File Changes for braney

v288_preview2 to v288_base (2013-08-13 to 2013-08-19) v288

• src/hg/hgTables/hal.c
  • lines changed 61, context: html, text, full: html, text
    make HAL linked in by default, fix the problem with mismatched bases nothaving the right chars in them, start adding HAL to the table browser.
    refs #10637
    
• src/hg/hgTables/hgTables.c
  • lines changed 4, context: html, text, full: html, text
    make HAL linked in by default, fix the problem with mismatched bases nothaving the right chars in them, start adding HAL to the table browser.
    refs #10637
    
• src/hg/hgTables/hgTables.h
  • lines changed 9, context: html, text, full: html, text
    make HAL linked in by default, fix the problem with mismatched bases nothaving the right chars in them, start adding HAL to the table browser.
    refs #10637
    
• src/hg/hgTables/joining.c
  • lines changed 12, context: html, text, full: html, text
    make HAL linked in by default, fix the problem with mismatched bases nothaving the right chars in them, start adding HAL to the table browser.
    refs #10637
    
• src/hg/hgTables/makefile
  • lines changed 1, context: html, text, full: html, text
    make HAL linked in by default, fix the problem with mismatched bases nothaving the right chars in them, start adding HAL to the table browser.
    refs #10637
    
• src/hg/hgTracks/snakeTrack.c
  • lines changed 12, context: html, text, full: html, text
    make HAL linked in by default, fix the problem with mismatched bases nothaving the right chars in them, start adding HAL to the table browser.
    refs #10637
    
• src/hg/makeDb/doc/hg19.txt
  • lines changed 68, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/makeDb/genbank/etc/euronode-copy
  • lines changed 1, context: html, text, full: html, text
    use hgwdev.sdsc.edu for euronode copy
• src/hg/utils/decipher/buildDecipher
  • lines changed 42, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/decipher/checkDecipher.sh
  • lines changed 104, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/decipher/decipher.tables
  • lines changed 4, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/decipher/decipherWrapper.sh
  • lines changed 8, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/decipher/validateDecipher.sh
  • lines changed 30, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/gwas/checkGwas.sh
  • lines changed 76, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/gwas/expectedColumns.txt
  • lines changed 34, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/gwas/gwasWrapper.sh
  • lines changed 8, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/gwas/makefile
  • lines changed 23, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/gwas/perlParser.pl
  • lines changed 38, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/gwas/validateGwas.sh
  • lines changed 30, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/isca/buildISCA.csh
  • lines changed 55, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/isca/checkISCA.sh
  • lines changed 72, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/isca/isca.tables
  • lines changed 9, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/isca/iscaWrapper.sh
  • lines changed 8, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/isca/makefile
  • lines changed 20, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/isca/validateISCA.sh
  • lines changed 35, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/omim/buildOmimTracks.csh
  • lines changed 175, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/omim/checkOmim.sh
  • lines changed 148, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/omim/checkOmimUpload.sh
  • lines changed 80, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/omim/doOmimAv/doOmimAv.c
  • lines changed 219, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/omim/doOmimAv/makefile
  • lines changed 21, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/omim/doOmimGene2/doOmimGene2.c
  • lines changed 98, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/omim/doOmimGene2/makefile
  • lines changed 21, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/omim/doOmimGeneSymbols/doOmimGeneSymbols.c
  • lines changed 81, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/omim/doOmimGeneSymbols/makefile
  • lines changed 21, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/omim/doOmimLocation/doOmimLocation.c
  • lines changed 311, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/omim/doOmimLocation/makefile
  • lines changed 21, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/omim/makefile
  • lines changed 21, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/omim/omim.tables
  • lines changed 9, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/omim/omimUploadWrapper.sh
  • lines changed 9, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/omim/omimWrapper.sh
  • lines changed 8, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/omim/parseGeneMap.pl
  • lines changed 221, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/omim/validateOmim.sh
  • lines changed 35, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/otto/decipher/buildDecipher
  • lines changed 42, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/otto/decipher/checkDecipher.sh
  • lines changed 104, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/otto/decipher/decipher.tables
  • lines changed 4, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/otto/decipher/decipherWrapper.sh
  • lines changed 8, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/otto/decipher/validateDecipher.sh
  • lines changed 30, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/otto/gwas/checkGwas.sh
  • lines changed 76, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/otto/gwas/expectedColumns.txt
  • lines changed 34, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/otto/gwas/gwasWrapper.sh
  • lines changed 8, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/otto/gwas/makefile
  • lines changed 23, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/otto/gwas/perlParser.pl
  • lines changed 38, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/otto/gwas/validateGwas.sh
  • lines changed 30, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/otto/isca/buildISCA.csh
  • lines changed 55, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/otto/isca/checkISCA.sh
  • lines changed 72, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/otto/isca/isca.tables
  • lines changed 9, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/otto/isca/iscaWrapper.sh
  • lines changed 8, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/otto/isca/makefile
  • lines changed 20, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/otto/isca/validateISCA.sh
  • lines changed 35, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/otto/omim/buildOmimTracks.csh
  • lines changed 175, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/otto/omim/checkOmim.sh
  • lines changed 148, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/otto/omim/checkOmimUpload.sh
  • lines changed 80, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/otto/omim/doOmimAv/doOmimAv.c
  • lines changed 219, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/otto/omim/doOmimAv/makefile
  • lines changed 21, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/otto/omim/doOmimGene2/doOmimGene2.c
  • lines changed 98, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/otto/omim/doOmimGene2/makefile
  • lines changed 21, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/otto/omim/doOmimGeneSymbols/doOmimGeneSymbols.c
  • lines changed 81, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/otto/omim/doOmimGeneSymbols/makefile
  • lines changed 21, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/otto/omim/doOmimLocation/doOmimLocation.c
  • lines changed 311, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/otto/omim/doOmimLocation/makefile
  • lines changed 21, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/otto/omim/makefile
  • lines changed 21, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/otto/omim/omim.tables
  • lines changed 9, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/otto/omim/omimUploadWrapper.sh
  • lines changed 9, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/otto/omim/omimWrapper.sh
  • lines changed 8, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/otto/omim/parseGeneMap.pl
  • lines changed 221, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/otto/omim/validateOmim.sh
  • lines changed 35, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/inc/common.mk
  • lines changed 13, context: html, text, full: html, text
    make HAL linked in by default, fix the problem with mismatched bases nothaving the right chars in them, start adding HAL to the table browser.
    refs #10637