Update GenerateFs for dadi VCF parser updates, and make --polarized u…

…nrequired if user uses --subsample

dadi_cli/GenerateFs.py

@@ -43,11 +43,12 @@ def generate_fs(
         extract_ploidy = True
         subsample_dict = {}
         for i in range(len(pop_ids)):
-            subsample_dict[pop_ids[i]] = int(subsample[i])
+            subsample_dict[pop_ids[i]] = subsample[i]
         dd, ploidy = dadi.Misc.make_data_dict_vcf(
             vcf_filename=vcf, popinfo_filename=pop_info, subsample=subsample_dict, calc_coverage=calc_coverage, extract_ploidy=extract_ploidy
         )
         projections = [individuals*ploidy for individuals in subsample]
+        print(projections, ploidy, subsample)
     else:
         dd = dadi.Misc.make_data_dict_vcf(vcf_filename=vcf, popinfo_filename=pop_info, calc_coverage=calc_coverage)
     if calc_coverage:    

dadi_cli/__main__.py

@@ -1413,11 +1413,15 @@ def dadi_cli_parser():
         help="Name of the file containing the population name of each sample.",
         dest="pop_info",
     )
+    # Check if subsamples are being requested to determin if --projections needed
+    proj_req = True
+    if "--subsample" in sys.argv:
+        proj_req = False
     parser.add_argument(
         "--projections",
         type=_check_positive_int,
         nargs="+",
-        required=True,
+        required=proj_req,
         help="Sample sizes after projection; If you do not want to project down your data, please input the original sample sizes of your data.",
     )
     parser.add_argument(
@@ -1437,6 +1441,7 @@ def dadi_cli_parser():
     )
     parser.add_argument(
         "--subsample",
+        type=_check_positive_int,
         default=[],
         nargs="+",
         dest="subsample",