--cutoff usage

[Shicheng-Guo]

Hi Felix,

Can you make it more explicit:

--cutoff [threshold] The minimum number of times a methylation state has to be seen for that nucleotide before its methylation percentage is reported. Default: 1.

It means the methylation read counts should be >=1 or total reads at the base should be >=1?

Thanks.

I think it should be

--cutoff [threshold] The minimum number of times a methylation state (M or U) has to be seen for that nucleotide before its methylation percentage is reported. Default: 1.

Isn't it?

Thanks.

[FelixKrueger]

For piece of mind I have altered the description slightly to:

--cutoff [threshold] The minimum number of times any methylation state (methylated or unmethylated) has to be seen for a nucleotide before its methylation percentage is reported. Default: 1.