q_pos and r_pos indexing

[paulaberry]

The outputs from alignment.dump() indicate a 1-indexed position number for the start and end of the matching region of the query and reference sequence. However, the output from alignment.r_pos and alignment.q_pos are 0-indexed. The output from alignment.r_end and alignment.q_end are the same as in the output from alignment.dum() and so appear to be 1-indexed. Is this expected behavior and output?