hiram: changes by commit

branch to review (2009-02-09 to 2009-02-17) v200

• Added sacCer2.
  • src/hg/makeDb/genbank/etc/genbank.conf 1.328 - lines changed: 16, context: html, text, full: html, text
• If we translate the type five_prime_UTR_intron to 5utr and use the -gtf option to ldHgGene then it seems to work OK.
  • src/hg/makeDb/outside/yeast/hgSgdGff3/sgdGffToGtf.pl 1.4 - lines changed: 1, context: html, text, full: html, text
• Ran the liftOver to sacCer2
  • src/hg/makeDb/doc/sacCer1.txt 1.7 - lines changed: 27, context: html, text, full: html, text
• Initial work has genome up and running, sgdGene tracks functioning, running genbank
  • src/hg/makeDb/doc/sacCer2.txt 1.1 - lines changed: 312, context: html, text, full: html, text
• Ran liftOver to rn5 back in December
  • src/hg/makeDb/doc/rn4.txt 1.32 - lines changed: 9, context: html, text, full: html, text
• Human proteins done by Brian, and multiple alignment in progress, genbank done
  • src/hg/makeDb/doc/sacCer2.txt 1.3 - lines changed: 165, context: html, text, full: html, text
• Straighten out business with fr2ScaffoldEnsemblLink()
  • src/hg/hgTracks/hgTracks.c 1.1554 - lines changed: 3, context: html, text, full: html, text
• Finished 7-way conservation business
  • src/hg/makeDb/doc/sacCer2.txt 1.4 - lines changed: 289, context: html, text, full: html, text
• Adding 7-way multiple conservation track
  • src/hg/makeDb/trackDb/sacCer/sacCer2/trackDb.ra 1.2 - lines changed: 43, context: html, text, full: html, text
• gap off, and most conserved on pack
  • src/hg/makeDb/trackDb/sacCer/sacCer2/trackDb.ra 1.3 - lines changed: 2, context: html, text, full: html, text