File Changes for hiram

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

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