Major Overhaul

1. Fisher's Test Removed 
-Contingency table set up incorrectly, thus p-value was meaningless
2. Empirical Bayes Test Removed 
-When read depth was too high, beta function would round off to zero, and division by zero would occur when calculating prb --> program crashes. 
3. Changed Default Parameters
4. Heteroplasmy Detection: 
-Expanded to variant detection (relative to rCRS), renamed accordingly 
-Conversion of location + ref allele (from hg19 --> rCRS) takes place BEFORE analysis, though basecall is still in original ref format
-Will check for heteroplasmy based on secondary allele (second most common allele) frequency 
    -If heteroplasmy, reports Heteroplasmic Frequency as [Alternate Allele Count]/[Total Allele Count]  (relative to rCRS)
    -If not heteroplasmy, checks if it is a homoplasmic variant. 
-Removed strand bias filter (because it removes ~1600 positions automatically), but strand bias is still shown for reference. 
-Displays Alternate Allele in table, removed Stat Test Results. 
5. Somatic Detection 
-Original somatic analysis required that the normal position had 100% support for a single allele. This is impractical as it assumes no noise in the data. 
-Somatic analysis expanded to look for changes in Heteroplasmic Frequency from Normal --> Tumor. 
-Requirement: HFDiff > sp
-Set depth filter for somatic detection
6. Relative Copy Number Changes
-Warning message: due to differences in exon enrichment protocols, it is impractical to compare mitochondrials reads and total reads. The differences in relative ratios would be attributed to the efficiency of the protocol rather than the actual mitochondrial DNA copy number. 
-Results generated from this are highly unreliable for exome data, but may be useful for Whole Genome data. 
7. MitoSeek.html (output page)
-Title changes: 
   "Heteroplasmy" --> "Variants"
   "Somatic Mutations" --> "Heteroplasmic Changes and Somatic Mutations"
-Changed Descriptions
8. General grammar, spelling, and format fixes