Add sequence file manipulation utilities.

[cnobles]

Absorb dualDemultiplexR, seqTrimR, seqFiltR, seqConsolidateR, and blatCoupleR code into gintools.

This should help with reducing code duplication and increase modularity, though the package will get quite large compared to it's current size. This will also mean that analytical functions such as standardize sites and refine_breakpoints, as well as others, will be available in the environment.