Restructuring dada2 R/python code

[jordenrabasco]

Improvement Description

• Restructuring of R code into a more condensed format
• Passing variables from python to R via option arguments.

Current Behavior

• There are separate R files (ex: "run_dada_single.R") dedicated to processing each tech-specific read type with the exception of pyro sequencing which utilizes the same script as single-end reads.
• Arguments are passed from the python script "_denoise.py" to the supporting R scripts through positional arguments.

Proposed Behavior

• With the large amount of redundant code between the various supporting R files I think it makes sense to condense these into one or two R files to more easily enable code to be shared between the various tech-specific data processing functionalities.
• Changing the method of argument passing from positional to optional (utilizing variable names); I believe, would make it easier to expand functionality further down the line as well as make it more explicit as to which variables are being passed and how they are being used.

Comments

1. Hi All! I just wanted to mention that I am working with @benjjneb as a grad student to look into implementing the changes described above.