A group of reads that have been deduplicated
A Read or Reads and the number of times that read signature has been seen Read signature meaning Position + UMI
Abstraction so ReadFreq can hold a single best read for it's read signature or hold all reads for it's read signature (used for --group_only).
Create a graph from the UmiMap TODO: Inline?
Create the connections between the umis via an all vs all comparison. A Connection will only be formed from a larger node to a smaller node. Larger being defined as node_a >= 2x node_b - 1, the provides the directionality. TODO: Keep a seen list here instead of later? Some connections will be redundant.
Group reads together based on their positions.
The main function to coordinate the deduplication process