SNP score 1.1

SNP score is for the analysis of SNP and the possible effects on having two different nucleotides might have on the binding of Transcription Factors. SNP score has three portions within it. 
The first portion is scoring the SNPs given in as input, score them against a directory of position frequency matrices within .pfm files, with an output of the top 5 transcription factor with the biggest differences in scores between the two SNP alleles for each SNP.
The second portion is the homology scoring portion which takes a file of homology sequences as input, and then scores the transcription factors against the homologous sequences.  It will then output the scores and sequences of the highest found within a table along with the human SNP sequences for comparison.
The last portion is an alignment portion which will take each possible sequence of size 40 in the SNP and do an alignment with each sequence of size 40 in each homology sequence. SNP score will then output the information within the same table as above.

Enhancements
- Options redone, now options and command line options can be interweaved together. Split program up to allow interfaces.
- Generated interface for input, scoring, and info.
- Integrated Get_SNP_Info with snpScore to make things easier and more intuitive.
- Added inline inputting type.