Rename _bwa_reg2_rapi_aln_se and add is_paired parameter
Fix method to get text names of RAPI errors
Provide a mapping from cigar code to operation letter
Avoid using temporary tag structure
Formatting and comments
typedef tag vector type
remove obsolete comment
Wrap rapi_alignment

Also reorder some of the SWIG code in a way that may be easier to
follow.
Extend unit tests to cover part of the alignment functionality