Setup tensorstore

Author: Will-Tyler

.Rbuildignore

@@ -1 +1,3 @@
 thirdParty/cget
+thirdParty/tensorstore-0.1.65
+src/build

.gitignore

@@ -7,5 +7,6 @@ thirdParty/bgen/.hg
 src/*.o
 src/*.so
 src/backup/*
+src/build
 extdata/input/nfam_100_nindep_0_step1_includeMoreRareVariants_poly.raw
 *.swp

src/CMakeLists.txt

@@ -0,0 +1,28 @@
+cmake_minimum_required(VERSION 3.1...3.29)
+
+set(CMAKE_BUILD_TYPE Debug)
+set(CMAKE_CXX_STANDARD 17)
+set(CMAKE_CXX_STANDARD_REQUIRED True)
+set(CMAKE_CXX_EXTENSIONS OFF)
+
+add_library(VCZ OBJECT VCZ.cpp)
+
+include(FetchContent)
+
+FetchContent_Declare(
+    tensorstore
+    URL "https://github.com/google/tensorstore/archive/refs/tags/v0.1.64.tar.gz"
+    URL_HASH SHA256=1dc632c6e9f83c033a2a16fe1a67ca38825902083ea0efe314769eee980c3126
+)
+
+# Additional FetchContent_Declare calls as needed...
+
+FetchContent_MakeAvailable(tensorstore)
+
+# Define a target that depends on TensorStore...
+
+target_link_libraries(
+    VCZ
+    PRIVATE
+    tensorstore::tensorstore tensorstore::all_drivers
+)

src/Main.cpp

@@ -20,6 +20,7 @@
 #include "PLINK.hpp"
 #include "BGEN.hpp"
 #include "VCF.hpp"
+#include "VCZ.hpp"
 #include "SAIGE_test.hpp"
 #include "UTIL.hpp"
 #include "CCT.hpp"
@@ -34,6 +35,7 @@
 static PLINK::PlinkClass* ptr_gPLINKobj = NULL;
 static BGEN::BgenClass* ptr_gBGENobj = NULL;
 static VCF::VcfClass* ptr_gVCFobj = NULL;
+static VCZ::VczClass* ptr_gVCZobj = NULL;
 // global objects for different analysis methods
 static SAIGE::SAIGEClass* ptr_gSAIGEobj = NULL;
 //single, SAIGE
@@ -813,7 +815,7 @@ bool isEnd = ptr_gVCFobj->check_iterator_end();
 
 // [[Rcpp::export]]
 void setVCZobjInCPP(std::string t_vczFileName, std::vector<std::string> &t_SampleInModel) {
-  // TODO
+  ptr_gVCZobj = new VCZ::VczClass(t_vczFileName, t_SampleInModel);
 }