File Changes for hiram

v267_preview to v267_preview2 (2012-05-01 to 2012-05-08) v267

• src/hg/gsBig/gsBig.c
  • lines changed 10, context: html, text, full: html, text
    after all these years, gsBig has been leaving garbage all over the place for no good reason. Fixed this bug
• src/hg/gsBig/makefile
  • lines changed 4, context: html, text, full: html, text
    add compile target
• src/hg/makeDb/doc/canFam2.txt
  • lines changed 28, context: html, text, full: html, text
    completed liftOver to canFam3
• src/hg/makeDb/doc/canFam3.txt
  • lines changed 87, context: html, text, full: html, text
    starting genbank run
  • lines changed 6, context: html, text, full: html, text
    done with genbank run
• src/hg/makeDb/doc/choHof1.txt
  • lines changed 25, context: html, text, full: html, text
    done with windowMasker track
• src/hg/makeDb/doc/dipOrd1.txt
  • lines changed 84, context: html, text, full: html, text
    done with windowMasker and running genbank
• src/hg/makeDb/doc/echTel1.txt
  • lines changed 35, context: html, text, full: html, text
    done with windowMasker
• src/hg/makeDb/doc/felCat5.txt
  • lines changed 123, context: html, text, full: html, text
    completed a tough genscan run
• src/hg/makeDb/doc/micMur1.txt
  • lines changed 18, context: html, text, full: html, text
    done with windowMasker
• src/hg/makeDb/doc/mm6.txt
  • lines changed 34, context: html, text, full: html, text
    constructing liftOver to Mm10
• src/hg/makeDb/doc/mm8.txt
  • lines changed 20, context: html, text, full: html, text
    constructing liftOver to Mm10
• src/hg/makeDb/doc/ochPri2.txt
  • lines changed 25, context: html, text, full: html, text
    completed windowMasker track
• src/hg/makeDb/doc/panTro4.txt
  • lines changed 125, context: html, text, full: html, text
    completed a difficult gencode run
  • lines changed 94, context: html, text, full: html, text
    completed genbank operations
• src/hg/makeDb/doc/papHam1.txt
  • lines changed 86, context: html, text, full: html, text
    completed windowMasker track
• src/hg/makeDb/doc/proCap1.txt
  • lines changed 25, context: html, text, full: html, text
    completed windowMasker track
• src/hg/makeDb/doc/pteVam1.txt
  • lines changed 30, context: html, text, full: html, text
    window masker done
• src/hg/makeDb/doc/rn5.txt
  • lines changed 120, context: html, text, full: html, text
    completed a complicated genscan run
• src/hg/makeDb/doc/tarSyr1.txt
  • lines changed 18, context: html, text, full: html, text
    done with windowMasker
• src/hg/makeDb/doc/tupBel1.txt
  • lines changed 25, context: html, text, full: html, text
    done with genscan track
  • lines changed 25, context: html, text, full: html, text
    completed windowMasker track
• src/hg/makeDb/doc/vicPac1.txt
  • lines changed 21, context: html, text, full: html, text
    completed windowMasker track
• src/hg/makeDb/genbank/etc/align.dbs
  • lines changed 1, context: html, text, full: html, text
    Added canFam3.
  • lines changed 1, context: html, text, full: html, text
    Added panTro4.
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 17, context: html, text, full: html, text
    adding definition for canFam3
  • lines changed 1, context: html, text, full: html, text
    unplacedChroms should be chrUn_*
  • lines changed 1, context: html, text, full: html, text
    unplacedChroms means any chrom with non-bridged gaps as marked in the lift file
  • lines changed 5, context: html, text, full: html, text
    canFam3 is labelled finished
  • lines changed 18, context: html, text, full: html, text
    adding choHof1 and removing blanks at end of line
  • lines changed 17, context: html, text, full: html, text
    adding chrPic1 painted turtle
  • lines changed 17, context: html, text, full: html, text
    adding dasNov3 painted turtle
  • lines changed 17, context: html, text, full: html, text
    adding dipOrd1 kangaroo rat
  • lines changed 19, context: html, text, full: html, text
    adding rn5 rat
  • lines changed 19, context: html, text, full: html, text
    adding felCat5 rat
  • lines changed 2, context: html, text, full: html, text
    broken definition for felCat5
  • lines changed 18, context: html, text, full: html, text
    adding galGal4 chicken
  • lines changed 21, context: html, text, full: html, text
    adding panTro4 chimp
  • lines changed 22, context: html, text, full: html, text
    adding susScr3 pig
  • lines changed 1, context: html, text, full: html, text
    correct specifications for panTro4
  • lines changed 1, context: html, text, full: html, text
    correct specifications for susScr3
  • lines changed 18, context: html, text, full: html, text
    adding otoGar3 bushbaby
  • lines changed 1, context: html, text, full: html, text
    need to say no for lift
  • lines changed 20, context: html, text, full: html, text
    adding hetGla2 painted turtle
  • lines changed 19, context: html, text, full: html, text
    adding nomLeu2 Gibbon
  • lines changed 19, context: html, text, full: html, text
    adding turTru2 Dolphin
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • lines changed 1, context: html, text, full: html, text
    Added canFam3.
  • lines changed 1, context: html, text, full: html, text
    Added panTro4.
• src/hg/makeDb/genbank/src/lib/gbGenome.c
  • lines changed 2, context: html, text, full: html, text
    adding definition for choHofNames Choloepus hoffmanni
  • lines changed 2, context: html, text, full: html, text
    adding definition for chrPicNames Chrysemys picta bellii
  • lines changed 2, context: html, text, full: html, text
    adding definition for dipOrdNames Dipodomys ordii
  • lines changed 2, context: html, text, full: html, text
    adding definition for otoGarNames Otolemur garnettii
  • lines changed 2, context: html, text, full: html, text
    adding definition for turTruNames Tursiops truncatus
• src/hg/utils/automation/doSameSpeciesLiftOver.pl
  • lines changed 16, context: html, text, full: html, text
    allow /hive/data/genomes/ to satisify the patch to the 2bit files
• src/hg/utils/automation/doWindowMasker.pl
  • lines changed 38, context: html, text, full: html, text
    adding the bits that used to be done manually after it was finished, cleaning the sequence of gaps