File Changes for angie

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

• src/hg/hgAi/hgAi.c
  • lines changed 6, context: html, text, full: html, text
    Add yet another special case for all_* tables.
    
• src/hg/js/react/hgAi/hgAi.jsx
  • lines changed 32, context: html, text, full: html, text
    Minor refactoring: instead of passing a schema link object into AddDataSource,
    make it locally.
    
• src/hg/lib/cartJson.c
  • lines changed 14, 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/makeDb/doc/hg19.txt
  • lines changed 18, 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/hg38/variation.txt
  • lines changed 18, 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/schema/all.joiner
  • lines changed 9, context: html, text, full: html, text
    Removing merge conflict caught by Kate. refs #14740
    
• src/hg/makeDb/trackDb/human/snp142.shared.html
  • lines changed 16, context: html, text, full: html, text
    Correcting the names of the dbSNP download files since they now tweak the paths for human.
    refs #14189
    
• src/hg/snp/snpLoad/snpNcbiToUcsc.c
  • lines changed 4, 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