
    Staging correction of controlId metaData for ENCODE HAIB TFBS refs #13476
• src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.ra
  • lines changed 1, context: html, text, full: html, text
    Adding source table that describes sourceIds in main bed table. Not currently used by hgc (which still uses inputTrackTable). It is there for VAI. refs 13490
  • lines changed 1, context: html, text, full: html, text
    Rename Cells table to Sources. refs #13490
• src/hg/makeDb/trackDb/human/hg38/centromeres.html
  • lines changed 7, context: html, text, full: html, text
    Updating centromere track references, refs #12689
• src/hg/makeDb/trackDb/mouse/cloneEnd.trackDb.ra
  • lines changed 155, context: html, text, full: html, text
    Made changes to make mm10 NCBI Ends track visible on hgwdev (redmine #10083)
• src/hg/makeDb/trackDb/mouse/cloneEndSuper.html
  • lines changed 16, context: html, text, full: html, text
    Made changes to make mm10 NCBI Ends track visible on hgwdev (redmine #10083)
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodeSydhHist.ra
  • lines changed 15, context: html, text, full: html, text
    Staging metaData md5sum info for mouse tar file correction refs #13404
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/wgEncodeSydhHist.ra
  • lines changed 15, context: html, text, full: html, text
    Staging metaData md5sum info for mouse tar file correction refs #13404
• src/hg/makeDb/trackDb/mouse/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    Made changes to make mm10 NCBI Ends track visible on hgwdev (redmine #10083)
• src/hg/utils/automation/EnsGeneAutomate.pm
  • lines changed 219, context: html, text, full: html, text
    adding v76 definitions refs #13774
  • lines changed 1, context: html, text, full: html, text
    fixup path name for dasNov3 refs #13774
• src/hg/utils/gff3ToGenePred/tests/expected/bogusQuotesTest.out
  • lines changed 1, context: html, text, full: html, text
    fix a test in gff3ToGenePred
• src/inc/textOut.h
  • lines changed 4, context: html, text, full: html, text
    Fixes #12559. GenomeSpace support added to hgTables.
• src/lib/gff3.c
  • lines changed 1, context: html, text, full: html, text
    add dash to error message about acceptable characters in tags
• src/lib/htmshell.c
  • lines changed 2, context: html, text, full: html, text
    Fixes #12559. GenomeSpace support added to hgTables.
• src/lib/textOut.c
  • lines changed 39, context: html, text, full: html, text
    Fixes #12559. GenomeSpace support added to hgTables.
• src/utils/newProg/newProg.c
  • lines changed 2, context: html, text, full: html, text
    The generated CGI .c call to cartWebStart was missing the db argument, so it didn't compile.
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    v304 final build refs #13703

• lines changed: 23849
• files changed: 102