Fixed bug whereby overlapping sequence was could be double counted if '--overlappingPairedEndCheck bismark' or '--overlappingPairedEndCheck none' was set.
Fixed bug whereby overlapping sequence was could be double counted if '--overlappingPairedEndCheck bismark' or '--overlappingPairedEndCheck none' was set.

PeteHaitch/methtuple,PeteHaitch/methtuple,PeteHaitch/methtuple