File Changes for angie

v321_preview to v321_preview2 (2015-08-10 to 2015-08-17) v321

• src/hg/hgVarAnnogrator/hgVarAnnogrator.c
  • lines changed 1, context: html, text, full: html, text
    Moved averaging of wiggle values back from annoFormatTab to annoGrateWig,
    so that it can be done properly across multiple regions with data.
    A user was trying to get average GC over 1MB regions, but averages of
    smaller subregions were returned instead.
    refs #15834
    
• src/hg/inc/annoGrateWigDb.h
  • lines changed 3, context: html, text, full: html, text
    Moved averaging of wiggle values back from annoFormatTab to annoGrateWig,
    so that it can be done properly across multiple regions with data.
    A user was trying to get average GC over 1MB regions, but averages of
    smaller subregions were returned instead.
    refs #15834
    
• src/hg/js/model/hgIntegrator/hgIntegratorModel.js
  • lines changed 1, context: html, text, full: html, text
    Oops, need to include maf along with wigMaf in order to exclude MAF custom tracks.
    fixes #15857
    
• src/hg/lib/annoFormatVep.c
  • lines changed 29, context: html, text, full: html, text
    Moved averaging of wiggle values back from annoFormatTab to annoGrateWig,
    so that it can be done properly across multiple regions with data.
    A user was trying to get average GC over 1MB regions, but averages of
    smaller subregions were returned instead.
    refs #15834
    
• src/hg/lib/annoGrateWigDb.c
  • lines changed 5, context: html, text, full: html, text
    Moved averaging of wiggle values back from annoFormatTab to annoGrateWig,
    so that it can be done properly across multiple regions with data.
    A user was trying to get average GC over 1MB regions, but averages of
    smaller subregions were returned instead.
    refs #15834
    
• src/hg/lib/annoStreamDb.c
  • lines changed 2, context: html, text, full: html, text
    Fixing corner-case that caused the last item(s) to be lost when merge-sorting
    large-bin items and all items are in large bins.
    fixes #15867
    
• src/hg/lib/annoStreamWig.c
  • lines changed 2, context: html, text, full: html, text
    Moved averaging of wiggle values back from annoFormatTab to annoGrateWig,
    so that it can be done properly across multiple regions with data.
    A user was trying to get average GC over 1MB regions, but averages of
    smaller subregions were returned instead.
    refs #15834
    
• src/hg/lib/cartJson.c
  • lines changed 2, context: html, text, full: html, text
    Work around some hgcentraltest genome values that unintentionally include extra whitespace.
    
• src/hg/lib/hAnno.c
  • lines changed 3, context: html, text, full: html, text
    Moved averaging of wiggle values back from annoFormatTab to annoGrateWig,
    so that it can be done properly across multiple regions with data.
    A user was trying to get average GC over 1MB regions, but averages of
    smaller subregions were returned instead.
    refs #15834
    
• src/hg/lib/tests/annoGratorTester.c
  • lines changed 8, context: html, text, full: html, text
    Moved averaging of wiggle values back from annoFormatTab to annoGrateWig,
    so that it can be done properly across multiple regions with data.
    A user was trying to get average GC over 1MB regions, but averages of
    smaller subregions were returned instead.
    refs #15834
    
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Disabling pop-up configuration for exacVariants subtrack because the js pop-up config code
    mangles the cart's multishad & value of checkbox group items.
    refs #14379, #15873
    
• src/inc/annoGrateWig.h
  • lines changed 12, context: html, text, full: html, text
    Moved averaging of wiggle values back from annoFormatTab to annoGrateWig,
    so that it can be done properly across multiple regions with data.
    A user was trying to get average GC over 1MB regions, but averages of
    smaller subregions were returned instead.
    refs #15834
    
• src/inc/annoRow.h
  • lines changed 13, context: html, text, full: html, text
    Moved averaging of wiggle values back from annoFormatTab to annoGrateWig,
    so that it can be done properly across multiple regions with data.
    A user was trying to get average GC over 1MB regions, but averages of
    smaller subregions were returned instead.
    refs #15834
    
• src/lib/annoFormatTab.c
  • lines changed 72, context: html, text, full: html, text
    Moved averaging of wiggle values back from annoFormatTab to annoGrateWig,
    so that it can be done properly across multiple regions with data.
    A user was trying to get average GC over 1MB regions, but averages of
    smaller subregions were returned instead.
    refs #15834
    
• src/lib/annoGrateWig.c
  • lines changed 5, context: html, text, full: html, text
    Use isnan instead of comparing to NAN, which does not work!
    
  • lines changed 105, context: html, text, full: html, text
    Moved averaging of wiggle values back from annoFormatTab to annoGrateWig,
    so that it can be done properly across multiple regions with data.
    A user was trying to get average GC over 1MB regions, but averages of
    smaller subregions were returned instead.
    refs #15834
    
• src/lib/annoRow.c
  • lines changed 25, context: html, text, full: html, text
    Moved averaging of wiggle values back from annoFormatTab to annoGrateWig,
    so that it can be done properly across multiple regions with data.
    A user was trying to get average GC over 1MB regions, but averages of
    smaller subregions were returned instead.
    refs #15834
    
• src/lib/annoStreamBigWig.c
  • lines changed 4, context: html, text, full: html, text
    Moved averaging of wiggle values back from annoFormatTab to annoGrateWig,
    so that it can be done properly across multiple regions with data.
    A user was trying to get average GC over 1MB regions, but averages of
    smaller subregions were returned instead.
    refs #15834