getCountsStrandedPerPosition is added which returns a list of counts per
basepair for a given annotation. Used for quantile trimming.
Major changes to Scripture. 
* Intermediate file writing is limited to 2-3 files. 
* unnecessary logging statements are debug only
* AddEndRNASeq now supports trimming for multiple gene ends.
Merge branch 'master' of https://github.com/mgarber/scriptureV2.git