Added walkHSP to Read class and residueCounts to TitleAlignments

Plus tests for both. There could probably be more tests, but it looks reasonably good, I think.

Fixes #265 

OK. I changed the docstring from "If the HSP specifies that the entire read matches the subject..." to "If the HSP specifies that the read matches the entire subject..."  To make it clearer that the match covers the whole subject but that the read still has unmatched bases to the left and right of the subject. Thanks.