--- a/diversity_pi.py	Fri Jul 26 12:51:13 2013 -0400
+++ b/diversity_pi.py	Fri Sep 20 13:25:27 2013 -0400
@@ -6,30 +6,55 @@
 
 ################################################################################
 
-if len(sys.argv) != 7:
-    gd_util.die('Usage')
-
-snp_input, coverage_input, indiv_input, min_coverage, output, ind_arg = sys.argv[1:]
+def load_pop(file, wrapped_dict):
+    if file == '/dev/null':
+        pop = None
+    else:
+        pop = Population()
+        pop.from_wrapped_dict(wrapped_dict)
+    return pop
 
-p_total = Population()
-p_total.from_wrapped_dict(ind_arg)
-
-p1 = Population()
-p1.from_population_file(indiv_input)
-if not p_total.is_superset(p1):
-    gd_util.die('There is an individual in the population individuals that is not in the SNP table')
+def append_tags(the_list, p, p_type, val):
+    if p is None:
+        return
+    for tag in p.tag_list():
+        column, name = tag.split(':')
+        if p_type == 'gd_genotype':
+            column = int(column) - 2
+        the_list.append('{0}:{1}:{2}'.format(val, column, name))
 
 ################################################################################
 
-prog = 'mt_pi'
+if len(sys.argv) != 11:
+    gd_util.die('Usage')
+
+snp_input, snp_ext, snp_arg, cov_input, cov_ext, cov_arg, indiv_input, min_coverage, req_thresh, output = sys.argv[1:]
+
+p_snp = load_pop(snp_input, snp_arg)
+p_cov = load_pop(cov_input, cov_arg)
+
+p_ind = Population()
+p_ind.from_population_file(indiv_input)
+
+if not p_snp.is_superset(p_ind):
+  gd_util.die('There is an individual in the population individuals that is not in the SNP/Genotype table')
+
+if p_cov is not None and (not p_cov.is_superset(p_ind)):
+  gd_util.die('There is an individual in the population individuals that is not in the Coverage table')
+
+################################################################################
+
+prog = 'mito_pi'
 
 args = [ prog ]
 args.append(snp_input)
-args.append(coverage_input)
+args.append(cov_input)
 args.append(min_coverage)
+args.append(req_thresh)
 
-for tag in p1.tag_list():
-    args.append(tag)
+append_tags(args, p_ind, 'gd_indivs', 0)
+append_tags(args, p_snp, snp_ext, 1)
+append_tags(args, p_cov, cov_ext, 2)
 
 with open(output, 'w') as fh:
     gd_util.run_program(prog, args, stdout=fh)