Commits for hiram

v259_preview to v259_preview2 (2011-10-25 to 2011-11-01) v259

• fixup ensGene name searches for the extra letters in the ENS gene names
  • src/hg/makeDb/trackDb/squirt/cioSav2/trackDb.ra - lines changed 34, context: html, text, full: html, text
• fixup gold search rule to allow all fragment names to match
  • src/hg/makeDb/trackDb/zebrafish/danRer7/trackDb.ra - lines changed 5, context: html, text, full: html, text
• fixup ensGene and flyBase gene search rules to match the new patterns
  • src/hg/makeDb/trackDb/drosophila/dm3/trackDb.ra - lines changed 31, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/drosophila/trackDb.ra - lines changed 2, context: html, text, full: html, text
• fixup sgpGene searchTable rule to match these scaffold names
  • src/hg/makeDb/trackDb/cat/felCat3/trackDb.ra - lines changed 4, context: html, text, full: html, text
• finished with lastz gorGor3 to rheMac2 and ponAbe2
  • src/hg/makeDb/doc/ponAbe2.txt - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/doc/rheMac2.txt - lines changed 7, context: html, text, full: html, text
• done with Chimp and Orangutan lastz
  • src/hg/makeDb/doc/gorGor3.txt - lines changed 40, context: html, text, full: html, text
• fixing up search rules
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/ce10/trackDb.ra - lines changed 34, context: html, text, full: html, text
• search rules to eliminate any errors from checkHgFindSpec -checkTermRegex
  • src/hg/makeDb/trackDb/worm/ce10/trackDb.ra - lines changed 16, context: html, text, full: html, text
• search rules to eliminate any errors from checkHgFindSpec -checkTermRegex
  • src/hg/makeDb/trackDb/stickleback/gasAcu1/trackDb.ra - lines changed 1, context: html, text, full: html, text
• search rules to eliminate any errors from checkHgFindSpec -checkTermRegex
  • src/hg/makeDb/trackDb/rhesus/rheMac2/trackDb.ra - lines changed 8, context: html, text, full: html, text
• extend ctgPos search rule to function OK here
  • src/hg/makeDb/trackDb/rat/rn4/trackDb.ra - lines changed 7, context: html, text, full: html, text
• update ensGene search rules to match the names in this genome
  • src/hg/makeDb/trackDb/sacCer/sacCer3/trackDb.ra - lines changed 33, context: html, text, full: html, text
• update ensGene search rules to work with the Ensembl naming pattern here
  • src/hg/makeDb/trackDb/fugu/fr1/trackDb.ra - lines changed 32, context: html, text, full: html, text
• finishing up the lastz runs to gorGor3
  • src/hg/makeDb/doc/calJac3.txt - lines changed 15, context: html, text, full: html, text
  • src/hg/makeDb/doc/gorGor3.txt - lines changed 97, context: html, text, full: html, text
  • src/hg/makeDb/doc/nomLeu1.txt - lines changed 24, context: html, text, full: html, text
  • src/hg/makeDb/doc/panTro3.txt - lines changed 30, context: html, text, full: html, text
• fixup checkHgFindSpec errors
  • src/hg/makeDb/trackDb/cow/bosTau4/trackDb.ra - lines changed 13, context: html, text, full: html, text
• fixup checkHgFindSpec errors
  • src/hg/makeDb/trackDb/worm/ce6/trackDb.ra - lines changed 33, context: html, text, full: html, text
• fixup search for gold and ctgPos2
  • src/hg/makeDb/trackDb/zebrafish/danRer4/trackDb.ra - lines changed 6, context: html, text, full: html, text
• fixup ctgPos2 search rule
  • src/hg/makeDb/trackDb/zebrafish/danRer3/trackDb.ra - lines changed 1, context: html, text, full: html, text
• fixup checkHgFindSpec errors
  • src/hg/makeDb/trackDb/zebrafish/danRer5/trackDb.ra - lines changed 9, context: html, text, full: html, text
• fixup checkHgFindSpec errors
  • src/hg/makeDb/trackDb/zebrafish/danRer6/trackDb.ra - lines changed 8, context: html, text, full: html, text
• fixup nscanGene checkHgFindSpec
  • src/hg/makeDb/trackDb/drosophila/dm2/trackDb.ra - lines changed 4, context: html, text, full: html, text
• same ensGene search rules for all sacCer assemblies
  • src/hg/makeDb/trackDb/sacCer/sacCer3/trackDb.ra - lines changed 33, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/sacCer/trackDb.ra - lines changed 33, context: html, text, full: html, text
• fixup some of the checkHgFindSpec errors
  • src/hg/makeDb/trackDb/tetraodon/tetNig1/trackDb.ra - lines changed 23, context: html, text, full: html, text
• fixup checkHgFindSpec errors
  • src/hg/makeDb/trackDb/worm/ce10/trackDb.ra - lines changed 1, context: html, text, full: html, text