Clangfix

I have fixed all but one of the issues causing blasr to file to compile on clang.  

Please double-check the one that I have flagged that "PACbio needs to check".  You have a situation in the code where the number of arguments expected by a constructor and those passed to the constructor differ, and it is not clear what you intend.

The other two fixes are simple bug fixes.

I am working on the fourth one, but it is harder  to track down.