Added support of newer TBB version

iminkin · iminkin · commit 292d8eaf4c9c · 2022-09-28T23:26:57.000-04:00
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,7 @@
+TwoPaCo 1.0.0
+=============
+* Added support of the newer version of TBB library
+
 TwoPaCo 0.9.4
 =============
 * Added the installation scripts
diff --git a/README.md b/README.md
@@ -1,6 +1,6 @@
-TwoPaCo 0.9.4
+TwoPaCo 1.0.0
 
-Release date: 25th September 2020
+Release date: 29th September 2022
 =============================
 
 Authors
diff --git a/src/graphconstructor/CMakeLists.txt b/src/graphconstructor/CMakeLists.txt
@@ -1,5 +1,4 @@
 project(twopaco CXX)
-cmake_minimum_required(VERSION 2.8)
 
 set(CMAKE_PROJECT_NAME twopaco)
 set(CMAKE_CXX_STANDARD 14)
@@ -10,6 +9,6 @@ include_directories(${twopaco_SOURCE_DIR} ${TBB_INCLUDE_DIR} "../common")
 target_link_libraries(twopaco  "tbb" "tbbmalloc" "tbbmalloc_proxy" "pthread" )
 install(TARGETS twopaco RUNTIME DESTINATION bin)
 
-set(CPACK_PACKAGE_VERSION_MAJOR "0")
-set(CPACK_PACKAGE_VERSION_MINOR "9")
-set(CPACK_PACKAGE_VERSION_PATCH "4")
+set(CPACK_PACKAGE_VERSION_MAJOR "1")
+set(CPACK_PACKAGE_VERSION_MINOR "0")
+set(CPACK_PACKAGE_VERSION_PATCH "0")
diff --git a/src/graphconstructor/assemblyedgeconstructor.h b/src/graphconstructor/assemblyedgeconstructor.h
@@ -8,7 +8,7 @@ namespace TwoPaCo
 	class AssemblyEdgeConstructor
 	{
 	public:
-		AssemblyEdgeConstructor(const std::vector<std::string> & inputFileName, const std::string & marksFileName, const VertexEnumerator & vertexEnumerator) : 				
+		AssemblyEdgeConstructor(const std::vector<std::string> & inputFileName, const std::string & marksFileName, const VertexEnumerator & vertexEnumerator) :
 				vertexEnumerator_(vertexEnumerator)
 		{
 			int64_t vertexLength = vertexEnumerator_.GetHashSeed().VertexLength();
@@ -20,11 +20,11 @@ namespace TwoPaCo
 			JunctionPositionReader junctionReader(marksFileName);
 //			std::unique_ptr<ConcurrentBitVector> bloomFilter = vertexEnumerator_.ReloadBloomFilter();
 			for (std::string chr; chrReader.NextChr(chr); chrNumber++)
-			{								
+			{
 				//Read the current vector of junction marks. Notice: should be done in order!
 				junctionMark.push_back(std::vector<bool>(chr.size(), false));
 				junctionReader.RestoreVector(junctionMark.back(), chrNumber);
-				//Init hash function				
+				//Init hash function
 				VertexRollingHash hash(vertexEnumerator.GetHashSeed(), chr.begin(), vertexEnumerator.GetHashSeed().HashFunctionsNumber());
 				for (int64_t i = 0; i <= int64_t(chr.size()) - edgeLength; i++)
 				{
@@ -35,7 +35,7 @@ namespace TwoPaCo
 					{
 						assert(IsIngoingEdgeInBloomFilter(hash, *bloomFilter, chr[i - 1]));
 					}
-					
+
 					//Check the if the vertex is a junction
 					if (vertexEnumerator_.GetId(vertex) != INVALID_VERTEX)
 					{
@@ -49,7 +49,7 @@ namespace TwoPaCo
 				}
 			}
 		}
-		
+
 	private:
 		const VertexEnumerator & vertexEnumerator_;
 		DISALLOW_COPY_AND_ASSIGN(AssemblyEdgeConstructor);
@@ -58,4 +58,4 @@ namespace TwoPaCo
 
 }
 
-#endif
+#endif
diff --git a/src/graphconstructor/common.h b/src/graphconstructor/common.h
@@ -38,7 +38,7 @@ namespace TwoPaCo
 		static const size_t TASK_SIZE = 32;
 #else
 		static const size_t TASK_SIZE = 1 << 19;
-#endif					
+#endif
 		static const size_t GAME_OVER = SIZE_MAX;
 		Task() {}
 		Task(uint64_t seqId, uint64_t start, uint64_t piece, uint64_t offset, bool isFinal, std::string && str) :
diff --git a/src/graphconstructor/constructor.cpp b/src/graphconstructor/constructor.cpp
@@ -56,7 +56,7 @@ int main(int argc, char * argv[])
 	OddConstraint constraint;
 	try
 	{
-		TCLAP::CmdLine cmd("Program for construction of the condensed de Bruijn graph from complete genomes", ' ', "0.9.4");
+		TCLAP::CmdLine cmd("Program for construction of the condensed de Bruijn graph from complete genomes", ' ', "1.0.0");
 
 		TCLAP::ValueArg<unsigned int> kvalue("k",
 			"kvalue",
diff --git a/src/graphdump/CMakeLists.txt b/src/graphdump/CMakeLists.txt
@@ -1,5 +1,4 @@
 project(graphdump CXX)
-cmake_minimum_required(VERSION 2.8)
 
 set(CMAKE_PROJECT_NAME graphdump)
 set(CMAKE_CXX_STANDARD 14)
@@ -10,6 +9,6 @@ include_directories(${twopaco_SOURCE_DIR} ${TBB_INCLUDE_DIR} "../common")
 target_link_libraries(graphdump  "tbb" "pthread")
 install(TARGETS graphdump RUNTIME DESTINATION bin)
 
-set(CPACK_PACKAGE_VERSION_MAJOR "0")
-set(CPACK_PACKAGE_VERSION_MINOR "9")
-set(CPACK_PACKAGE_VERSION_PATCH "4")
+set(CPACK_PACKAGE_VERSION_MAJOR "1")
+set(CPACK_PACKAGE_VERSION_MINOR "0")
+set(CPACK_PACKAGE_VERSION_PATCH "0")

Original file line number	Diff line number	Diff line change
`@@ -8,7 +8,7 @@ namespace TwoPaCo`
`8`	`8`	`class AssemblyEdgeConstructor`
`9`	`9`	`{`
`10`	`10`	`public:`
`11`		`- AssemblyEdgeConstructor(const std::vector<std::string> & inputFileName, const std::string & marksFileName, const VertexEnumerator & vertexEnumerator) :`
	`11`	`+ AssemblyEdgeConstructor(const std::vector<std::string> & inputFileName, const std::string & marksFileName, const VertexEnumerator & vertexEnumerator) :`
`12`	`12`	`vertexEnumerator_(vertexEnumerator)`
`13`	`13`	`{`
`14`	`14`	`int64_t vertexLength = vertexEnumerator_.GetHashSeed().VertexLength();`
`@@ -20,11 +20,11 @@ namespace TwoPaCo`
`20`	`20`	`JunctionPositionReader junctionReader(marksFileName);`
`21`	`21`	`// std::unique_ptr<ConcurrentBitVector> bloomFilter = vertexEnumerator_.ReloadBloomFilter();`
`22`	`22`	`for (std::string chr; chrReader.NextChr(chr); chrNumber++)`
`23`		`- {`
	`23`	`+ {`
`24`	`24`	`//Read the current vector of junction marks. Notice: should be done in order!`
`25`	`25`	`junctionMark.push_back(std::vector<bool>(chr.size(), false));`
`26`	`26`	`junctionReader.RestoreVector(junctionMark.back(), chrNumber);`
`27`		`- //Init hash function`
	`27`	`+ //Init hash function`
`28`	`28`	`VertexRollingHash hash(vertexEnumerator.GetHashSeed(), chr.begin(), vertexEnumerator.GetHashSeed().HashFunctionsNumber());`
`29`	`29`	`for (int64_t i = 0; i <= int64_t(chr.size()) - edgeLength; i++)`
`30`	`30`	`{`
`@@ -35,7 +35,7 @@ namespace TwoPaCo`
`35`	`35`	`{`
`36`	`36`	`assert(IsIngoingEdgeInBloomFilter(hash, *bloomFilter, chr[i - 1]));`
`37`	`37`	`}`
`38`		`-`
	`38`	`+`
`39`	`39`	`//Check the if the vertex is a junction`
`40`	`40`	`if (vertexEnumerator_.GetId(vertex) != INVALID_VERTEX)`
`41`	`41`	`{`
`@@ -49,7 +49,7 @@ namespace TwoPaCo`
`49`	`49`	`}`
`50`	`50`	`}`
`51`	`51`	`}`
`52`		`-`
	`52`	`+`
`53`	`53`	`private:`
`54`	`54`	`const VertexEnumerator & vertexEnumerator_;`
`55`	`55`	`DISALLOW_COPY_AND_ASSIGN(AssemblyEdgeConstructor);`
`@@ -58,4 +58,4 @@ namespace TwoPaCo`
`58`	`58`
`59`	`59`	`}`
`60`	`60`
`61`		`-#endif`
	`61`	`+#endif`
Original file line number	Diff line number	Diff line change
`@@ -56,7 +56,7 @@ int main(int argc, char * argv[])`
`56`	`56`	`OddConstraint constraint;`
`57`	`57`	`try`
`58`	`58`	`{`
`59`		`- TCLAP::CmdLine cmd("Program for construction of the condensed de Bruijn graph from complete genomes", ' ', "0.9.4");`
	`59`	`+ TCLAP::CmdLine cmd("Program for construction of the condensed de Bruijn graph from complete genomes", ' ', "1.0.0");`
`60`	`60`
`61`	`61`	`TCLAP::ValueArg<unsigned int> kvalue("k",`
`62`	`62`	`"kvalue",`