hiram: changes by file

review to branch (2010-03-30 to 2010-04-06) v228

• src/hg/hgTracks/hgTracks.c
  • 1.1636 lines changed: 9, context: html, text, full: html, text
    allow oryCun2 to find equivalent Ensembl scaffold names for blue bar
• src/hg/hgTracks/wigTrack.c
  • 1.102 lines changed: 6, context: html, text, full: html, text
    Fix one last place where long strings in custom tracks cause problems
• src/hg/makeDb/doc/bosTau4.txt
  • 1.23 lines changed: 59, context: html, text, full: html, text
    never got susScr1 to work finished with susScr2 lastz
• src/hg/makeDb/doc/calJac3.txt
  • 1.6 lines changed: 45, context: html, text, full: html, text
    adding ctgPos2 track
  • 1.5 lines changed: 557, context: html, text, full: html, text
    done and in the pushQ except for the multiz track
• src/hg/makeDb/doc/gorGor2.txt
  • 1.4 lines changed: 18, context: html, text, full: html, text
    have blat server and default location
• src/hg/makeDb/doc/makeEnsembl.txt
  • 1.15 lines changed: 443, context: html, text, full: html, text
    first set of v57 done
• src/hg/makeDb/doc/oryCun2.txt
  • 1.7 lines changed: 30, context: html, text, full: html, text
    ensGene v57 added and in the pushQ
• src/hg/makeDb/doc/rn4.txt
  • 1.40 lines changed: 11, context: html, text, full: html, text
    done with Panda ailMel1 lastz
• src/hg/makeDb/doc/susScr2.txt
  • 1.3 lines changed: 231, context: html, text, full: html, text
    susScr2 done and in the pushQ
• src/hg/makeDb/genbank/etc/align.dbs
  • 1.114 lines changed: 1, context: html, text, full: html, text
    Added susScr2 - Pig
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • 1.118 lines changed: 1, context: html, text, full: html, text
    Added susScr2 - Pig
• src/hg/makeDb/schema/all.joiner
  • 1.776 lines changed: 30, context: html, text, full: html, text
    adding susScr2 ailMel1 and fixing up chain checks
• src/hg/makeDb/schema/joinerCheck/joinerCheck.c
  • 1.41 lines changed: 5, context: html, text, full: html, text
    add verbose output to table check to find out who, what, why, where, when
• src/hg/makeDb/trackDb/trackDb.chainNet.ra
  • 1.88 lines changed: 1, context: html, text, full: html, text
    o_db is sufficient at this time for felCatV17e
• src/hg/makeDb/trackDb/marmoset/calJac3/ctgPos2.html
  • 1.1 lines changed: 16, context: html, text, full: html, text
    now showing scaffold names
• src/hg/makeDb/trackDb/panda/ailMel1/description.html
  • 1.4 lines changed: 14, context: html, text, full: html, text
    finalizing these document pages
• src/hg/makeDb/trackDb/panda/ailMel1/gap.html
  • 1.2 lines changed: 47, context: html, text, full: html, text
    finalizing these document pages
• src/hg/makeDb/trackDb/panda/ailMel1/gold.html
  • 1.2 lines changed: 8, context: html, text, full: html, text
    finalizing these document pages
• src/hg/makeDb/trackDb/pig/susScr2/bosTau4ChainPileUp.html
  • 1.3 lines changed: 7, context: html, text, full: html, text
    escaping the dollar signs in the html and the backslashes
  • 1.2 lines changed: 7, context: html, text, full: html, text
    can not use shell dollar sign strings in our html files
  • 1.1 lines changed: 50, context: html, text, full: html, text
    adding bosTau4ChainPileUp track
• src/hg/makeDb/trackDb/pig/susScr2/trackDb.ra
  • 1.4 lines changed: 2, context: html, text, full: html, text
    escaping the dollar signs in the html and the backslashes
  • 1.3 lines changed: 31, context: html, text, full: html, text
    add wiggle and bedGraph formats for comparison
  • 1.2 lines changed: 7, context: html, text, full: html, text
    adding bosTau4ChainPileUp track
• src/hg/makeDb/trackDb/rabbit/oryCun2/gap.html
  • 1.2 lines changed: 43, context: html, text, full: html, text
    finalizing gap,gold descriptions
• src/hg/makeDb/trackDb/rabbit/oryCun2/gold.html
  • 1.2 lines changed: 10, context: html, text, full: html, text
    finalizing gap,gold descriptions
• src/hg/utils/automation/EnsGeneAutomate.pm
  • 1.23 lines changed: 50, context: html, text, full: html, text
    ftp directories have underscore not period for separator
  • 1.22 lines changed: 6, context: html, text, full: html, text
    Ensembl calJac3 is not our calJac3
• src/hg/utils/automation/doEnsGeneUpdate.pl
  • 1.24 lines changed: 3, context: html, text, full: html, text
    need quotes around a string in a SQL insert statement
• src/hg/utils/phyloTrees/49way.dissect.txt
  • 1.1 lines changed: 679, context: html, text, full: html, text
    adding Sheep OviAra to a 49-way tree
• src/hg/utils/phyloTrees/49way.nh
  • 1.1 lines changed: 23, context: html, text, full: html, text
    adding Sheep OviAra to a 49-way tree
• src/hg/utils/phyloTrees/chainNet.pl
  • 1.5 lines changed: 7, context: html, text, full: html, text
    adding Sheep OviAra to a 49-way tree
• src/hg/utils/phyloTrees/placentals.txt
  • 1.1 lines changed: 57, context: html, text, full: html, text
    From NCBI taxonomy viewer, species name lists
• src/hg/utils/phyloTrees/primates.txt
  • 1.1 lines changed: 25, context: html, text, full: html, text
    From NCBI taxonomy viewer, species name lists
• src/hg/utils/phyloTrees/vertebrates.txt
  • 1.1 lines changed: 30, context: html, text, full: html, text
    From NCBI taxonomy viewer, species name lists
• src/product/scripts/README
  • 1.3 lines changed: 2, context: html, text, full: html, text
    adding printEnv.pl
• src/product/scripts/printEnv.pl
  • 1.1 lines changed: 25, context: html, text, full: html, text
    initial source