File Changes for angie

v304_preview to v304_preview2 (2014-07-28 to 2014-08-04) v304

• src/hg/hgGenome/import.c
  • lines changed 1, context: html, text, full: html, text
    Ugh, forgot to remove external dependencies on jsWriteFunctions in b7b15a261.
• src/hg/hgGenome/mainPage.c
  • lines changed 2, context: html, text, full: html, text
    Ugh, forgot to remove external dependencies on jsWriteFunctions in b7b15a261.
• src/hg/hgTables/mainPage.c
  • lines changed 1, context: html, text, full: html, text
    Ugh, forgot to remove external dependencies on jsWriteFunctions in b7b15a261.
• src/hg/hgTracks/variation.c
  • lines changed 2, context: html, text, full: html, text
    When showing SNPs' alleles on the reference genome + strand, if the userclicks "reverse" (revCmplDisp) show them on the - strand like other
    base displays (Base Position track, pgSnp/VCF, multiz). refs #13694
    
• src/hg/hgVai/hgVai.c
  • lines changed 4, context: html, text, full: html, text
    Added jsMakeSetClearContainer / jsEndContainer to jsHelper.c, and apppliedthem to a couple long lists of checkboxes in hgVai. While at it, I moved
    jsHelper.c's javascript-inlined-in-HTML out to a new .js file, jsHelper.js.
    
• src/hg/hgc/vcfClick.c
  • lines changed 4, context: html, text, full: html, text
    David pointed out how confusing it is to see the 'Haplotype sorting order' optionto change the central variant, when haplotype clustering is disabled. So don't
    show the option unless haplotype clustering is enabled.
    
  • lines changed 10, context: html, text, full: html, text
    David pointed out that it is inappropriate to show Hardy-Weinberg equilibriumfrequencies on the VCF details page unless the VCF data are from a population
    study -- so at this point, pretty much only 1000 Genomes. So I added a new
    trackDb setting for vcf/vcfTabix, showHardyWeinberg, and added it to the
    1000 Genomes track def.
    
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
  • lines changed 26, context: html, text, full: html, text
    Documentation of new trackDb settings for initial config of VCF tracks.
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.html
  • lines changed 26, context: html, text, full: html, text
    Documentation of new trackDb settings for initial config of VCF tracks.
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 68, context: html, text, full: html, text
    Documentation of new trackDb settings for initial config of VCF tracks.
• src/hg/htdocs/goldenPath/help/vcf.html
  • lines changed 14, context: html, text, full: html, text
    Documentation of new trackDb settings for initial config of VCF tracks.
• src/hg/inc/jsHelper.h
  • lines changed 11, context: html, text, full: html, text
    Removed unused function jsMakeSetClearButton (which should remain unused -- it does a form submit!).
  • lines changed 7, context: html, text, full: html, text
    Added jsMakeSetClearContainer / jsEndContainer to jsHelper.c, and apppliedthem to a couple long lists of checkboxes in hgVai. While at it, I moved
    jsHelper.c's javascript-inlined-in-HTML out to a new .js file, jsHelper.js.
    
  • lines changed 5, context: html, text, full: html, text
    Ugh, forgot to remove external dependencies on jsWriteFunctions in b7b15a261.
• src/hg/inc/vcfUi.h
  • lines changed 2, context: html, text, full: html, text
    David pointed out that it is inappropriate to show Hardy-Weinberg equilibriumfrequencies on the VCF details page unless the VCF data are from a population
    study -- so at this point, pretty much only 1000 Genomes. So I added a new
    trackDb setting for vcf/vcfTabix, showHardyWeinberg, and added it to the
    1000 Genomes track def.
    
• src/hg/js/jsHelper.js
  • lines changed 121, context: html, text, full: html, text
    Added jsMakeSetClearContainer / jsEndContainer to jsHelper.c, and apppliedthem to a couple long lists of checkboxes in hgVai. While at it, I moved
    jsHelper.c's javascript-inlined-in-HTML out to a new .js file, jsHelper.js.
    
  • lines changed 4, context: html, text, full: html, text
    Oops, left in some console.log calls in jsHelper.js -- removing them.
• src/hg/js/makefile
  • lines changed 1, context: html, text, full: html, text
    Added jsHelper.js.
• src/hg/lib/jsHelper.c
  • lines changed 42, context: html, text, full: html, text
    Removed unused function jsMakeSetClearButton (which should remain unused -- it does a form submit!).
  • lines changed 120, context: html, text, full: html, text
    Added jsMakeSetClearContainer / jsEndContainer to jsHelper.c, and apppliedthem to a couple long lists of checkboxes in hgVai. While at it, I moved
    jsHelper.c's javascript-inlined-in-HTML out to a new .js file, jsHelper.js.
    
  • lines changed 2, context: html, text, full: html, text
    Ugh, forgot to remove external dependencies on jsWriteFunctions in b7b15a261.
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    David pointed out that it is inappropriate to show Hardy-Weinberg equilibriumfrequencies on the VCF details page unless the VCF data are from a population
    study -- so at this point, pretty much only 1000 Genomes. So I added a new
    trackDb setting for vcf/vcfTabix, showHardyWeinberg, and added it to the
    1000 Genomes track def.
    
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 9, context: html, text, full: html, text
    David pointed out that it is inappropriate to show Hardy-Weinberg equilibriumfrequencies on the VCF details page unless the VCF data are from a population
    study -- so at this point, pretty much only 1000 Genomes. So I added a new
    trackDb setting for vcf/vcfTabix, showHardyWeinberg, and added it to the
    1000 Genomes track def.