Fixed to get individuals from ped files

trio_whole_exome_create_parameter_files.pl

@@ -89,7 +89,7 @@ my $family_id_out_fh = new IO::File;
 $family_id_out_fh->open(sprintf("%s.family_ids.txt", $output_prefix), "w") or die "Could not open $output_prefix.family_ids.txt\n$!";
 
 my $ped_out_fh = new IO::File;
-foreach my $family_id (keys %family)
+foreach my $family_id (keys %ped)
 {
 	my $pcr_plate_id = $family{$family_id}{'pcr_plate_id'};
 	my $new_family_id = sprintf("%s_%s", $pcr_plate_id, $family_id);
@@ -98,7 +98,7 @@ foreach my $family_id (keys %family)
 
 	$ped_out_fh->open(sprintf("%s_%s.ped", $output_prefix, $new_family_id), "w") or die "Could not open $output_prefix.$new_family_id.ped\n$!";
 
-	foreach my $individual_id (keys %{ $family{$family_id}{'individual_id'} })
+	foreach my $individual_id (keys %{ $ped{$family_id} })
 	{
 		my $father_id = $ped{$family_id}{$individual_id}{'father_id'};
 		my $mother_id = $ped{$family_id}{$individual_id}{'mother_id'};