Commits for kent

v248_preview2 to v248_base (2011-03-01 to 2011-03-08) v248

• Working on some mm9 ucscGenes issues from Pauline, related to redmine issue 2682. Commented out some Robert Baertsch retroGene stuff from all.joiner that was never made public, and had fallen out of date. Regenerating some tables with time stamps that are off.
  • src/hg/makeDb/doc/mm9.txt - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/schema/all.joiner - lines changed 14, context: html, text, full: html, text
• Adding hAllocConn parameter.
  • src/hg/protein/kgBioCyc0/kgBioCyc0.c - lines changed 2, context: html, text, full: html, text
• Added new utility to check if two columns look joinable in a database.
  • src/hg/makeDb/schema/joinTwoInfo/joinTwoInfo.c - lines changed 105, context: html, text, full: html, text
  • src/hg/makeDb/schema/joinTwoInfo/makefile - lines changed 18, context: html, text, full: html, text
• Made the transMapGeneUcscGenesId identifier fuzzy, since the transMap table covers known genes for all assemblies, and you can't really express this in all.joiner precisely, but it is still worthwhile to join on that column.
  • src/hg/makeDb/schema/all.joiner - lines changed 3, context: html, text, full: html, text
• Making all.joiner tolerate empty UniProt fields in some UCSC genes related tables.
  • src/hg/makeDb/schema/all.joiner - lines changed 4, context: html, text, full: html, text
• Adding count of unique overlapping fields.
  • src/hg/makeDb/schema/joinTwoInfo/joinTwoInfo.c - lines changed 24, context: html, text, full: html, text
• Fixing typo that caused an old version of the ucsc gene alignment table to be loaded.
  • src/hg/makeDb/doc/mm9.txt - lines changed 2, context: html, text, full: html, text
• Fixed taxon human/mouse mixup. Have to rerun the whole thing now though! Also fixed missing knownToSnpCds table.
  • src/hg/makeDb/doc/ucscGenes/mm9.ucscGenes12.csh - lines changed 22, context: html, text, full: html, text