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
Awesome, thank you!

Also, with the doxygen comments in particular, I don't think it is necessary or a good idea to try to line up all of the comments across an entire file. This pushes many comments way too far outside of the typical text editor viewing area, and introduces tons of these annoying whitespace changes. At most I think that we should go for "local alignment" (see sam.h for an example) where we just try to line up comments in each separate cluster of functions (in separate commits, when things get messy)