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@golobor finally, I've made something to address https://github.com/mirnylab/pairsamtools/issues/55
Sorry it took so long!
This more of a conversation starter, rather than the final version.
It is working correctly on your test
mock.4dedup.pairsam
, producing correct stats and outputs (checked for different mismatch radii).Haven't tested performance or larger data.
Once we finalize this thing it would be much easier to update distiller