BLASR:
  Fixed -rbao (Refine Between Anchors Only) to allow very long (multi megabase) sequence alignment.
  Added -p to print progress.
MappingParameters.h:
  Added -p, added -m sanity check.
FASTQReader.h:
  Fixed memory leak.
GraphPaper.h:
  Fixed optimization.
SDPAlign.h:
  Added graph paper optimization.
FindMaxInterval.h:
  Added more sensitive search.
SuffixArray.h:
  Slow change to fix header includes.