angie: changes by commit

review to branch (2009-06-16 to 2009-06-23) v209

• hgFindSpec tweaks: for the more restrictive stsMapAliasMrnaAcc search, don't require that all aliases match the termRegex. Broaden sgpGene and geneid termRegexes to accomodate hg19.
  • src/hg/makeDb/trackDb/trackDb.ra 1.512 - lines changed: 3, context: html, text, full: html, text
• Fixed termRegex for ctgPos2.
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra 1.30 - lines changed: 1, context: html, text, full: html, text
• When selecting fields for output, automatically include any tables specified in trackDb setting defaultLinkedTables.
  • src/hg/hgTables/filterFields.c 1.77 - lines changed: 16, context: html, text, full: html, text
• Added new defaultLinkedTables setting to knownGene so kgXref will appear by default when selecting output fields in hgTables.
  • src/hg/makeDb/trackDb/human/hg18/trackDb.ra 1.397 - lines changed: 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/trackDb.ra 1.513 - lines changed: 1, context: html, text, full: html, text
• Make UCSC Genes the default label for knownGene going forward.
  • src/hg/makeDb/trackDb/trackDb.ra 1.514 - lines changed: 2, context: html, text, full: html, text
• Removed local knownGene definition (duplicate of top level now).
  • src/hg/makeDb/trackDb/mouse/mm9/trackDb.ra 1.50 - lines changed: 27, context: html, text, full: html, text
• Add override labels for knownGene (now UCSC Genes at top level).
  • src/hg/makeDb/trackDb/human/hg15/trackDb.ra 1.85 - lines changed: 4, context: html, text, full: html, text
• Convert knownGene to override, to simplify and to inherit new top-level settings.
  • src/hg/makeDb/trackDb/human/hg16/trackDb.ra 1.573 - lines changed: 11, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg17/trackDb.ra 1.425 - lines changed: 12, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/trackDb.ra 1.398 - lines changed: 14, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm6/trackDb.ra 1.53 - lines changed: 12, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm7/trackDb.ra 1.55 - lines changed: 12, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm8/trackDb.ra 1.55 - lines changed: 12, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rat/rn3/trackDb.ra 1.60 - lines changed: 12, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rat/rn4/trackDb.ra 1.35 - lines changed: 12, context: html, text, full: html, text
• Added mm6 back to mm -- it is still on hgwdev.
  • src/hg/makeDb/schema/all.joiner 1.720 - lines changed: 1, context: html, text, full: html, text
• Added NULL check -- this can happen when a trackDb setting specifies a table that isn't properly linked in all.joiner.
  • src/hg/hgTables/joining.c 1.56 - lines changed: 2, context: html, text, full: html, text
• Added new setting defaultLinkedTables.
  • src/hg/makeDb/trackDb/README 1.78 - lines changed: 2, context: html, text, full: html, text
• Yet another duplicate to ignore.
  • src/test/buildTableDescriptions.pl 1.43 - lines changed: 1, context: html, text, full: html, text
• Added clarification for meaning of cds-reference / "Reference (coding)".
  • src/hg/makeDb/trackDb/snp128.html 1.12 - lines changed: 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/snp129.html 1.10 - lines changed: 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/snp130.html 1.5 - lines changed: 2, context: html, text, full: html, text
• Added new SNP-specific setting defaultGeneTracks, to enable functional annotations of SNPs relative to some gene track(s).
  • src/hg/hgTrackUi/hgTrackUi.c 1.493 - lines changed: 6, context: html, text, full: html, text
  • src/hg/hgc/hgc.c 1.1556 - lines changed: 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/README 1.79 - lines changed: 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/trackDb.ra 1.515 - lines changed: 2, context: html, text, full: html, text
• Added note that HDGP geographical allele images may show alleles from the - strand (thanks David).
  • src/hg/hgc/hgc.c 1.1557 - lines changed: 4, context: html, text, full: html, text