Add code for bipartite-graph checking.

[samuelklee]

To support #1. Not sure if this is a notebook/script or a WDL, but happy to take a look once it's merged in any form and WDLize it, if needed. I will also take responsibility for integrating it into the megaWDL once it is added. Might be nice to see an example run and an explanation of the inputs/outputs; please feel free to start a conversation in the Discussions section of the repo.

[samuelklee]

This can just be a script that operates on a single sample and outputs machine-readable metrics, say in a tabular or json file; perhaps any per-sample plots that might be useful as well.

Please use a self-documenting schema that allows a downstream script to easily gather files and summarize metrics across samples. E.g., per-sample tables should include the sample name in one of the columns.

I will take this single-sample script, WDLize it, and add code/task for the downstream multisample summarizing.

[samuelklee]

@fabio-cunial any updates or plans you'd like to record here?

[fabio-cunial]

Bipartite graph checking is useful only for unphased genotypes (e.g. it's a way to compare SV genotypers like snifflesGT, cutesvGT, and svjedi, which output only unphased genotypes: one would like to know how far from phased those assignments are).

Is this still something useful to add, or has it been superseded by the collision removal tool?

[samuelklee]

Sorry for the delayed response---sure, we can deprioritize for now. Let's leave this open in case we expand upstream.