From 07ed2d0b01d7540115d6c2ef438ed049705184a7 Mon Sep 17 00:00:00 2001
From: Xiuwen Zheng <zhengxwen@users.noreply.github.com>
Date: Fri, 29 Mar 2024 22:30:10 -0500
Subject: [PATCH] system headers go first

---
 src/ConvToGDS.cpp   |  6 +++---
 src/SNPRelate.cpp   | 16 ++++++++--------
 src/ThreadPool.h    | 11 +++++------
 src/dGenGWAS.h      |  2 +-
 src/genBeta.cpp     | 12 ++++++------
 src/genEIGMIX.cpp   |  4 ++--
 src/genFst.cpp      | 10 +++++-----
 src/genHWE.cpp      |  8 ++++----
 src/genIBD.cpp      | 10 +++++-----
 src/genIBS.cpp      | 12 ++++++------
 src/genKING.cpp     | 12 ++++++------
 src/genLD.cpp       |  8 ++++----
 src/genPCA.cpp      |  6 +++---
 src/genSlideWin.cpp |  8 ++++----
 14 files changed, 62 insertions(+), 63 deletions(-)

diff --git a/src/ConvToGDS.cpp b/src/ConvToGDS.cpp
index a39ada9..90aa337 100755
--- a/src/ConvToGDS.cpp
+++ b/src/ConvToGDS.cpp
@@ -2,7 +2,7 @@
 //
 // ConvToGDS.cpp: PED/VCF to GDS Format
 //
-// Copyright (C) 2013-2023    Xiuwen Zheng
+// Copyright (C) 2013-2024    Xiuwen Zheng
 //
 // This file is part of SeqArray.
 //
@@ -19,16 +19,16 @@
 // along with SeqArray.
 // If not, see <http://www.gnu.org/licenses/>.
 
-#include <R_GDS_CPP.h>
 #include <string>
 #include <vector>
 #include <map>
 #include <algorithm>
+#include <fstream>
 
+#include <R_GDS_CPP.h>
 using namespace CoreArray;
 
 #include <dGenGWAS.h>
-#include <fstream>
 using namespace GWAS;
 
 
diff --git a/src/SNPRelate.cpp b/src/SNPRelate.cpp
index d03e960..37a637b 100755
--- a/src/SNPRelate.cpp
+++ b/src/SNPRelate.cpp
@@ -9,7 +9,7 @@
 // SNPRelate.cpp: Relatedness, Linkage Disequilibrium and
 //				  Principal Component Analysis
 //
-// Copyright (C) 2011-2018    Xiuwen Zheng [zhengxwen@gmail.com]
+// Copyright (C) 2011-2024    Xiuwen Zheng [zhengx@u.washington.edu]
 //
 // This file is part of SNPRelate.
 //
@@ -27,13 +27,6 @@
 // If not, see <http://www.gnu.org/licenses/>.
 
 
-#include <dGenGWAS.h>
-#include <dVect.h>
-
-#include <Rinternals.h>
-#include <R_ext/Lapack.h>
-#include <R_ext/Rdynload.h>
-
 #include <fstream>
 #include <vector>
 #include <set>
@@ -41,6 +34,13 @@
 #include <utility>
 #include <algorithm>
 
+#include <dGenGWAS.h>
+#include <dVect.h>
+
+#include <Rinternals.h>
+#include <R_ext/Lapack.h>
+#include <R_ext/Rdynload.h>
+
 
 using namespace std;
 using namespace CoreArray;
diff --git a/src/ThreadPool.h b/src/ThreadPool.h
index 0624c41..63b876c 100755
--- a/src/ThreadPool.h
+++ b/src/ThreadPool.h
@@ -2,7 +2,7 @@
 //
 // ThreadPool.h: a C++ implementation of thread pool
 //
-// Copyright (C) 2016-2017    Xiuwen Zheng
+// Copyright (C) 2016-2024    Xiuwen Zheng
 //
 // This file is part of SNPRelate.
 //
@@ -21,9 +21,9 @@
 
 /**
  *	\file     ThreadPool.h
- *	\author   Xiuwen Zheng [zhengxwen@gmail.com]
+ *	\author   Xiuwen Zheng [zhengx@u.washington.edu]
  *	\version  1.0
- *	\date     2016-2017
+ *	\date     2016-2024
  *	\brief    a C++ implementation of thread pool
  *	\details
 **/
@@ -31,19 +31,18 @@
 #ifndef _HEADER_THREAD_POOL_
 #define _HEADER_THREAD_POOL_
 
-#include <CoreDEF.h>
-#include <R_GDS_CPP.h>
 #include <vector>
 #include <queue>
+#include <CoreDEF.h>
 
 #ifdef COREARRAY_PLATFORM_WINDOWS
 #   include <windows.h>
 #endif
-
 #ifdef COREARRAY_POSIX_THREAD
 #   include <pthread.h>
 #endif
 
+#include <R_GDS_CPP.h>
 
 namespace CoreArray
 {
diff --git a/src/dGenGWAS.h b/src/dGenGWAS.h
index beab959..bb1bcdd 100755
--- a/src/dGenGWAS.h
+++ b/src/dGenGWAS.h
@@ -22,13 +22,13 @@
 #ifndef _HEADER_GWAS_
 #define _HEADER_GWAS_
 
-#include <R_GDS_CPP.h>
 #include <ctime>
 #include <vector>
 #include <string>
 #include <algorithm>
 #include <memory>
 
+#include <R_GDS_CPP.h>
 #include "ThreadPool.h"
 #include "dVect.h"
 
diff --git a/src/genBeta.cpp b/src/genBeta.cpp
index 6192bd1..65d27ba 100755
--- a/src/genBeta.cpp
+++ b/src/genBeta.cpp
@@ -2,7 +2,7 @@
 //
 // genBeta.cpp: Individual Inbreeding and Relatedness (Beta) on GWAS
 //
-// Copyright (C) 2016-2018    Xiuwen Zheng
+// Copyright (C) 2016-2024    Xiuwen Zheng
 //
 // This file is part of SNPRelate.
 //
@@ -22,17 +22,17 @@
 #ifndef _HEADER_IBD_BETA_
 #define _HEADER_IBD_BETA_
 
-// CoreArray library header
-#include <dGenGWAS.h>
-#include <dVect.h>
-#include "ThreadPool.h"
-
 // Standard library header
 #include <cmath>
 #include <cfloat>
 #include <memory>
 #include <algorithm>
 
+// CoreArray library header
+#include <dGenGWAS.h>
+#include <dVect.h>
+#include "ThreadPool.h"
+
 
 namespace IBD_BETA
 {
diff --git a/src/genEIGMIX.cpp b/src/genEIGMIX.cpp
index fdfa71f..3b6abda 100755
--- a/src/genEIGMIX.cpp
+++ b/src/genEIGMIX.cpp
@@ -2,7 +2,7 @@
 //
 // genEIGMIX.cpp: Eigen-analysis with admixture on GWAS
 //
-// Copyright (C) 2017    Xiuwen Zheng
+// Copyright (C) 2017-2024    Xiuwen Zheng
 //
 // This file is part of SNPRelate.
 //
@@ -23,8 +23,8 @@
 #ifndef _HEADER_EIGMIX_
 #define _HEADER_EIGMIX_
 
-#include "genPCA.h"
 #include <algorithm>
+#include "genPCA.h"
 
 
 namespace EIGMIX
diff --git a/src/genFst.cpp b/src/genFst.cpp
index 82518db..33fe32a 100755
--- a/src/genFst.cpp
+++ b/src/genFst.cpp
@@ -2,7 +2,7 @@
 //
 // genFst.cpp: Fixation index (Fst) Estimation
 //
-// Copyright (C) 2015-2017    Xiuwen Zheng
+// Copyright (C) 2015-2024    Xiuwen Zheng
 //
 // This file is part of SNPRelate.
 //
@@ -22,14 +22,14 @@
 #ifndef _HEADER_FST_
 #define _HEADER_FST_
 
-// CoreArray library header
-#include "dGenGWAS.h"
-#include "dVect.h"
-
 // Standard library header
 #include <vector>
 #include <cmath>
 
+// CoreArray library header
+#include "dGenGWAS.h"
+#include "dVect.h"
+
 namespace Fst
 {
 	class COREARRAY_DLL_LOCAL ClassFst_WH15
diff --git a/src/genHWE.cpp b/src/genHWE.cpp
index 12a6a0b..f4bfa39 100755
--- a/src/genHWE.cpp
+++ b/src/genHWE.cpp
@@ -2,7 +2,7 @@
 //
 // genHWE.cpp: Hardy-Weinberg Equilibrium Test on SNPs
 //
-// Copyright (C) 2015-2017    Xiuwen Zheng
+// Copyright (C) 2015-2024    Xiuwen Zheng
 //
 // This file is part of SNPRelate.
 //
@@ -22,13 +22,13 @@
 #ifndef _HEADER_HWE_
 #define _HEADER_HWE_
 
-// CoreArray library header
-#include "dGenGWAS.h"
-
 // Standard library header
 #include <vector>
 #include <cmath>
 
+// CoreArray library header
+#include "dGenGWAS.h"
+
 // using namespace
 using namespace std;
 using namespace GWAS;
diff --git a/src/genIBD.cpp b/src/genIBD.cpp
index c331093..5693860 100755
--- a/src/genIBD.cpp
+++ b/src/genIBD.cpp
@@ -2,7 +2,7 @@
 //
 // genIBD.cpp: Identity by descent (IBD) Analysis on GWAS
 //
-// Copyright (C) 2011-2018    Xiuwen Zheng
+// Copyright (C) 2011-2024    Xiuwen Zheng
 //
 // This file is part of SNPRelate.
 //
@@ -23,10 +23,6 @@
 #ifndef _HEADER_IBD_
 #define _HEADER_IBD_
 
-// CoreArray library header
-#include "dGenGWAS.h"
-#include "dVect.h"
-
 // Standard library header
 #include <limits>
 #include <vector>
@@ -35,6 +31,10 @@
 #include <memory>
 #include <algorithm>
 
+// CoreArray library header
+#include "dGenGWAS.h"
+#include "dVect.h"
+
 
 #ifdef COREARRAY_SIMD_SSE
 #include <xmmintrin.h>
diff --git a/src/genIBS.cpp b/src/genIBS.cpp
index 184c991..9df6535 100755
--- a/src/genIBS.cpp
+++ b/src/genIBS.cpp
@@ -2,7 +2,7 @@
 //
 // genIBS.cpp: Identity by state (IBS) Analysis on GWAS
 //
-// Copyright (C) 2011-2018    Xiuwen Zheng
+// Copyright (C) 2011-2024    Xiuwen Zheng
 //
 // This file is part of SNPRelate.
 //
@@ -23,17 +23,17 @@
 #ifndef _HEADER_IBS_
 #define _HEADER_IBS_
 
-// CoreArray library header
-#include "dGenGWAS.h"
-#include "dVect.h"
-#include "ThreadPool.h"
-
 // Standard library header
 #include <cmath>
 #include <cfloat>
 #include <memory>
 #include <algorithm>
 
+// CoreArray library header
+#include "dGenGWAS.h"
+#include "dVect.h"
+#include "ThreadPool.h"
+
 
 namespace IBS
 {
diff --git a/src/genKING.cpp b/src/genKING.cpp
index 5582dda..5755095 100755
--- a/src/genKING.cpp
+++ b/src/genKING.cpp
@@ -2,7 +2,7 @@
 //
 // genKING.cpp: KINK Identity-by-descent (IBD) Analysis on GWAS
 //
-// Copyright (C) 2011-2018    Xiuwen Zheng
+// Copyright (C) 2011-2024    Xiuwen Zheng
 //
 // This file is part of SNPRelate.
 //
@@ -22,17 +22,17 @@
 #ifndef _HEADER_IBD_KING_
 #define _HEADER_IBD_KING_
 
-// CoreArray library header
-#include <dGenGWAS.h>
-#include <dVect.h>
-#include "ThreadPool.h"
-
 // Standard library header
 #include <cmath>
 #include <cfloat>
 #include <memory>
 #include <algorithm>
 
+// CoreArray library header
+#include <dGenGWAS.h>
+#include <dVect.h>
+#include "ThreadPool.h"
+
 
 namespace IBD_KING
 {
diff --git a/src/genLD.cpp b/src/genLD.cpp
index d684114..87e760a 100755
--- a/src/genLD.cpp
+++ b/src/genLD.cpp
@@ -23,10 +23,6 @@
 #ifndef _HEADER_LD_
 #define _HEADER_LD_
 
-// CoreArray library header
-#include <dGenGWAS.h>
-#include <dVect.h>
-
 // Standard library header
 #include <cmath>
 #include <cfloat>
@@ -34,6 +30,10 @@
 #include <list>
 #include <algorithm>
 
+// CoreArray library header
+#include <dGenGWAS.h>
+#include <dVect.h>
+
 
 #ifdef COREARRAY_SIMD_SSE
 #include <xmmintrin.h>
diff --git a/src/genPCA.cpp b/src/genPCA.cpp
index 71e5f74..4a12209 100755
--- a/src/genPCA.cpp
+++ b/src/genPCA.cpp
@@ -2,7 +2,7 @@
 //
 // genPCA.cpp: Principal Component Analysis on GWAS
 //
-// Copyright (C) 2011-2020    Xiuwen Zheng
+// Copyright (C) 2011-2024    Xiuwen Zheng
 //
 // This file is part of SNPRelate.
 //
@@ -19,11 +19,11 @@
 // with SNPRelate.
 // If not, see <http://www.gnu.org/licenses/>.
 
-#include "genPCA.h"
-#include <R_ext/Lapack.h>
 #include <cmath>
 #include <memory>
 #include <algorithm>
+#include "genPCA.h"
+#include <R_ext/Lapack.h>
 
 #ifndef FCONE
 #   define FCONE
diff --git a/src/genSlideWin.cpp b/src/genSlideWin.cpp
index fa5a08b..a324660 100755
--- a/src/genSlideWin.cpp
+++ b/src/genSlideWin.cpp
@@ -2,7 +2,7 @@
 //
 // genSlideWin.cpp: The Method of Sliding Windows
 //
-// Copyright (C) 2015-2017    Xiuwen Zheng
+// Copyright (C) 2015-2024    Xiuwen Zheng
 //
 // This file is part of SNPRelate.
 //
@@ -22,13 +22,13 @@
 #ifndef _HEADER_SLIDE_WINDOW_
 #define _HEADER_SLIDE_WINDOW_
 
-// CoreArray library header
-#include "dGenGWAS.h"
-
 // Standard library header
 #include <vector>
 #include <cmath>
 
+// CoreArray library header
+#include "dGenGWAS.h"
+
 // using namespace
 using namespace std;
 using namespace GWAS;