Commits for angie

v254_preview to v254_preview2 (2011-07-05 to 2011-07-12) v254

• MLQ #4463 (problem w/intersection):enabling intersection for bigWig uncovered a couple new bugs: 1. The secondary-table-fetching code didn't handle the bigWig case. Fix: added bigWigIntervalsToBed and hooked it up in bitsForIntersectingTable. 2. The code for intersecting w/bigWig primary table had been written but never tested, and the code for incompletely covered items from the primary table was incorrect.
  • src/hg/hgTables/bigWig.c - lines changed 26, context: html, text, full: html, text
  • src/hg/hgTables/hgTables.h - lines changed 5, context: html, text, full: html, text
  • src/hg/hgTables/intersect.c - lines changed 8, context: html, text, full: html, text
• Getting rid of compile warning on Ubuntu (format arg has to be a proper format string).
  • src/hg/hgHubConnect/hgHubConnect.c - lines changed 1, context: html, text, full: html, text
• Bug #4263 (track items not being drawn in hgTracks when zoomed way in):Building on Fan's fix for integer overflow in bedPlusLabelDrawAt's x1 calculation, I changed the x1 and x2 calculations to use pre-clipped chromosome coordinates so that they're using reasonably small inputs. The ISCA Retrospective track (bedDrawSimpleAt) had the same problem with long items and large scale factor causing integer overflow, so I applied the same fix there. hgTracks code still has ~50 places that use the same round((double)(... method, but it takes extreme conditions to cause integer overflow so I'll leave those alone for now.
  • src/hg/hgTracks/bedTrack.c - lines changed 11, context: html, text, full: html, text
  • src/hg/hgTracks/simpleTracks.c - lines changed 11, context: html, text, full: html, text
• Removed comment that had become incorrect.
  • src/lib/portimpl.c - lines changed 1, context: html, text, full: html, text
• Bug #4263 (track items not being drawn in hgTracks when zoomed way in):fixing same integer overflow problem, for RGD tracks -- thanks Brooke for catching those.
  • src/hg/hgTracks/simpleTracks.c - lines changed 5, context: html, text, full: html, text
• Track #671 (BDTNP): updated BDTNP DNase references, requested by Mark Biggin.
  • src/hg/makeDb/trackDb/drosophila/bdtnpDnase.html - lines changed 19, context: html, text, full: html, text
• Track #671 (BDTNP): oops, fixing a couple things caught by Brooke.
  • src/hg/makeDb/trackDb/drosophila/bdtnpDnase.html - lines changed 17, context: html, text, full: html, text
• Fix stricter-gcc warning: pass in a proper format string instead of a plain old char * variable.
  • src/hg/hgHubConnect/hgHubConnect.c - lines changed 1, context: html, text, full: html, text