Parameterize and wrap the demultiplexing code

[hillst]

The reading of data (from fastqs/barcode files, whatever) should be decoupled from the main unit of work (demultiplexing). Using the generator your wrote for FASTQs, write a method that accepts a fastq record and barcode collection that returns a barcode assignment

[rafischulman]

Last step: help message and kick out with wrong arguments

[hillst]

Switch to the argparse module in python

[rafischulman]

Last step before closing this: switch to argparse

[rafischulman]

Started implementing argparse, need to finish. Add optional argument: len of cutsite report. It should have default.