Find way of representing haplotype phase of a read in a compact way

[aays]

This needs to be a way to succinctly represent the haplotype phase (i.e. to detect phase changes) for recombination event classification.

Things to think about:

1. How do we include length? (e.g. for putative gene conversions)
2. How do we account for PE reads? Do we store reads separately and link them, or combine info from both reads somehow?
3. How do we represent 'no-match' sites?

[jiyvliu]

From Tuesday 5/19 discussion:

This will most likely require a change of the cigar function (the one we've built) to pass back a list of tuples that include the haplotype and the location instead of just the haploytypes

[jiyvliu]

Data represented as class structures in Python, closed for now