Commits for hiram

v257_base to v258_preview (2011-09-19 to 2011-09-27) v258

• adding ending marker after section
  • src/hg/makeDb/doc/xenTro3.txt - lines changed 2, context: html, text, full: html, text
• starting xenTro3 lastz
  • src/hg/makeDb/doc/anoCar2.txt - lines changed 73, context: html, text, full: html, text
• adding liftOver to xenTro3
  • src/hg/makeDb/doc/xenTro2.txt - lines changed 18, context: html, text, full: html, text
• danRer6 becomes danRer7
  • src/hg/hgGene/hgGeneData/S_cerevisiae/sacCer2/otherOrgs.ra - lines changed 1, context: html, text, full: html, text
• running lastz xenTro3 vs. these others
  • src/hg/makeDb/doc/anoCar2.txt - lines changed 42, context: html, text, full: html, text
  • src/hg/makeDb/doc/danRer7.txt - lines changed 57, context: html, text, full: html, text
  • src/hg/makeDb/doc/galGal3.txt - lines changed 56, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg19.txt - lines changed 56, context: html, text, full: html, text
  • src/hg/makeDb/doc/mm9.txt - lines changed 54, context: html, text, full: html, text
  • src/hg/makeDb/doc/xenTro3.txt - lines changed 121, context: html, text, full: html, text
• better gold fragment name search
  • src/hg/makeDb/trackDb/xenTro/xenTro3/trackDb.ra - lines changed 10, context: html, text, full: html, text
• starting lastz on xenTro3
  • src/hg/makeDb/doc/rn4.txt - lines changed 37, context: html, text, full: html, text
• starting lastz on xenTro3
  • src/hg/makeDb/doc/monDom5.txt - lines changed 57, context: html, text, full: html, text
• starting xenTro3 lastz
  • src/hg/makeDb/doc/melGal1.txt - lines changed 53, context: html, text, full: html, text
• allow ctgPos2 search to find the chrM contig name too
  • src/hg/makeDb/trackDb/xenTro/xenTro3/trackDb.ra - lines changed 1, context: html, text, full: html, text
• adding xenTro3 chain net
  • src/hg/makeDb/trackDb/trackDb.chainNet.ra - lines changed 51, context: html, text, full: html, text
• xenTro3 lastz finished
  • src/hg/makeDb/doc/melGal1.txt - lines changed 11, context: html, text, full: html, text
• xenTro3 lastz chain net completed
  • src/hg/makeDb/doc/rn4.txt - lines changed 22, context: html, text, full: html, text
• better searches for gold and ctgPos2 tables
  • src/hg/makeDb/trackDb/turkey/melGal1/trackDb.ra - lines changed 17, context: html, text, full: html, text
• done with lastz chain net runs for xenTro3
  • src/hg/makeDb/doc/monDom5.txt - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/doc/xenTro3.txt - lines changed 71, context: html, text, full: html, text
• clarify the relationship between db table name and track definition in the .ra file
  • src/product/README.trackDb - lines changed 7, context: html, text, full: html, text
• initial source checks all dbs blast tabs
  • src/hg/utils/automation/checkBlastTabs.sh - lines changed 98, context: html, text, full: html, text