All File Changes

v313_base to v314_preview (2015-03-09 to 2015-03-16) v314

• src/hg/hgBeacon/makefile
  • lines changed 1, context: html, text, full: html, text
    makeing sure testBeacon is copied into the bin dir, refs #14963
    
• src/hg/hgConvert/hgConvert.c
  • lines changed 2, context: html, text, full: html, text
    allow using different names for the following tables: dbDb, defaultDb,
    genomeClade, and clade. This will allow for testing of alternate
    versions of these tables on hgwdev.
    
• src/hg/hgLiftOver/hgLiftOver.c
  • lines changed 3, context: html, text, full: html, text
    allow using different names for the following tables: dbDb, defaultDb,
    genomeClade, and clade. This will allow for testing of alternate
    versions of these tables on hgwdev.
    
• src/hg/hgTables/identifiers.c
  • lines changed 1, context: html, text, full: html, text
    a mirror that has the failover connection (=hgdownload) enabled
    currently just crashes in hgTables. Adding an additional check
    to catch this condition and suppress printing the example values,
    just like what we do for custom tracks.
    refs #14945
    
• src/hg/hgTracks/hgTracks.c
  • lines changed 2, context: html, text, full: html, text
    Code review feedback from Kate. refs #14965
    
• src/hg/hgc/rmskJoinedClick.c
  • lines changed 3, context: html, text, full: html, text
    fixup cgi encoding for getDna clicks from these items refs #9741
    
• src/hg/htdocs/admin/500.html
  • lines changed 27, context: html, text, full: html, text
    making 500 error message adapt to the server where the apache is
    running. refs #14718
    
• src/hg/inc/hdb.h
  • lines changed 20, context: html, text, full: html, text
    allow using different names for the following tables: dbDb, defaultDb,
    genomeClade, and clade. This will allow for testing of alternate
    versions of these tables on hgwdev.
    
• src/hg/inc/jksql.h
  • lines changed 4, context: html, text, full: html, text
    a mirror that has the failover connection (=hgdownload) enabled
    currently just crashes in hgTables. Adding an additional check
    to catch this condition and suppress printing the example values,
    just like what we do for custom tracks.
    refs #14945
    
• src/hg/lib/cartJson.c
  • lines changed 3, context: html, text, full: html, text
    Fixing a few cases of assuming the database is in mysql (could be assembly hub!).
    
• src/hg/lib/hAnno.c
  • lines changed 17, context: html, text, full: html, text
    Fixing a few cases of assuming the database is in mysql (could be assembly hub!).
    
• src/hg/lib/hdb.c
  • lines changed 438, context: html, text, full: html, text
    allow using different names for the following tables: dbDb, defaultDb,
    genomeClade, and clade. This will allow for testing of alternate
    versions of these tables on hgwdev.
    
• src/hg/lib/hgSeq.c
  • lines changed 1, context: html, text, full: html, text
    Fixing item name buffer overflow: fixes #14966
    
• src/hg/lib/jksql.c
  • lines changed 26, context: html, text, full: html, text
    a mirror that has the failover connection (=hgdownload) enabled
    currently just crashes in hgTables. Adding an additional check
    to catch this condition and suppress printing the example values,
    just like what we do for custom tracks.
    refs #14945
    
• src/hg/lib/web.c
  • lines changed 41, context: html, text, full: html, text
    allow using different names for the following tables: dbDb, defaultDb,
    genomeClade, and clade. This will allow for testing of alternate
    versions of these tables on hgwdev.
    
• src/hg/makeDb/doc/danRer10/initialBuild.txt
  • lines changed 52, context: html, text, full: html, text
    add fixup procedure for gold table frag name search rule in trackDb refs #14017
    
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 23, context: html, text, full: html, text
    Added bisBis1; refs #14560
    
• src/hg/makeDb/genbank/src/lib/gbGenome.c
  • lines changed 2, context: html, text, full: html, text
    Added bisBis Bison bison bison refs #14560
    
• src/hg/makeDb/schema/all.joiner
  • lines changed 12, context: html, text, full: html, text
    adding xenTro7 rules refs #9868
    
• src/hg/makeDb/trackDb/human/hg38/cons17way.html
  • lines changed 13, context: html, text, full: html, text
    Fixing up things on Conservation track description pages, refs #14410 #14970
    
• src/hg/makeDb/trackDb/human/hg38/trackDb.17way.ra
  • lines changed 2, context: html, text, full: html, text
    corrected phylo ordering from 4D calculation refs #14970
    
  • lines changed 1, context: html, text, full: html, text
    stray blank line caused settings to be missed refs #14970
    
• src/hg/makeDb/trackDb/makefile
  • lines changed 1, context: html, text, full: html, text
    adding ornAna2 to the build refs #14560
    
• src/hg/makeDb/trackDb/platypus/ornAna2/description.html
  • lines changed 63, context: html, text, full: html, text
    adding ornAna2 to the build refs #14560
    
• src/hg/makeDb/trackDb/platypus/ornAna2/gap.html
  • lines changed 30, context: html, text, full: html, text
    adding ornAna2 to the build refs #14560
    
• src/hg/makeDb/trackDb/platypus/ornAna2/gold.html
  • lines changed 34, context: html, text, full: html, text
    adding ornAna2 to the build refs #14560
    
• src/hg/makeDb/trackDb/platypus/ornAna2/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    adding ornAna2 to the build refs #14560
    
  • lines changed 5, context: html, text, full: html, text
    add search rule for gold table refs #14560
    
• src/hg/makeDb/trackDb/tarsier/tarSyr2/cons17way.html
  • lines changed 1, context: html, text, full: html, text
    Fixing up things on Conservation track description pages, refs #14410 #14970
    
• src/hg/makeDb/trackDb/tarsier/tarSyr2/trackDb.17way.ra
  • lines changed 1, context: html, text, full: html, text
    order by phylo distance from 4D estimates refs #14410
    
• src/hg/makeDb/trackDb/zebrafish/danRer10/trackDb.ra
  • lines changed 5, context: html, text, full: html, text
    fixup gold table search on frag names refs #14017
    
• src/hg/mouseStuff/axtChain/axtChain.c
  • lines changed 4, context: html, text, full: html, text
    clarify usage message to avoid confusion refs #14955
    
  • lines changed 1, context: html, text, full: html, text
    clarify usage message to avoid confusion refs #14955
    
• src/utils/qa/qaAutoTrack.sh
  • lines changed 163, context: html, text, full: html, text
    Changes based on Code Review, refs #14895
    
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 1, context: html, text, full: html, text
    revert temporary donnak email address back to ann refs #14887
    
  • lines changed 2, context: html, text, full: html, text
    v314 preview1 refs #14887
    
• src/utils/qa/weeklybld/doNewBranch.csh
  • lines changed 4, context: html, text, full: html, text
    revert temporary donnak email address back to ann refs #14887
    
• src/utils/qa/weeklybld/doNewReview.csh
  • lines changed 1, context: html, text, full: html, text
    revert temporary donnak email address back to ann refs #14887
    
• src/utils/qa/weeklybld/doNewReview2.csh
  • lines changed 1, context: html, text, full: html, text
    revert temporary donnak email address back to ann refs #14887
    

• lines changed: 1019
• files changed: 39