Commits for angie

v290_preview to v290_preview2 (2013-09-16 to 2013-09-23) v290

• Adding all dgv* tracks to tablesIgnored.
  • src/hg/makeDb/schema/all.joiner - lines changed 1, context: html, text, full: html, text
• Incorporating corrections from Jeff MacDonald.refs #11200
  
  • src/hg/makeDb/trackDb/human/dgvPlus.html - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/trackDb.ra - lines changed 2, context: html, text, full: html, text
• Yikes, when querying at the cart position instead of the whole genome,annoStreamVcf was skipping rows that it shouldn't have!
  
  • src/lib/annoStreamVcf.c - lines changed 1, context: html, text, full: html, text
• Handle IE's unique behavior of window.location.replace when the newURL (including stuff after '?') is the same as the current URL.
  fixes #11443
  
  • src/hg/lib/jsHelper.c - lines changed 12, context: html, text, full: html, text
• Avoid double-linebreak in VEP header when dbSNP is not included.
  • src/hg/lib/annoFormatVep.c - lines changed 2, context: html, text, full: html, text
• Fixing a URL (copy-paste error).
  • src/hg/hgVai/hgVai.c - lines changed 2, context: html, text, full: html, text
• Oops, forgot to correct test file after fixing intron off-by-one in 099102d. Too bad I didn't notice it in the test file to begin with...
  • src/hg/lib/tests/expected/annoGrator/gpFx.txt - lines changed 4, context: html, text, full: html, text
• Fixing bug reported by user in MLQ #11775: VCF that is sorted bystart position might not be sorted by UCSC-start position, specifically
  when at the same VCF start position there is an indel followed by a
  substitution. VCF start coords for indels are actually one base to
  the left of the actual inserted or deleted bases. So we internally
  adjust those to be one base to the right, which can make them out-of-order
  when followed by a non-indel variant.
  
  To restore sorting order, indels are now saved aside in a queue until
  we know it's safe to let them out because either
  a) we got a substitution whose start is greater than the indel start
  b) we got an indel whose start is greater than the queued indel start
  c) we hit EOF.
  When condition (a) or (b) is met, we have to do something with the
  new record while the indel queue drains, so it's saved aside in the
  nextPosQ (which never holds more than one row). If it's (b), then
  when indelQ is empty, we move the nextPosQ indel to indelQ because
  we can't let that indel out until one of the 3 conditions is met.
  
  fixes #11787
  
  • src/lib/annoStreamVcf.c - lines changed 149, context: html, text, full: html, text