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
My point is that is took me 3x as long as it otherwise would have to review this pull request just because I had to examine each of these lines to look for differences, when all but one line was just whitespace changes. This should never happen -- it is unfair to the reviewer.

Whitespace-only changes, if we ever find them necessary (ie., things get really messy or screwed up), should be in a separate branch, so that we don't have to go hunting for real changes inside the sea of indentation changes.