Initial features request

[alexbarrera]

Recap of the discussion points that originated this repository.

• Extracting and tallying basecalls from mpileup
  - currently bash scripting and a python script from Alex
  - partition multiallelic sites
• Consolidating mpileup data into an input file
  - currently python script from Alex
• Options to threshold on DNA and/or RNA counts
• Add a parallelization option that includes creation of the variable file
• Option to include counts in the output file
• Generation of QC plots
  - distribution of preg values
  - distribution of theta values

Important scripts and template code to follow