Provide warning/notification if 0 is in affected_status column of ped

[mvelinder]

To let the user know slivar is treating 0 as unafffected

[seboyden]

I'd like support for s.unaffected and s.unknown.

Treating "affected" as a Boolean (only allowing s.affected or !s.affected) doesn't distinguish between unaffected (phenotype 1) and unknown (phenotype 0). If you don't want to filter either way based on phenotype unknown, only workaround is to delete those samples from the ped file, which isn't ideal because then those samples don't appear in the filtered VCF. I'd like to filter explicitly based on affected and unaffected, but still retain the sample columns for unknowns in the output.

[brentp]

@seboyden if you want to use phenotype directly, you can. from the readme:

phenotype is a string taken directly from the pedigree file while affected is a boolean.