From 8cb8d1c59637a0e9d3f8917b6d0ef940ebd6a9a6 Mon Sep 17 00:00:00 2001
From: Jana Ebler <ebler@hhu.de>
Date: Thu, 23 Mar 2023 13:26:38 +0100
Subject: [PATCH] set default subsampling size to 45. Subsampling is only done
 if the panelsize is over 90 since the new version of PanGenie is fast enough
 to handle panels of larger sizes.

---
 src/pggtyper.cpp | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/pggtyper.cpp b/src/pggtyper.cpp
index 36f3ba7..0fc0fdf 100644
--- 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;		
 		}