ng there are 4 positions in the window (5mC) and this read reports 5mC, followed by a filtered call, and 2 more 5mC calls.
This read will match to patterns <code>[mhmm mmmm mCmm]</code> (<code>m</code> = 5mC, <code>h</code> = 5hmC, and <code>C</code> is canonical cytosine).
When the <code>--num-positions</code> parameter gets large the number of potential patterns becomes large.
Most patterns will probably not have any reads matching to them, so instead of enumerating all possible patterns modkit uses a pre