Commits for chinhli

v259_base to v260_preview (2011-11-07 to 2011-11-15) v260

• LASTZ for Gibbon (nomLeu1) vs Human (hg19)
  • src/hg/makeDb/doc/hg19.txt - lines changed 64, context: html, text, full: html, text
  • src/hg/makeDb/doc/nomLeu1.txt - lines changed 25, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/trackDb.chainNet.ra - lines changed 54, context: html, text, full: html, text
• Correct the name of the tree model used in the 6 way conservation. redmine bug #5771.
  • src/hg/makeDb/doc/felCat4.txt - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cat/felCat4/cons6way.html - lines changed 6, context: html, text, full: html, text
• Provide liftOver files from sacCer3 to sacCer1 and sacCer2.
  • src/hg/makeDb/doc/sacCer3.txt - lines changed 32, context: html, text, full: html, text
• add lincRNAsCTTemp.as for two extra field description.
  • src/hg/lib/lincRNAsCTTemp.as - lines changed 11, context: html, text, full: html, text
• Initial description of gibbon nomLeu1
  • src/hg/makeDb/trackDb/gibbon/nomLeu1/description.html - lines changed 28, context: html, text, full: html, text
• Finished html for gibbon nomLeu1 assembly
  • src/hg/makeDb/doc/nomLeu1.txt - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/gibbon/nomLeu1/gap.html - lines changed 26, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/gibbon/nomLeu1/gold.html - lines changed 22, context: html, text, full: html, text
• Ignore tables for geneReviews and lincRNAs tracks.
  • src/hg/makeDb/schema/all.joiner - lines changed 28, context: html, text, full: html, text
• Change the search term for nomLeu1
  • src/hg/makeDb/trackDb/gibbon/nomLeu1/description.html - lines changed 28, context: html, text, full: html, text
• Add geneReviews tables to the geneReviews rule. No need to ignore them
  • src/hg/makeDb/schema/all.joiner - lines changed 8, context: html, text, full: html, text
• Add minCheck=0.85 filter to geneReviews and geneReviewRefGene table.
  • src/hg/makeDb/schema/all.joiner - lines changed 2, context: html, text, full: html, text
• Finished initial release of gibbon nomLeu1.
  • src/hg/makeDb/doc/nomLeu1.txt - lines changed 38, context: html, text, full: html, text
• When searching geneReviews using disease name, instead of useing '&search_param==begins_with', use '&search_param==begins_with'.
  • src/hg/hgc/hgc.c - lines changed 3, context: html, text, full: html, text