Commits for angie

v311_base to v312_preview (2015-01-26 to 2015-02-02) v312

• Correcting the names of the dbSNP download files since they now tweak the paths for human.
  refs #14189
  
  • src/hg/makeDb/trackDb/human/snp142.shared.html - lines changed 16, context: html, text, full: html, text
• Jonathan found that snp*ExceptionDesc's NonIntegerChromCount was more
  than twice the number of rows in the snp table with that exception.
  Turns out it was incremented in a loop on alleles. Rebuilt w/corrected
  counts. Note: ExceptionDesc counts can still be slightly higher than
  snp table counts because several exceptions are logged before the point
  at which we decide whether to keep or discard a variant.
  refs #14189
  
  • src/hg/makeDb/doc/hg19.txt - lines changed 18, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg38/variation.txt - lines changed 18, context: html, text, full: html, text
  • src/hg/snp/snpLoad/snpNcbiToUcsc.c - lines changed 4, context: html, text, full: html, text
• Removing merge conflict caught by Kate. refs #14740
  
  • src/hg/makeDb/schema/all.joiner - lines changed 9, context: html, text, full: html, text
• All Tracks / All Tables groups are not yet working in hgAi; I have a
  plan to fix it right, but for now, just omit those groups.
  refs #14579
  
  • src/hg/lib/cartJson.c - lines changed 14, context: html, text, full: html, text
• Add yet another special case for all_* tables.
  
  • src/hg/hgAi/hgAi.c - lines changed 6, context: html, text, full: html, text
• Minor refactoring: instead of passing a schema link object into AddDataSource,
  make it locally.
  
  • src/hg/js/react/hgAi/hgAi.jsx - lines changed 32, context: html, text, full: html, text