Add option to specify sample and molecular barcode design

[martinaryee]

demultiplex.py should have an option to specify how to construct the sample and molecular barcodes. e.g.:

python demultiplex.py --sample_barcode i1:2-8,i2:2-8 --molecular_barcode i2:9-16 . . .

to specify a 14bp sample barcode that consists of bases 2-8 of Index read 1 and bases 2-8 of index read 2. The molecular barcode in this example is found in bases 8-16 of index read 2.

[rchowe]

I would approach this in the following way:

1. Split the option up based on which file the range is acting on. So i1:2-8,i2:2-8 becomes the array ['i1:2-8', 'i2:2-8'].
2. For each item in the array, find out which file it references and the range, either using .split or using a regular expression.

import re

x = 'i1:2-8,i2:2-8'
parts = x.split(',')
for part in parts:
    m = re.match(r'(?P<filename>.+):(?P<lower_bound>\d+)-(?P<upper_bound>\d+)', part)
    filename = m.group('filename')
    lower_bound = m.group('lower_bound')
    upper_bound = m.group('upper_bound')

    # Process the barcodes based on this.

EDIT: I fixed a bug in the code.