[ENH] Making `calculate_counts` generic

[paulhibbing]

This is mostly a note to self, but may be interesting to others.

Currently, calculate_counts assumes data were read using read.gt3x. I sometimes use AGread, and it would be nice to accommodate this. Making calculate_counts into an S3 generic would be an easy way of doing this.

The current code can be the default method, and others can be set up for specific classes that arise from other approaches (e.g. the RAW class from AGread).