Low level pair coalescence counts

[nspope]

Low level extension of #2915

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 89.62%. Comparing base (e6483fc) to head (62069ec).

Additional details and impacted files

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  Coverage   89.62%   89.62%           
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c-tests	86.21% <ø> (ø)
lwt-tests	80.78% <ø> (ø)
python-c-tests	88.72% <ø> (ø)
python-tests	98.97% <ø> (ø)

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[nspope]

I'd like to generalize this algorithm slightly:

• Currently, the output is either a num_windows by num_nodes array (which is very large), or a num_windows by num_time_windows array where the counts are summed within time windows.
• Conceptually, the "nodes" output gives the empirical distribution of pair coalescence times in windows across the genome. That is, for each window we have a vector of RVs (node times) and a vector of weights (pair coalescence counts).
• From this distributional viewpoint, there's lots of useful things that may be calculated: the empirical CDF, quantiles, moments, coalescence rates, etc. (of which the "sum in time windows" option of the current implementation is one special case)

So, I think it'd be useful to take the current algorithm, and have it apply a summary function at the end of each window. This would let us calculate any useful summary statistic without having to create a potentially humongous array (windows by nodes by indexes) as an intermediate.

The API would stay the same-- later on, we could add named methods for various summary statistics, and potentially eventually expose a "general summary stat" interface, like is done for the other statistics.

[jeromekelleher]

Looks good to me - do you want to add the summary func stuff now before we start porting to C? Probably a good idea, if you want to do this in the short term.