angie: changes by file

review to branch (2010-06-01 to 2010-06-07) v233

• src/hg/hgTables/schema.c
  • 1.66 lines changed: 12, context: html, text, full: html, text
    For bigWig and BAM, provide link to format/info.
• src/hg/hgTrackUi/hgTrackUi.c
  • 1.527 lines changed: 3, context: html, text, full: html, text
    DGV: don't second-guess user filtering by include and deselecting all items.
  • 1.526 lines changed: 10, context: html, text, full: html, text
    Improvements to SNP controls' explanatory text -- thanks Mary!
• src/hg/hgTracks/simpleTracks.c
  • 1.148 lines changed: 3, context: html, text, full: html, text
    loadDgv: don't skip filtering when filterPmIds is NULL -- if the user has deselected everything but wants the filter to be include, we do need to filter.
• src/hg/hgTracks/variation.c
  • 1.148 lines changed: 1, context: html, text, full: html, text
    Comment tweak.
• src/hg/makeDb/doc/hg18.txt
  • 1.422 lines changed: 10, context: html, text, full: html, text
    Updated gwasCatalog.
• src/hg/makeDb/doc/hg19.txt
  • 1.117 lines changed: 45, context: html, text, full: html, text
    Regenerated snp131Exceptions, and snp131OrthoPt2Rm2Pa2 which depends on the exceptions. Multiple alignments were flagged even when there were single alignments to a chrom and chrom_hap, which had the effect of excluding haplo regions (even on main chroms) from ortho alignments.
  • 1.116 lines changed: 9, context: html, text, full: html, text
    Updated gwasCatalog: both new catalog data, and use just-released snp131 instead of snp130.
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • 1.120 lines changed: 4, context: html, text, full: html, text
    Updated gwasCatalog: both new catalog data, and use just-released snp131 instead of snp130.
• src/hg/snp/snpLoad/snpNcbiToUcsc.c
  • 1.12 lines changed: 46, context: html, text, full: html, text
    Fixed detection of multiple mappings to handle chr*_hap correctly, e.g. if a SNP maps to one chr6 pos and one chr6_cox_hap2 pos it is not multiply mapped. Other misc changes to accomodate human snp131.