is_missing renamed to missing

Renamed the is_missing functionality across the library to match the more STL-like missing() calls. Also renamed is_empty() to empty() in the sam_builder class. The two separate commits reflect both changes.

fixes #152
reverted, but you do realize that once you make changes to a line that has end-of-line comments, the indentation of the end-of-line comments will change. You have the option to leave it messed up or fix all the other lines. You're advocating for:

1. leaving it messed up 
2. fix the indentation on a separate commit

I disagree with 1 ,and agree with 2 on a theoretical basis, but in practice it will be very hard to separate the two. Not in this case though. This case was trivial and I could have totally done it.