angie: changes by commit

branch to review (2009-06-09 to 2009-06-16) v208

• Some code for codons smaller than 3 bases was erroneously applied to noncoding blocks smaller than 3 bases.
  • src/hg/hgTracks/cds.c 1.100 - lines changed: 12, context: html, text, full: html, text
• Added sacCer2 (why was it missing?).
  • src/hg/makeDb/trackDb/makefile 1.269 - lines changed: 1, context: html, text, full: html, text
• wgEncodeGencode names are not specific enough to warrant semiShortCircuit -- that was excluding UCSC Genes and other matches.
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.342 - lines changed: 8, context: html, text, full: html, text
• Added section describing settings specific to the snp125 (or later) tracks -- Kate's review feedback.
  • src/hg/makeDb/trackDb/README 1.77 - lines changed: 14, context: html, text, full: html, text
• Merged some duplicate notification messages about custom tracks and blat results when creating a session -- Thanks Ann.
  • src/hg/hgSession/hgSession.c 1.51 - lines changed: 44, context: html, text, full: html, text
• Added stderr logging (a la htmlVaWarn) to cartEarlyWarningHandler, so we get an informative message along with the stack dump.
  • src/hg/lib/cart.c 1.110 - lines changed: 9, context: html, text, full: html, text
• Prevent stack dump in case of stoopid invocation (googlebots).
  • src/hg/hgGene/hgGene.c 1.115 - lines changed: 8, context: html, text, full: html, text