angie: changes by commit

review to branch (2009-08-25 to 2009-09-02) v214

• Added check for table existence to printSnp125CodingAnnotations so an extra trackDb setting is ignored instead of errAborting.
  • src/hg/hgc/hgc.c 1.1569 - lines changed: 2, context: html, text, full: html, text
• Adding local overrides for snp130 (*provisional* b37 coord release by dbSNP).
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra 1.49 - lines changed: 12, context: html, text, full: html, text
• If refNCBI is wrong size (or snp coords are wrong), make an error instead of aborting. Don't abort on between+in-del -- between size is 0, min observed size can be 0 (-).
  • src/hg/snp/snpLoad/snpNcbiToUcsc.c 1.11 - lines changed: 10, context: html, text, full: html, text
• Added snp130: dbSNP's provisional mapping from b36 to GRCh37 coords. Also added orthologous allele table for snp130.
  • src/hg/makeDb/doc/hg19.txt 1.36 - lines changed: 302, context: html, text, full: html, text
• Adding minCheck to snp130Exceptions.name -- sometimes a snp can trigger an exception before we detect a real error and omit it from snp130.
  • src/hg/makeDb/schema/all.joiner 1.733 - lines changed: 1, context: html, text, full: html, text