Similarity of Variants (before and after data)

[DBecker7]

Jaccard similarity of all pairwise combinations of variants.

Extract the set of mutations for each variant, then compare pairwise across all variants.

There are a couple of interesting cases:

• One variant is a subset of another (all the same mutations, but one has more)
  • One variant is almost a subset of the other.
• Two variants differ by one mutation.
• Jaccard similarity
• TN93 distance?

The function should be able to calculate these before data are fused (i.e. with varmat) as well as after (i.e. with the fused data).

[DBecker7]

Output format should be matrices, similar to something like cov(data). This makes it nice to plot as a heatmap for easy visual inspection.

[DBecker7]

Some good work has been done. However, the Jaccard similarity is not calculated correctly, and the code could use some clean-up. I also need to make the plotting functions easier to differentiate, or add them to one function with arguments/dispatch to specify which.