From 303f40dd45c1bef3c3a456a15ee3b34022abf17e Mon Sep 17 00:00:00 2001
From: Xiuwen Zheng <zhengxwen@users.noreply.github.com>
Date: Thu, 7 Mar 2024 21:41:39 -0600
Subject: [PATCH] faster snpgdsLDpruning()

---
 DESCRIPTION   |  4 ++--
 NEWS          |  8 ++++++++
 src/genLD.cpp | 26 ++++++++++++--------------
 3 files changed, 22 insertions(+), 16 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 86fc8cd..a1f027c 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -2,8 +2,8 @@ Package: SNPRelate
 Type: Package
 Title: Parallel Computing Toolset for Relatedness and Principal Component
         Analysis of SNP Data
-Version: 1.36.1
-Date: 2024-01-19
+Version: 1.37.2
+Date: 2024-03-08
 Depends: R (>= 2.15), gdsfmt (>= 1.8.3)
 LinkingTo: gdsfmt
 Imports: methods
diff --git a/NEWS b/NEWS
index e967f23..6139e83 100644
--- a/NEWS
+++ b/NEWS
@@ -1,3 +1,11 @@
+CHANGES IN VERSION 1.37.2
+-------------------------
+
+UTILITIES
+
+    o faster `snpgdsLDpruning()`
+
+
 CHANGES IN VERSION 1.36.1
 -------------------------
 
diff --git a/src/genLD.cpp b/src/genLD.cpp
index 408ff18..afd81b1 100755
--- a/src/genLD.cpp
+++ b/src/genLD.cpp
@@ -780,19 +780,18 @@ namespace LD
 			BufSNP.ReadPackedGeno(i, &buf[0]);
 			progress.Forward(1, verbose);
 			// detect LD
-			int TotalCnt = 0, ValidCnt = 0;
-			list<TSNP>::iterator it;
-			for (it=ListGeno.begin(); it != ListGeno.end(); TotalCnt++)
+			bool to_include = true;
+			for (list<TSNP>::iterator it=ListGeno.begin(); it != ListGeno.end(); )
 			{
 				// check whether it is in the sliding window
 				if ((abs(i - it->idx) <= slide_max_n) &&
 					(abs(pos_bp[i] - it->pos_bp) <= slide_max_bp))
 				{
-					if (fabs(_CalcLD(&(it->genobuf[0]), &buf[0])) <= LD_threshold)
-						ValidCnt ++;
+					if (to_include &&
+						(fabs(_CalcLD(&(it->genobuf[0]), &buf[0])) > LD_threshold))
+						to_include = false;
 					it ++;
 				} else {
-					ValidCnt ++;
 					// delete it
 					list<TSNP>::iterator tmp_it = it;
 					it ++;
@@ -800,7 +799,7 @@ namespace LD
 				}
 			}
 			// handle
-			out_SNP[i] = (ValidCnt == TotalCnt);
+			out_SNP[i] = to_include;
 			if (out_SNP[i])
 			{
 				ListGeno.push_back(TSNP(i, pos_bp[i], nPackedSamp));
@@ -837,19 +836,18 @@ namespace LD
 			BufSNP.ReadPackedGeno(i, &buf[0]);
 			progress.Forward(1, verbose);
 			// detect LD
-			int TotalCnt = 0, ValidCnt = 0;
-			list<TSNP>::iterator it;
-			for (it=ListGeno.begin(); it != ListGeno.end(); TotalCnt++)
+			bool to_include = true;
+			for (list<TSNP>::iterator it=ListGeno.begin(); it != ListGeno.end(); )
 			{
 				// check whether it is in the sliding window
 				if ((abs(i - it->idx) <= slide_max_n) &&
 					(abs(pos_bp[i] - it->pos_bp) <= slide_max_bp))
 				{
-					if (fabs(_CalcLD(&(it->genobuf[0]), &buf[0])) <= LD_threshold)
-						ValidCnt ++;
+					if (to_include &&
+						(fabs(_CalcLD(&(it->genobuf[0]), &buf[0])) > LD_threshold))
+						to_include = false;
 					it++;
 				} else {
-					ValidCnt ++;
 					// delete it
 					list<TSNP>::iterator tmp_it = it;
 					it++;
@@ -857,7 +855,7 @@ namespace LD
 				}
 			}
 			// handle
-			out_SNP[i] = (ValidCnt == TotalCnt);
+			out_SNP[i] = to_include;
 			if (out_SNP[i])
 			{
 				ListGeno.push_front(TSNP(i, pos_bp[i], nPackedSamp));