All File Changes

v320_preview to v320_preview2 (2015-07-20 to 2015-07-27) v320

• src/hg/hgGene/hgGeneData/Human/hg38/links.ra
  • lines changed 6, context: html, text, full: html, text
    add link outs to ExonPrimer from hg38 #15656
    
• src/hg/hgTables/bigBed.c
  • lines changed 1, context: html, text, full: html, text
    fix a couple of problems where sql tables were assumed #15756
    
• src/hg/hgTables/identifiers.c
  • lines changed 1, context: html, text, full: html, text
    fix a couple of problems where sql tables were assumed #15756
    
• src/hg/hgTables/sumStats.c
  • lines changed 1, context: html, text, full: html, text
    fix summary stats on assembly hubs #15756
    
• src/hg/hgTracks/extTools.c
  • lines changed 7, context: html, text, full: html, text
    adding a $returnUrl option to the extTools.ra file, refs #15113
    
• src/hg/hgTracks/menu.c
  • lines changed 3, context: html, text, full: html, text
    Changing menu bar colors, refs #15389
    
• src/hg/htdocs/goldenPath/help/cutters.html
  • lines changed 1, context: html, text, full: html, text
    Replacing absolute links in track descriptions with relative links, refs #8231
    
• src/hg/htdocs/goldenPath/help/oligoMatch.html
  • lines changed 1, context: html, text, full: html, text
    Replacing absolute links in track descriptions with relative links, refs #8231
    
• src/hg/htdocs/images/hgTracksHomeIconSprite.png
  • lines changed 0, context: html, text, full: html, text
    Changing menu bar colors, refs #15389
    
• src/hg/htdocs/images/homeIconSprite.png
  • lines changed 0, context: html, text, full: html, text
    Changing menu bar colors, refs #15389
    
• src/hg/htdocs/style/nice_menu.css
  • lines changed 25, context: html, text, full: html, text
    Changing menu bar colors, refs #15389
    
• src/hg/htdocs/training/index.html
  • lines changed 2, context: html, text, full: html, text
    added new window spawn to UC Davis link and dropped an o from Icahn schoool. per steve code review. refs #15732
    
  • lines changed 1, context: html, text, full: html, text
    adding map of training locations past and future and linking to it from index page. refs #15730
    
• src/hg/htdocs/training/trainingMap.html
  • lines changed 9, context: html, text, full: html, text
    adding map of training locations past and future and linking to it from index page. refs #15730
    
• src/hg/inc/jksql.h
  • lines changed 13, context: html, text, full: html, text
    Fixes RM#15751. Fixes a minor problem with sql string escaping. Also added a new function sqlSafefAppend because it use handy when you need to safely append a little formatted string, but you do not want to be bothered with using dyStrings.
    
• src/hg/lib/hgFind.c
  • lines changed 9, context: html, text, full: html, text
    Fixes RM#15751. Fixes a minor problem with sql string escaping. Also added a new function sqlSafefAppend because it use handy when you need to safely append a little formatted string, but you do not want to be bothered with using dyStrings.
    
• src/hg/lib/jksql.c
  • lines changed 19, context: html, text, full: html, text
    Fixes RM#15751. Fixes a minor problem with sql string escaping. Also added a new function sqlSafefAppend because it use handy when you need to safely append a little formatted string, but you do not want to be bothered with using dyStrings.
    
• src/hg/makeDb/doc/caeSp111.txt
  • lines changed 5, context: html, text, full: html, text
    now has a scientific name refs #15209
    
  • lines changed 2, context: html, text, full: html, text
    and the organism/common name updates too refs @15209
    
• src/hg/makeDb/doc/ce11/lastzRuns.txt
  • lines changed 515, context: html, text, full: html, text
    done with lastz runs for loaLoa1 ancCey1 triSui1 triSpi1 priExs1 dirImm1 ascSuu1 hetBac1 necAme1 refs #15209
    
• src/hg/makeDb/doc/hg18.txt
  • lines changed 6, context: html, text, full: html, text
    Note from Valerie that our hg18.altLocations are valid.
    
• src/hg/makeDb/doc/hg19.txt
  • lines changed 175, context: html, text, full: html, text
    mafSnp mode for hg19 100 way
    
  • lines changed 2, context: html, text, full: html, text
    Fixed typo in hg19 makedoc; refs #9391
    
• src/hg/makeDb/doc/worms/ancCey1.txt
  • lines changed 68, context: html, text, full: html, text
    done with basic tracks refs #15209
    
• src/hg/makeDb/doc/worms/ascSuu1.txt
  • lines changed 46, context: html, text, full: html, text
    done with basic tracks refs @15209
    
• src/hg/makeDb/doc/worms/bruMal2.txt
  • lines changed 98, context: html, text, full: html, text
    done with basic set of tracks refs #15209
    
• src/hg/makeDb/doc/worms/dirImm1.txt
  • lines changed 36, context: html, text, full: html, text
    done with basic tracks refs #15209
    
• src/hg/makeDb/doc/worms/hetBac1.txt
  • lines changed 83, context: html, text, full: html, text
    done with basic tracks refs #15209
    
• src/hg/makeDb/doc/worms/loaLoa1.txt
  • lines changed 41, context: html, text, full: html, text
    done with basic tracks refs #15209
    
  • lines changed 1, context: html, text, full: html, text
    correct name at the top refs #15209
    
• src/hg/makeDb/doc/worms/necAme1.txt
  • lines changed 45, context: html, text, full: html, text
    done with basic tracks refs #15209
    
• src/hg/makeDb/doc/worms/oncVol1.txt
  • lines changed 40, context: html, text, full: html, text
    done with basic tracks refs #15209
    
• src/hg/makeDb/doc/worms/priExs1.txt
  • lines changed 77, context: html, text, full: html, text
    done with basic tracks refs #15209
    
• src/hg/makeDb/doc/worms/triSpi1.txt
  • lines changed 44, context: html, text, full: html, text
    done with basic tracks refs #15209
    
• src/hg/makeDb/doc/worms/triSui1.txt
  • lines changed 45, context: html, text, full: html, text
    done with basic tracks refs #15209
    
• src/hg/makeDb/genbank/src/ccds/ccdsMkTables.c
  • lines changed 3, context: html, text, full: html, text
    some tweaks to CCDS processing (no redmine)
    
• src/hg/makeDb/genbank/src/ccds/createTables.sql
  • lines changed 2, context: html, text, full: html, text
    some tweaks to CCDS processing (no redmine)
    
• src/hg/makeDb/genbank/src/ccds/ncbiSql/createTables.sql
  • lines changed 2, context: html, text, full: html, text
    some tweaks to CCDS processing (no redmine)
    
• src/hg/makeDb/trackDb/augustusGene.html
  • lines changed 46, context: html, text, full: html, text
    Expanding section about training species used when scanning different clades, refs #13088
    
  • lines changed 3, context: html, text, full: html, text
    Fixing spelling errors found in CR, refs #15735
    
• src/hg/makeDb/trackDb/est.html
  • lines changed 3, context: html, text, full: html, text
    Replacing absolute links in track descriptions with relative links, refs #8231
    
• src/hg/makeDb/trackDb/est.new.html
  • lines changed 3, context: html, text, full: html, text
    Replacing absolute links in track descriptions with relative links, refs #8231
    
• src/hg/makeDb/trackDb/mrna.html
  • lines changed 3, context: html, text, full: html, text
    Replacing absolute links in track descriptions with relative links, refs #8231
    
• src/hg/makeDb/trackDb/refGene.html
  • lines changed 2, context: html, text, full: html, text
    Replacing absolute links in track descriptions with relative links, refs #8231
    
• src/hg/makeDb/trackDb/refGene.new.html
  • lines changed 2, context: html, text, full: html, text
    Replacing absolute links in track descriptions with relative links, refs #8231
    
• src/hg/makeDb/trackDb/trackDb.chainNet.nematode.ra
  • lines changed 675, context: html, text, full: html, text
    seperate out nematode definitions since there are a number to come refs #15209
    
• src/hg/makeDb/trackDb/trackDb.chainNet.ra
  • lines changed 671, context: html, text, full: html, text
    seperate out nematode definitions since there are a number to come refs #15209
    
• src/hg/makeDb/trackDb/xenoEst.html
  • lines changed 2, context: html, text, full: html, text
    Replacing absolute links in track descriptions with relative links, refs #8231
    
• src/hg/makeDb/trackDb/xenoMrna.html
  • lines changed 3, context: html, text, full: html, text
    Replacing absolute links in track descriptions with relative links, refs #8231
    
• src/hg/utils/automation/doDbSnpMaskSequence.pl
  • lines changed 4, context: html, text, full: html, text
    Use use File::Basename as suggested by Hiram. refs #15739
    
• src/hg/utils/automation/doDbSnpOrthoAlleles.pl
  • lines changed 4, context: html, text, full: html, text
    Use use File::Basename as suggested by Hiram. refs #15739
    
• src/hg/utils/genePredToBigGenePred/genePredToBigGenePred.c
  • lines changed 2, context: html, text, full: html, text
    eom teaks to make genePredToBigGenePred easier to use #15390
    
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    v320 preview2 refs #15731
    

• lines changed: 2861
• files changed: 53