Implements #78 without adding any new flags to the input.
If multiple regions are specified:
For cis, the union of snps within those regions (+- window_size) are tested.
For trans, the intersection of snps outside those regions (+- window_size) is tested.
Still to-do:
Only allow multiple regions to be specified if a given input flag is passed in. At the moment, the user is blind to this if they unintentionally specified multiple regions for one feature.
Subset features properly when running analysis on one chromosome. At present, if a feature has any regions on a given chromosome, that feature will be tested in that chromosome's run. This will obviously cause issues if
Implements #78 without adding any new flags to the input.
If multiple regions are specified:
For cis, the union of snps within those regions (+- window_size) are tested. For trans, the intersection of snps outside those regions (+- window_size) is tested.
Still to-do: