File Changes for hiram

v266_base to v267_preview (2012-04-24 to 2012-05-01) v267

• src/hg/makeDb/doc/canFam3.txt
  • lines changed 9, context: html, text, full: html, text
    adding cpgIslandExt track
  • lines changed 12, context: html, text, full: html, text
    completed genscan track
• src/hg/makeDb/doc/choHof1.txt
  • lines changed 17, context: html, text, full: html, text
    adding cpgIslandExt track
  • lines changed 12, context: html, text, full: html, text
    completed genscan track
• src/hg/makeDb/doc/chrPic1.txt
  • lines changed 9, context: html, text, full: html, text
    adding cpgIslandExt track
  • lines changed 18, context: html, text, full: html, text
    done with genscan track build
• src/hg/makeDb/doc/dasNov3.txt
  • lines changed 10, context: html, text, full: html, text
    adding cpgIslandExt track
  • lines changed 12, context: html, text, full: html, text
    done with genscan track build
• src/hg/makeDb/doc/dipOrd1.txt
  • lines changed 14, context: html, text, full: html, text
    adding cpgIslandExt track
  • lines changed 20, context: html, text, full: html, text
    done with genscan track build
• src/hg/makeDb/doc/echTel1.txt
  • lines changed 16, context: html, text, full: html, text
    adding cpgIslandExt track
  • lines changed 21, context: html, text, full: html, text
    done with genscan track build
• src/hg/makeDb/doc/eriEur1.txt
  • lines changed 15, context: html, text, full: html, text
    adding cpgIslandExt track
  • lines changed 12, context: html, text, full: html, text
    completed genscan track
• src/hg/makeDb/doc/felCat5.txt
  • lines changed 10, context: html, text, full: html, text
    adding cpgIslandExt track
• src/hg/makeDb/doc/fr3.txt
  • lines changed 3, context: html, text, full: html, text
    adding cpgIslandExt track
• src/hg/makeDb/doc/gadMor1.txt
  • lines changed 21, context: html, text, full: html, text
    adding cpgIslandExt track
  • lines changed 12, context: html, text, full: html, text
    completed genscan track
• src/hg/makeDb/doc/galGal4.txt
  • lines changed 10, context: html, text, full: html, text
    adding cpgIslandExt track
  • lines changed 19, context: html, text, full: html, text
    done with genscan track build
• src/hg/makeDb/doc/hetGla2.txt
  • lines changed 9, context: html, text, full: html, text
    adding cpgIslandExt track
  • lines changed 28, context: html, text, full: html, text
    completed genscan track
• src/hg/makeDb/doc/latCha1.txt
  • lines changed 10, context: html, text, full: html, text
    adding cpgIslandExt track
  • lines changed 12, context: html, text, full: html, text
    done with genscan track build
• src/hg/makeDb/doc/melUnd1.txt
  • lines changed 9, context: html, text, full: html, text
    adding cpgIslandExt track
  • lines changed 17, context: html, text, full: html, text
    done with genscan track build
• src/hg/makeDb/doc/micMur1.txt
  • lines changed 11, context: html, text, full: html, text
    adding cpgIslandExt track
  • lines changed 21, context: html, text, full: html, text
    done with genscan track build
• src/hg/makeDb/doc/nomLeu2.txt
  • lines changed 9, context: html, text, full: html, text
    adding cpgIslandExt track
  • lines changed 12, context: html, text, full: html, text
    done with genscan track build
• src/hg/makeDb/doc/ochPri2.txt
  • lines changed 15, context: html, text, full: html, text
    adding cpgIslandExt track
  • lines changed 21, context: html, text, full: html, text
    done with genscan track build
• src/hg/makeDb/doc/oreNil1.txt
  • lines changed 11, context: html, text, full: html, text
    adding cpgIslandExt track
  • lines changed 12, context: html, text, full: html, text
    completed genscan track
• src/hg/makeDb/doc/oreNil2.txt
  • lines changed 11, context: html, text, full: html, text
    adding cpgIslandExt track
  • lines changed 19, context: html, text, full: html, text
    done with genscan track build
• src/hg/makeDb/doc/otoGar3.txt
  • lines changed 11, context: html, text, full: html, text
    adding cpgIslandExt track
  • lines changed 18, context: html, text, full: html, text
    done with genscan track build
• src/hg/makeDb/doc/panTro4.txt
  • lines changed 10, context: html, text, full: html, text
    adding cpgIslandExt track
• src/hg/makeDb/doc/papHam1.txt
  • lines changed 15, context: html, text, full: html, text
    adding cpgIslandExt track
  • lines changed 12, context: html, text, full: html, text
    completed genscan track
• src/hg/makeDb/doc/proCap1.txt
  • lines changed 15, context: html, text, full: html, text
    adding cpgIslandExt track
  • lines changed 17, context: html, text, full: html, text
    done with genscan track build
• src/hg/makeDb/doc/pteVam1.txt
  • lines changed 10, context: html, text, full: html, text
    adding cpgIslandExt track
  • lines changed 12, context: html, text, full: html, text
    done with genscan track build
• src/hg/makeDb/doc/rheMac3.txt
  • lines changed 1, context: html, text, full: html, text
    done with genscan track build
• src/hg/makeDb/doc/rn5.txt
  • lines changed 10, context: html, text, full: html, text
    adding cpgIslandExt track
• src/hg/makeDb/doc/saiBol1.txt
  • lines changed 10, context: html, text, full: html, text
    adding cpgIslandExt track
  • lines changed 26, context: html, text, full: html, text
    completed genscan track
• src/hg/makeDb/doc/sorAra1.txt
  • lines changed 15, context: html, text, full: html, text
    adding cpgIslandExt track
  • lines changed 18, context: html, text, full: html, text
    done with genscan track build
• src/hg/makeDb/doc/speTri2.txt
  • lines changed 11, context: html, text, full: html, text
    adding cpgIslandExt track
  • lines changed 12, context: html, text, full: html, text
    completed genscan track
• src/hg/makeDb/doc/susScr3.txt
  • lines changed 10, context: html, text, full: html, text
    adding cpgIslandExt track
  • lines changed 18, context: html, text, full: html, text
    completed genscan track
• src/hg/makeDb/doc/tarSyr1.txt
  • lines changed 19, context: html, text, full: html, text
    adding cpgIslandExt track
  • lines changed 12, context: html, text, full: html, text
    completed genscan track
• src/hg/makeDb/doc/triMan1.txt
  • lines changed 10, context: html, text, full: html, text
    adding cpgIslandExt track
  • lines changed 21, context: html, text, full: html, text
    done with genscan track build
• src/hg/makeDb/doc/tupBel1.txt
  • lines changed 10, context: html, text, full: html, text
    adding cpgIslandExt track
• src/hg/makeDb/doc/turTru2.txt
  • lines changed 12, context: html, text, full: html, text
    adding cpgIslandExt track
  • lines changed 20, context: html, text, full: html, text
    done with genscan track build
• src/hg/makeDb/doc/vicPac1.txt
  • lines changed 15, context: html, text, full: html, text
    adding cpgIslandExt track
  • lines changed 17, context: html, text, full: html, text
    done with genscan track build
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    expand list of chroms for vegaGene redmine 7403
• src/hg/makeDb/trackDb/makefile
  • lines changed 1, context: html, text, full: html, text
    vicVic1 is actually vicPac1
• src/hg/utils/automation/doCpgIslands.pl
  • lines changed 1, context: html, text, full: html, text
    fix error in using head in a pipe in csh
• src/hg/utils/automation/doGenscan.pl
  • lines changed 354, context: html, text, full: html, text
    similar to doCpgIslands.pl and more robust
  • lines changed 19, context: html, text, full: html, text
    properly protect each step from repeats or missing previous step
• src/hg/utils/automation/grcIncidentUpdate.sh
  • lines changed 111, context: html, text, full: html, text
    present copy of update.sh used by grcIncidentDb.pl
• src/hg/utils/automation/grcRunIncidentUpdate.sh
  • lines changed 45, context: html, text, full: html, text
    current copy of runUpdate.sh used by grcIncidentDb.pl
• src/hg/utils/automation/ncbiIncidentDb.pl
  • lines changed 303, context: html, text, full: html, text
    now taken care of in grcIncidentDb.pl
• src/hg/utils/automation/ncbiIncidentUpdate.sh
  • lines changed 83, context: html, text, full: html, text
    now contained in grcRunIncidentUpdate.sh and grcIncidentUpdate.sh
• src/hg/utils/automation/ncbiRunIncidentUpdate.sh
  • lines changed 30, context: html, text, full: html, text
    now contained in grcRunIncidentUpdate.sh and grcIncidentUpdate.sh
• src/hg/utils/phyloTrees/60way.nh
  • lines changed 1, context: html, text, full: html, text
    update mm9 to mm10
• src/hg/utils/phyloTrees/placentals.txt
  • lines changed 30, context: html, text, full: html, text
    updating comments about which is what
• src/hg/utils/phyloTrees/vertebrates.txt
  • lines changed 26, context: html, text, full: html, text
    adding melUnd1 lepOcu1 hapBur1 neoBri1 mayZeb1 punNye1 xipMac1 oreNil1
• src/product/scripts/allDatabaseUpdate.sh
  • lines changed 1, context: html, text, full: html, text
    using bash instead of just sh so the include of browserEnvironment.txt will work without a full path
• src/product/scripts/fetchFullGbdb.sh
  • lines changed 1, context: html, text, full: html, text
    using bash instead of just sh so the include of browserEnvironment.txt will work without a full path
• src/product/scripts/fetchFullGoldenPath.sh
  • lines changed 1, context: html, text, full: html, text
    using bash instead of just sh so the include of browserEnvironment.txt will work without a full path
• src/product/scripts/fetchMinimalGbdb.sh
  • lines changed 1, context: html, text, full: html, text
    using bash instead of just sh so the include of browserEnvironment.txt will work without a full path
• src/product/scripts/fetchMinimalGoldenPath.sh
  • lines changed 1, context: html, text, full: html, text
    using bash instead of just sh so the include of browserEnvironment.txt will work without a full path
• src/product/scripts/kentSrcUpdate.sh
  • lines changed 1, context: html, text, full: html, text
    using bash instead of just sh so the include of browserEnvironment.txt will work without a full path
• src/product/scripts/loadDb.sh
  • lines changed 1, context: html, text, full: html, text
    using bash instead of just sh so the include of browserEnvironment.txt will work without a full path
• src/product/scripts/loadUpdateGoldenPath.sh
  • lines changed 1, context: html, text, full: html, text
    using bash instead of just sh so the include of browserEnvironment.txt will work without a full path
• src/product/scripts/tagGoldenPath.sh
  • lines changed 1, context: html, text, full: html, text
    using bash instead of just sh so the include of browserEnvironment.txt will work without a full path
• src/product/scripts/updateHtml.sh
  • lines changed 1, context: html, text, full: html, text
    using bash instead of just sh so the include of browserEnvironment.txt will work without a full path