File Changes for hiram

v275_preview2 to v275_base (2012-10-23 to 2012-10-30) v275

• src/hg/makeDb/doc/cerSim1.txt
  • lines changed 4, context: html, text, full: html, text
    blat servers assigned
  • lines changed 44, context: html, text, full: html, text
    lastz done hg19 and mm10 to cerSim1
• src/hg/makeDb/doc/galGal4.txt
  • lines changed 65, context: html, text, full: html, text
    done with lastz for chicken lamprey
• src/hg/makeDb/doc/hetGla1.txt
  • lines changed 22, context: html, text, full: html, text
    fixup labels on naked mole rat lastz
• src/hg/makeDb/doc/hg19.txt
  • lines changed 6, context: html, text, full: html, text
    lastz done hg19 and mm10 to cerSim1
• src/hg/makeDb/doc/melUnd1.txt
  • lines changed 22, context: html, text, full: html, text
    duplicate lastz entry for mm10
• src/hg/makeDb/doc/mm10.txt
  • lines changed 66, context: html, text, full: html, text
    lastz mm10 petMar2 done
  • lines changed 60, context: html, text, full: html, text
    lastz done hg19 and mm10 to cerSim1
  • lines changed 4, context: html, text, full: html, text
    fixup some comment names in lastz sections
  • lines changed 3, context: html, text, full: html, text
    fixup labels on naked mole rat lastz
• src/hg/makeDb/doc/oryLat2.txt
  • lines changed 64, context: html, text, full: html, text
    lastz done to petMar2
• src/hg/makeDb/doc/panTro4.txt
  • lines changed 22, context: html, text, full: html, text
    lastz for mm10 swap procedure included here
• src/hg/makeDb/doc/petMar2.txt
  • lines changed 22, context: html, text, full: html, text
    lastz mm10 petMar2 done
  • lines changed 8, context: html, text, full: html, text
    default position set and in the pushQ
  • lines changed 3, context: html, text, full: html, text
    blat servers assigned
  • lines changed 46, context: html, text, full: html, text
    lastz done for monDom5 and oryLat2
  • lines changed 19, context: html, text, full: html, text
    done with lastz for chicken lamprey
• src/hg/makeDb/schema/all.joiner
  • lines changed 1, context: html, text, full: html, text
    not petMar2 on the proteinAccession identifier
  • lines changed 9, context: html, text, full: html, text
    adding braFlo2
• src/hg/makeDb/trackDb/lamprey/trackDb.chainNet.ra
  • lines changed 6, context: html, text, full: html, text
    overrides for Mm10 chainNet
• src/hg/makeDb/trackDb/trackDb.chainNet.ra
  • lines changed 156, context: html, text, full: html, text
    adding petMar2 braFlo2 and cerSim1
  • lines changed 306, context: html, text, full: html, text
    adding sections for Dolphin, Alpaca, Pig, Coelacanth, Atlantic cod
  • lines changed 51, context: html, text, full: html, text
    addind in Atlantic Cod gadMor1
• src/hg/utils/automation/doBlastzChainNet.pl
  • lines changed 1, context: html, text, full: html, text
    removing ; from ;: situation in an article reference, redmine 8887 note 64
  • lines changed 1, context: html, text, full: html, text
    remove stray paren, redmine 8887 note 66
  • lines changed 4, context: html, text, full: html, text
    fixup md5sum of axtNet when single file in there, redmine 8887 note 70
• src/hg/utils/automation/extractRepeats
  • lines changed 73, context: html, text, full: html, text
    copy from bin/scripts from March 2006
• src/hg/utils/phyloTrees/64way.dissect.txt
  • lines changed 889, context: html, text, full: html, text
    need 64 way dissect tree
• src/hg/utils/phyloTrees/64way.nh
  • lines changed 27, context: html, text, full: html, text
    brought up to 64-way species
• src/hg/utils/phyloTrees/64wayChainNet.pl
  • lines changed 136, context: html, text, full: html, text
    brought up to 64-way species
• src/hg/utils/phyloTrees/65way.dissect.txt
  • lines changed 903, context: html, text, full: html, text
    adding chiLan1 Chinchilla
• src/hg/utils/phyloTrees/65way.nh
  • lines changed 28, context: html, text, full: html, text
    adding chiLan1 Chinchilla
• src/hg/utils/phyloTrees/chainNet.pl
  • lines changed 28, context: html, text, full: html, text
    brought up to 64-way species