Commits for angie

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

• 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.
  
  • src/hg/hgc/vcfClick.c - lines changed 4, 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/hgTracks/variation.c - 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/hgc/vcfClick.c - lines changed 10, context: html, text, full: html, text
  • src/hg/inc/vcfUi.h - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/tagTypes.tab - lines changed 9, context: html, text, full: html, text
• Documentation of new trackDb settings for initial config of VCF tracks.
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html - lines changed 26, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.html - lines changed 26, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml - lines changed 68, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/vcf.html - lines changed 14, context: html, text, full: html, text
• Removed unused function jsMakeSetClearButton (which should remain unused -- it does a form submit!).
  • src/hg/inc/jsHelper.h - lines changed 11, context: html, text, full: html, text
  • src/hg/lib/jsHelper.c - lines changed 42, 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/hgVai/hgVai.c - lines changed 4, context: html, text, full: html, text
  • src/hg/inc/jsHelper.h - lines changed 7, context: html, text, full: html, text
  • src/hg/js/jsHelper.js - lines changed 121, context: html, text, full: html, text
  • src/hg/lib/jsHelper.c - lines changed 120, context: html, text, full: html, text
• Added jsHelper.js.
  • src/hg/js/makefile - lines changed 1, context: html, text, full: html, text
• Oops, left in some console.log calls in jsHelper.js -- removing them.
  • src/hg/js/jsHelper.js - lines changed 4, context: html, text, full: html, text
• Ugh, forgot to remove external dependencies on jsWriteFunctions in b7b15a261.
  • src/hg/hgGenome/import.c - lines changed 1, context: html, text, full: html, text
  • src/hg/hgGenome/mainPage.c - lines changed 2, context: html, text, full: html, text
  • src/hg/hgTables/mainPage.c - lines changed 1, context: html, text, full: html, text
  • src/hg/inc/jsHelper.h - lines changed 5, context: html, text, full: html, text
  • src/hg/lib/jsHelper.c - lines changed 2, context: html, text, full: html, text