Support zero depth sites

[y9c]

For analyzing multiple samples together, it is useful to accept sites whose depth is 0 within some samples.

[Sfeng666]

For analyzing multiple samples together, it is useful to accept sites whose depth is 0 within some samples.

I agree.

It also make more sense to allow coverage = 0. Both the mapping quality (-m) and base call quality (-q) filterings allow no filtering (threshold = 0).

[piechottam]

I will try to incorporate -m and -q with threshold 0.
A coverage of 0 requires extensive updates to how the test-statistic is calculated - I'll check this.