File Changes for angie

v289_preview2 to v289_base (2013-09-02 to 2013-09-09) v289

• src/hg/hgGenome/mainPage.c
  • lines changed 1, context: html, text, full: html, text
    Fixing linker warnings that appear on Mac OS X 10.8, caused byarguments passed to functions that don't take any arguments.
    
• src/hg/hgTables/compositeTrack.c
  • lines changed 1, context: html, text, full: html, text
    Fixing linker warnings that appear on Mac OS X 10.8, caused byarguments passed to functions that don't take any arguments.
    
• src/hg/hgTables/hgTables.c
  • lines changed 1, context: html, text, full: html, text
    Fixing linker warnings that appear on Mac OS X 10.8, caused byarguments passed to functions that don't take any arguments.
    
• src/hg/hgTracks/snakeTrack.c
  • lines changed 2, context: html, text, full: html, text
    Fixing Mac OS X portability issue.
  • lines changed 1, context: html, text, full: html, text
    Fixing compiler warning that appears only when compiling with -O.
• src/hg/hgVai/hgVai.c
  • lines changed 34, context: html, text, full: html, text
    hgVai can now handle assembly hubs, but if they have no genePred tracks, itcan't really do anything useful so it just suggests that the user choose a different assembly.
    fixes #11306
    
• src/hg/lib/annoFormatVep.c
  • lines changed 18, context: html, text, full: html, text
    VCF annoRows need to have corrected coords for indels, otherwise it messesup coord comparison in annoGrator. Also, that lets us get rid of the
    ugly skippedFirstBase hack in annoFormatVep and annoGratorGpVar.
    
• src/hg/lib/annoGratorGpVar.c
  • lines changed 3, context: html, text, full: html, text
    VCF annoRows need to have corrected coords for indels, otherwise it messesup coord comparison in annoGrator. Also, that lets us get rid of the
    ugly skippedFirstBase hack in annoFormatVep and annoGratorGpVar.
    
• src/hg/lib/tests/expected/annoGrator/snpBigWigToTabOut.txt
  • lines changed 3, context: html, text, full: html, text
    snp135 got some new rows when it was rebuilt (#11544), so we get some new rows of output.
• src/hg/lib/tests/expected/annoGrator/vepOut.txt
  • lines changed 11, context: html, text, full: html, text
    VCF annoRows need to have corrected coords for indels, otherwise it messesup coord comparison in annoGrator. Also, that lets us get rid of the
    ugly skippedFirstBase hack in annoFormatVep and annoGratorGpVar.
    
• src/inc/vcf.h
  • lines changed 2, context: html, text, full: html, text
    VCF annoRows need to have corrected coords for indels, otherwise it messesup coord comparison in annoGrator. Also, that lets us get rid of the
    ugly skippedFirstBase hack in annoFormatVep and annoGratorGpVar.
    
• src/lib/annoGrator.c
  • lines changed 13, context: html, text, full: html, text
    In order to detect the overlap of two 0-length (insertion) items, we needto expand at least one of their ranges to the two surrounding bases.
    
• src/lib/annoStreamVcf.c
  • lines changed 1, context: html, text, full: html, text
    VCF annoRows need to have corrected coords for indels, otherwise it messesup coord comparison in annoGrator. Also, that lets us get rid of the
    ugly skippedFirstBase hack in annoFormatVep and annoGratorGpVar.
    
• src/lib/vcf.c
  • lines changed 4, context: html, text, full: html, text
    VCF annoRows need to have corrected coords for indels, otherwise it messesup coord comparison in annoGrator. Also, that lets us get rid of the
    ugly skippedFirstBase hack in annoFormatVep and annoGratorGpVar.