angie: changes by file

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

• src/hg/hgTables/filterFields.c
  • 1.77 lines changed: 16, context: html, text, full: html, text
    When selecting fields for output, automatically include any tables specified in trackDb setting defaultLinkedTables.
• src/hg/hgTables/joining.c
  • 1.56 lines changed: 2, 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/hgTrackUi/hgTrackUi.c
  • 1.493 lines changed: 6, 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/hgc/hgc.c
  • 1.1557 lines changed: 4, context: html, text, full: html, text
    Added note that HDGP geographical allele images may show alleles from the - strand (thanks David).
  • 1.1556 lines changed: 6, 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/makeDb/schema/all.joiner
  • 1.720 lines changed: 1, context: html, text, full: html, text
    Added mm6 back to mm -- it is still on hgwdev.
• src/hg/makeDb/trackDb/README
  • 1.79 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).
  • 1.78 lines changed: 2, context: html, text, full: html, text
    Added new setting defaultLinkedTables.
• src/hg/makeDb/trackDb/snp128.html
  • 1.12 lines changed: 2, context: html, text, full: html, text
    Added clarification for meaning of cds-reference / "Reference (coding)".
• src/hg/makeDb/trackDb/snp129.html
  • 1.10 lines changed: 2, context: html, text, full: html, text
    Added clarification for meaning of cds-reference / "Reference (coding)".
• src/hg/makeDb/trackDb/snp130.html
  • 1.5 lines changed: 2, context: html, text, full: html, text
    Added clarification for meaning of cds-reference / "Reference (coding)".
• src/hg/makeDb/trackDb/trackDb.ra
  • 1.515 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).
  • 1.514 lines changed: 2, context: html, text, full: html, text
    Make UCSC Genes the default label for knownGene going forward.
  • 1.513 lines changed: 1, context: html, text, full: html, text
    Added new defaultLinkedTables setting to knownGene so kgXref will appear by default when selecting output fields in hgTables.
  • 1.512 lines changed: 3, context: html, text, full: html, text
    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/human/hg15/trackDb.ra
  • 1.85 lines changed: 4, context: html, text, full: html, text
    Add override labels for knownGene (now UCSC Genes at top level).
• src/hg/makeDb/trackDb/human/hg16/trackDb.ra
  • 1.573 lines changed: 11, context: html, text, full: html, text
    Convert knownGene to override, to simplify and to inherit new top-level settings.
• src/hg/makeDb/trackDb/human/hg17/trackDb.ra
  • 1.425 lines changed: 12, context: html, text, full: html, text
    Convert knownGene to override, to simplify and to inherit new top-level settings.
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • 1.398 lines changed: 14, context: html, text, full: html, text
    Convert knownGene to override, to simplify and to inherit new top-level settings.
  • 1.397 lines changed: 1, 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/hg19/trackDb.ra
  • 1.30 lines changed: 1, context: html, text, full: html, text
    Fixed termRegex for ctgPos2.
• src/hg/makeDb/trackDb/mouse/mm6/trackDb.ra
  • 1.53 lines changed: 12, context: html, text, full: html, text
    Convert knownGene to override, to simplify and to inherit new top-level settings.
• src/hg/makeDb/trackDb/mouse/mm7/trackDb.ra
  • 1.55 lines changed: 12, context: html, text, full: html, text
    Convert knownGene to override, to simplify and to inherit new top-level settings.
• src/hg/makeDb/trackDb/mouse/mm8/trackDb.ra
  • 1.55 lines changed: 12, context: html, text, full: html, text
    Convert knownGene to override, to simplify and to inherit new top-level settings.
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.ra
  • 1.50 lines changed: 27, context: html, text, full: html, text
    Removed local knownGene definition (duplicate of top level now).
• src/hg/makeDb/trackDb/rat/rn3/trackDb.ra
  • 1.60 lines changed: 12, context: html, text, full: html, text
    Convert knownGene to override, to simplify and to inherit new top-level settings.
• src/hg/makeDb/trackDb/rat/rn4/trackDb.ra
  • 1.35 lines changed: 12, context: html, text, full: html, text
    Convert knownGene to override, to simplify and to inherit new top-level settings.
• src/test/buildTableDescriptions.pl
  • 1.43 lines changed: 1, context: html, text, full: html, text
    Yet another duplicate to ignore.