Commits for braney

v273_preview2 to v273_base (2012-09-11 to 2012-09-18) v273

• take off verbose flag for initial rsync
  • src/hg/makeDb/genbank/etc/euronode-copy - lines changed 1, context: html, text, full: html, text
• move things around in the printf in hgGene that prints out the transcript start and stop, and CDS start and stop (#8249)
  • src/hg/hgGene/hgGene.c - lines changed 30, context: html, text, full: html, text
• fix problems with duplicate lines in refGene due to overlapping blat regions (#9008)
  • src/hg/makeDb/genbank/src/align/gbAlignFinish - lines changed 1, context: html, text, full: html, text
• more twiddling of the info about a gene (#8249)
  • src/hg/hgGene/hgGene.c - lines changed 3, context: html, text, full: html, text
• more twiddling (#8249)
  • src/hg/hgGene/hgGene.c - lines changed 3, context: html, text, full: html, text
• rebuilt to fix up kg5ToKg6 (#7045)
  • src/hg/makeDb/doc/ucscGenes/mm10.ucscGenes13.csh - lines changed 38, context: html, text, full: html, text
• eliminated pointless check for .2bit suffix in file name. There's checks elsewhere for file signature (#9095)
  • src/lib/twoBit.c - lines changed 5, context: html, text, full: html, text
• fix twoBit recognition logic (#9095). Look for signature in file rather than .2bit suffix
  • src/lib/twoBit.c - lines changed 36, context: html, text, full: html, text
• one more fix for this
  • src/utils/twoBitToFa/twoBitToFa.c - lines changed 4, context: html, text, full: html, text
• add a track that has the lifted over mm9 ucsc genes (#7045)
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra - lines changed 10, context: html, text, full: html, text
• add track of Pfam domains in UCSC genes (#8968)
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra - lines changed 9, context: html, text, full: html, text