counting in readMutString at end of sequences

[anthonymustoe]

readMutString increments windows past the end of the read, assuming that the end is not the actual end of the RNA (e.g. with Nextera data). For RNAs with actual ends, we don't want this behavior which causes weird correlations at the end.

[anthonymustoe]

Fixed by checking against the sequence length and breaking out of the forward scanning loop in readMutStrings.pyx