set default subsampling size to 45. Subsampling is only done if the p…

…anelsize is over 90 since the new version of PanGenie is fast enough to handle panels of larger sizes.
eblerjana · Mar 23, 2023 · 8cb8d1c · 8cb8d1c
1 parent 8e99a84
commit 8cb8d1c
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/src/pggtyper.cpp b/src/pggtyper.cpp
@@ -321,8 +321,8 @@ int main (int argc, char* argv[])
 	if (nr_paths > 200) cerr << "Warning: panel is large and PanGenie might take a long time genotyping. Try reducing the panel size prior to genotyping." << endl;
 	// handle case when sampling_size is not set
 	if (sampling_size == 0) {
-		if (nr_paths > 25) {
-			sampling_size = 14;
+		if (nr_paths > 90) {
+			sampling_size = 45;
 		} else {
 			sampling_size = nr_paths;		
 		}