Commits for angie

v286_preview to v286_preview2 (2013-06-24 to 2013-07-02) v286

• First draft of hgVai documentation. refs #6152
  • src/hg/htdocs/goldenPath/help/hgVaiHelpText.html - lines changed 322, context: html, text, full: html, text
• minor tweak: put tool's short/common name first, followed by long name.
  • src/hg/htdocs/goldenPath/help/hgVaiHelpText.html - lines changed 2, context: html, text, full: html, text
• Updating Complete Genomics samples and references. refs #683
  • src/hg/makeDb/trackDb/human/hg19/pgSnp.html - lines changed 78, context: html, text, full: html, text
• Added a cautionary note for the next dbSNP build, to look for rs IDs that havebeen mapped to assembly patch contigs but not the primary reference, because
  in at least some of those cases, mappings to the primary assembly show up on
  dbSNP's website but not in the download files. refs #8360
  
  • src/hg/makeDb/doc/hg19.txt - lines changed 33, context: html, text, full: html, text
• Clarifying which Genome Variants subtracks are native to hg19 and whichwere lifted. Unfortunately the per-subtrack origAssembly/pennantIcon
  settings aren't reflected in the hgTrackUi table of subtracks; that
  would be a nice feature.
  
  • src/hg/makeDb/trackDb/human/hg19/pgSnp.html - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra - lines changed 28, context: html, text, full: html, text
• Shortening too-longLabel per Brooke's suggestion. refs #683
  • src/hg/makeDb/trackDb/human/trackDb.pgSnp.ra - lines changed 1, context: html, text, full: html, text
• Updating links & small fixes - thanks Brooke! refs #683
  • src/hg/makeDb/trackDb/human/hg19/pgSnp.html - lines changed 80, context: html, text, full: html, text