Remove subset PED step in CleanVcf after merging CleanVcf rewrite

[epiercehoffman]

The subset PED step added in #250 (two tasks: GetSampleIdsFromVcf and SubsetPedFile) will become unnecessary after the rewrite of CleanVcf is merged, so it should be removed at that time.

Details:
This task was added because CleanVcf1_20 errors out if there is a) a header line in the PED file or b) extra samples with sex=0 in the PED file that are not in the VCF. The rewrite of CleanVcf appears to circumvent these issues by using the VCF sample IDs as a starting point, so the subset PED step should be unnecessary after those updates are merged. It appears that steps prior to CleanVcf are able to handle the header line in the PED file as users did not encounter errors until CleanVcf1_20.

[epiercehoffman]

Addressed in #288