Robustness of padding code

[rkretsch]

Padding code should be organized and options documented better.

Options are the following:

Whether sequences should share same pad:

• all different pad
• all sequences of same length have same pad
• all same pad with sequences of different length simply taking truncated versions of that pad

Structure of pad:

• A specified sequence
• A specified bias of sequence (eg lots A)
• A random or polyA hang on the sequence side
• A completely unpaired region
• A stem-loop(s) structure

Location of pad:

• Shared between 3' and 5'
• All 3'
• All 5'

Additionally robustness to the following parameters should be tested:

• length of pad
• whether we also need to reduce probabilities when it has failed enough
• How many sequences/mutants need to be tested

[rkretsch]

The code is updated to perform these action, but test cases and testing robustness to length of pad etc is needed.

[rkretsch]

A potential robustness add is the ability to mutate the polyA region (if present) or constant loop (if present) if no solution is being found (see barcode code for example).

[rkretsch]

Now with add_library_elements, also need to move over some of the previous barcode and padding over