kent: changes by file

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

• src/hg/makeDb/doc/hg19.txt
  • 1.41 lines changed: 102, context: html, text, full: html, text
    Doing stuff to get gnfAtlas2 data in.
  • 1.40 lines changed: 31, context: html, text, full: html, text
    Adding Allen Brain track to hg19.
• src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes12.csh
  • 1.6 lines changed: 14, context: html, text, full: html, text
    Did old to new mapping.
  • 1.5 lines changed: 12, context: html, text, full: html, text
    Making a few more knownTo tables
  • 1.4 lines changed: 36, context: html, text, full: html, text
    Doing/redoing some knownTo tables and pfam.
• src/hg/makeDb/doc/ucscGenes/mm9.ucscGenes12.csh
  • 1.1 lines changed: 1206, context: html, text, full: html, text
    Starting new build of mouse UCSC Genes.
• src/hg/makeDb/hgLoadSeq/hgLoadSeq.c
  • 1.15 lines changed: 2, 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/protein/pbCalResStdGlobal/pbCalResStdGlobal.c
  • 1.9 lines changed: 1, context: html, text, full: html, text
    Fixed typo in comment
• src/hg/txGene/txGeneAddOldUnmapped/makefile
  • 1.1 lines changed: 18, 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/txGeneAddOldUnmapped.c
  • 1.1 lines changed: 67, 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/txGeneExplainUpdate2/txGeneExplainUpdate2.c
  • 1.2 lines changed: 22, context: html, text, full: html, text
    Adding -unmapped and -oldAsm options.
• src/hg/utils/automation/doHgNearBlastp.pl
  • 1.11 lines changed: 1, context: html, text, full: html, text
    Made it treat 'tmpFoo' as a mammal for updates in place of the database.
• src/lib/bwgCreate.c
  • 1.17 lines changed: 3, context: html, text, full: html, text
    Improving error message.