Sam: implementation of mate operations

* fix off-by-one bug on Sam::alignment_stop (it was reporting the base after the last inclusive base, contradicting the docs)
* refactor cigar operator parsing routine from SamBuilder to Cigar class for mutual use
* add consumes_read_bases and consumes_reference_bases as static methods to the Cigar class
* add tests to the new API and all new functions

fixes #6
Please put them into a separate pull request so that we can merge the stuff I've reviewed. I am not going to be able to look at the mate_unclipped stuff until tomorrow. It should be easy to extract into a separate branch.