hiram: changes by file

branch to review (2010-02-16 to 2010-02-23) v226

• src/hg/makeDb/doc/calJac3.txt
  • 1.4 lines changed: 265, context: html, text, full: html, text
    trying to lastz papHam1 ogoGar1 micMur1 and tarSyr1 with difficulty
• src/hg/makeDb/doc/gorGor2.txt
  • 1.3 lines changed: 53, context: html, text, full: html, text
    done with genbank run
  • 1.2 lines changed: 100, context: html, text, full: html, text
    adding other gaps and ready for kluster scratch/data rsync
  • 1.1 lines changed: 110, context: html, text, full: html, text
    initial assembly build and done with repeatMasker and simpleRepeats
• src/hg/makeDb/genbank/etc/align.dbs
  • 1.112 lines changed: 1, context: html, text, full: html, text
    Added gorGor2 - Gorilla Gorilla
• src/hg/makeDb/genbank/etc/genbank.conf
  • 1.364 lines changed: 19, context: html, text, full: html, text
    adding gorilla gorGor2
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • 1.116 lines changed: 1, context: html, text, full: html, text
    Added gorGor2 - Gorilla Gorilla
• src/hg/makeDb/genbank/src/lib/gbGenome.c
  • 1.76 lines changed: 2, context: html, text, full: html, text
    adding names for gorilla species
• src/hg/makeDb/trackDb/marmoset/calJac3/description.html
  • 1.2 lines changed: 72, context: html, text, full: html, text
    cleaned up discussion and references, ready to go
• src/hg/makeDb/trackDb/marmoset/calJac3/gap.html
  • 1.2 lines changed: 41, context: html, text, full: html, text
    cleaned up gap types to cover all included in this assembly
• src/hg/makeDb/trackDb/marmoset/calJac3/gold.html
  • 1.2 lines changed: 9, context: html, text, full: html, text
    Correct text
• src/hg/makeDb/trackDb/marmoset/calJac3/trackDb.ra
  • 1.2 lines changed: 36, context: html, text, full: html, text
    Adding an 8-way conservation
• src/hg/makeDb/trackDb/tetraodon/tetNig2/trackDb.chainNet.ra
  • 1.3 lines changed: 8, context: html, text, full: html, text
    some better defaults on initial track visibilities
• src/hg/makeDb/trackDb/tetraodon/tetNig2/trackDb.ra
  • 1.5 lines changed: 2, context: html, text, full: html, text
    some better defaults on initial track visibilities
• src/hg/utils/automation/doBlastzChainNet.pl
  • 1.32 lines changed: 11, context: html, text, full: html, text
    adding an elapsed time calculation when successful completion
• src/hg/utils/automation/n50.pl
  • 1.3 lines changed: 13, context: html, text, full: html, text
    working even if contig names are identical and ignoring extra columns on input