Because of this, features present in exactly 10 samples (or whatever min-feature-count is) will get filtered out and samples with exactly 1000 counts (or whatever min-sample-count is) will get filtered out, even though these are described as the minimum acceptable values:
It looks like the filtering code uses
>when it should use>=:https://github.com/biocore/songbird/blob/2727c04f1d9c7145a2a4a865cfce0e9904f0baa1/songbird/util.py#L154-L158
Because of this, features present in exactly 10 samples (or whatever
min-feature-countis) will get filtered out and samples with exactly 1000 counts (or whatevermin-sample-countis) will get filtered out, even though these are described as the minimum acceptable values:https://github.com/biocore/songbird/blob/2727c04f1d9c7145a2a4a865cfce0e9904f0baa1/songbird/parameter_info.py#L30-L37