Commits for hiram

v275_base to v276_preview (2012-10-30 to 2012-11-06) v276

• completed Lamprey petMar2 and Rhino cerSim1 lastz to Opossum
  • src/hg/makeDb/doc/cerSim1.txt - lines changed 23, context: html, text, full: html, text
  • src/hg/makeDb/doc/monDom5.txt - lines changed 141, context: html, text, full: html, text
• tuning up the chain net tracks to be accurate locations and parameters
  • src/hg/makeDb/trackDb/lamprey/trackDb.chainNet.ra - lines changed 19, context: html, text, full: html, text
• fixup petMar2 and geoFor1 priority overrides
  • src/hg/makeDb/trackDb/chicken/trackDb.chainNet.ra - lines changed 6, context: html, text, full: html, text
• correct priority for petMar2 chain net
  • src/hg/makeDb/trackDb/medaka/trackDb.chainNet.ra - lines changed 3, context: html, text, full: html, text
• correct priority for petMar2 chain net
  • src/hg/makeDb/trackDb/opossum/trackDb.chainNet.ra - lines changed 2, context: html, text, full: html, text
• cow v. rhino lastz done
  • src/hg/makeDb/doc/bosTau7.txt - lines changed 61, context: html, text, full: html, text
  • src/hg/makeDb/doc/cerSim1.txt - lines changed 24, context: html, text, full: html, text
• starting 7-way alignment
  • src/hg/makeDb/doc/petMar2.txt - lines changed 220, context: html, text, full: html, text
• gap and frame annotation added to the 7-way
  • src/hg/makeDb/doc/petMar2.txt - lines changed 239, context: html, text, full: html, text
• initial display of the 7-way conservation
  • src/hg/makeDb/trackDb/lamprey/petMar2/cons7way.html - lines changed 388, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/lamprey/petMar2/trackDb.7way.ra - lines changed 103, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/lamprey/petMar2/trackDb.ra - lines changed 1, context: html, text, full: html, text
• phylo tree estimate done from the 7-way maf file
  • src/hg/makeDb/doc/petMar2.txt - lines changed 140, context: html, text, full: html, text
• done with phastCons7way
  • src/hg/makeDb/doc/petMar2.txt - lines changed 277, context: html, text, full: html, text
• done with phyloP7way
  • src/hg/makeDb/doc/petMar2.txt - lines changed 187, context: html, text, full: html, text
• setting the phyloP viewLimits
  • src/hg/makeDb/trackDb/lamprey/petMar2/trackDb.7way.ra - lines changed 4, context: html, text, full: html, text
• liftOver to rn4 done
  • src/hg/makeDb/doc/rn5.txt - lines changed 16, context: html, text, full: html, text
• correct histogram of the phyloP data
  • src/hg/makeDb/doc/petMar2.txt - lines changed 13, context: html, text, full: html, text
• revisit the phyloP histogram graph
  • src/hg/makeDb/doc/geoFor1.txt - lines changed 16, context: html, text, full: html, text