Sam: implementation of mate_alignment_stop()

* 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

This sets the base for issue #6
This entire loop can be replaced with a call into htslib's bam_cigar2rlen() (and should be, so that we don't have to maintain this duplicate implementation)