Commits for hiram

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

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