kent: changes by commit

branch to review (2009-09-29 to 2009-10-06) v217

• Starting new build of mouse UCSC Genes.
  • src/hg/makeDb/doc/ucscGenes/mm9.ucscGenes12.csh 1.1 - lines changed: 1206, context: html, text, full: html, text
• Improving error message.
  • src/lib/bwgCreate.c 1.17 - lines changed: 3, context: html, text, full: html, text
• Adding Allen Brain track to hg19.
  • src/hg/makeDb/doc/hg19.txt 1.40 - lines changed: 31, context: html, text, full: html, text
• Fixed typo in comment
  • src/hg/protein/pbCalResStdGlobal/pbCalResStdGlobal.c 1.9 - lines changed: 1, context: html, text, full: html, text
• Doing/redoing some knownTo tables and pfam.
  • src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes12.csh 1.4 - lines changed: 36, context: html, text, full: html, text
• Adding a little more detail to history table record of hgLoadSeq. It still is giving warnings, I think maybe because of the missing gbDate field.
  • src/hg/makeDb/hgLoadSeq/hgLoadSeq.c 1.15 - lines changed: 2, context: html, text, full: html, text
• Making a few more knownTo tables
  • src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes12.csh 1.5 - lines changed: 12, context: html, text, full: html, text
• Doing stuff to get gnfAtlas2 data in.
  • src/hg/makeDb/doc/hg19.txt 1.41 - lines changed: 102, context: html, text, full: html, text
• Made it treat 'tmpFoo' as a mammal for updates in place of the database.
  • src/hg/utils/automation/doHgNearBlastp.pl 1.11 - lines changed: 1, context: html, text, full: html, text
• Utility to add in genes that couldn't be mapped from previous assembly to oldToNew table seems to work.
  • src/hg/txGene/txGeneAddOldUnmapped/makefile 1.1 - lines changed: 18, context: html, text, full: html, text
  • src/hg/txGene/txGeneAddOldUnmapped/txGeneAddOldUnmapped.c 1.1 - lines changed: 67, context: html, text, full: html, text
• Adding -unmapped and -oldAsm options.
  • src/hg/txGene/txGeneExplainUpdate2/txGeneExplainUpdate2.c 1.2 - lines changed: 22, context: html, text, full: html, text
• Did old to new mapping.
  • src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes12.csh 1.6 - lines changed: 14, context: html, text, full: html, text