Process and validate command line arguments

[kwade4]

The main pre-processing steps (common to all sequences) include:

• [x] Checking sequences are the same length
• [x] Compressing sequences
• [x] Categorizing sequences based on number of gaps and variants
• [x] Calculating initial pairwise hamming distances

In the original source code, the sequences are divided into chunks of 4 nucleotides and then converted to integers.

Upon installation of the program, the pairwise hamming distance is calculated for all 625 possible combinations of 5 characters (ATGC-) and these values are written to a file. During execution of the program, these values are stored in a lookup table, queried, and used to calculate the hamming distance.

[kwade4]

Rather than caching the distances, I opted to encode the sequences as bit arrays and I calculate hamming distance by counting the 1's from bitseq1 XOR bitseq2. For now, performance seems fine, but if performance becomes an issue, I'll look into the caching approach.