Extend the rSNAPsim fileparser and default dictionaries for common nucleotide modifications

[Will-Raymond]

The rSNAPsim does not currently support common nucleotide modifications such as m6a or pseudouridine; Instead, these are parsed out to A, U, G, or C. Support for these modifications could be added, however many functions check the length of the sequence so a small function would be needed to convert multicharacter modifications to a single character to work with the code as is.