Added walkHSP to Read class and residueCounts to TitleAlignments and tests for both. There could probably be more tests, but it looks good so far.
Fixed merge conflicts from master.
Improved comments on HSP base class and in test_reads.py
Merge pull request #266 from terrycojones/title-reads-consensus

Added walkHSP to Read class and residueCounts to TitleAlignments.