Add confidence scores to each putative acceptor / poly-adenylation site

[khughitt]

Currently, each read which passes the specified thresholds are treated the same. It may be useful for some downstream analyses (e.g. determining primary UTR boundaries) to vary the score contributed by each read. For example, A site which was detected in a read with a 25nt suffix of the SL sequence would contribute a higher score to it's supported site than a read which contains only 4nt of the SL sequence.

This is probably most useful in cases where only a few reads map in the inter-CDS region for a given gene, and it is desirable to choose which site is the most-likely "true" acceptor/poly(a) site.