Commits for angie

v279_preview2 to v279_base (2013-02-05 to 2013-02-12) v279

• Trimming of trailing whitespace in e9a3d621 caused hgTrackDb to fail -- putting it back.
  • src/hg/makeDb/trackDb/human/trackDb.ra - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
• Adding maxWindowToDraw to a couple very dense VCF tracks after Pauline found that chr1 load runs out of mem (#8886 note 47).
  • src/hg/makeDb/trackDb/human/hg19/trackDb.denisova.ra - lines changed 1, 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 1, context: html, text, full: html, text
• For #8886 (Denisova tracks) Pauline found that some data tables appearedempty in the Table Browser. Turns out that insertion items (length=0) were
  dropped by bigbedIntervalQuery because it required a positive rangeIntersection.
  Fix: instead, compare start and end coords of search range and item.
  Note: In order to catch an insertion item, the search range has to encompass
  the item (>=1 base to left and >=1 base to right).
  
  • src/lib/bigBed.c - lines changed 1, context: html, text, full: html, text
• Passing an item's coords as the range to bigBedIntervalQuery worksfor retrieving the item -- except when the item is an insertion (length=0).
  In that case, the search range must be expanded to 2 bases, one base
  to the left of an item and one base to the right, so starts and ends
  will overlap.
  
  • src/hg/hgc/bigBedClick.c - lines changed 8, context: html, text, full: html, text
• Encapsulating hgVarAnnogrator.js into a single global object (hgva)with public methods for page events.
  
  • src/hg/hgVarAnnogrator/hgVarAnnogrator.c - lines changed 4, context: html, text, full: html, text
  • src/hg/js/hgVarAnnogrator.js - lines changed 197, context: html, text, full: html, text
• Track #9401 (need DGV update): reloaded in order to pick up missing IDs. Still waiting for missing Iafrate items in hg18.
  • src/hg/makeDb/doc/hg17.txt - lines changed 14, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg18.txt - lines changed 16, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg19.txt - lines changed 17, context: html, text, full: html, text