rolling back to old pufferfish b/c of the optimizations that made the…

… previous unusable for longer k-mers

CMakeLists.txt

@@ -81,10 +81,16 @@ set(GAT_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR})
 ###
 
 ## Try and find TBB first
-find_package(TBB 2018.0 COMPONENTS tbb tbbmalloc tbbmalloc_proxy)
+find_package(TBB 2019.0 COMPONENTS tbb tbbmalloc tbbmalloc_proxy)
+
+## NOTE: we actually require at least 2019 U4 or greater
+## since we are using tbb::global_control.  However, they 
+## seem not to have tagged minor version numbers in their 
+## source.  Check before release if we can bump to the 2020
+## version (requires having tbb 2020 for OSX).
 
 if (${TBB_FOUND})
-  if (${TBB_VERSION} VERSION_GREATER_EQUAL 2018.0)
+  if (${TBB_VERSION} VERSION_GREATER_EQUAL 2019.0)
   message("FOUND SUITABLE TBB VERSION : ${TBB_VERSION}")
   set(TBB_TARGET_EXISTED TRUE)
   else()
@@ -112,7 +118,8 @@ endif()
 message("Build system will fetch and build Intel Threading Building Blocks")
 message("==================================================================")
 # These are useful for the custom install step we'll do later
-set(TBB_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/oneTBB-2019_U8)
+set(TBB_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/oneTBB-2020.2)
+#set(TBB_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/oneTBB-2019_U8)
 #set(TBB_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/tbb-2019_U8)
 set(TBB_INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install)
 
@@ -126,10 +133,10 @@ set(TBB_CXXFLAGS "${TBB_CXXFLAGS} ${CXXSTDFLAG}")
 
 externalproject_add(libtbb
   DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
-  DOWNLOAD_COMMAND curl -k -L https://github.com/intel/tbb/archive/2019_U8.tar.gz -o tbb-2019_U8.tgz &&
-    ${SHASUM} 6b540118cbc79f9cbc06a35033c18156c21b84ab7b6cf56d773b168ad2b68566 tbb-2019_U8.tgz &&
-    tar -xzvf tbb-2019_U8.tgz
-  SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/oneTBB-2019_U8
+  DOWNLOAD_COMMAND curl -k -L https://github.com/oneapi-src/oneTBB/archive/v2020.2.tar.gz  -o tbb-2020_U2.tgz &&
+    ${SHASUM} 4804320e1e6cbe3a5421997b52199e3c1a3829b2ecb6489641da4b8e32faf500 tbb-2020_U2.tgz &&
+    tar -xzvf tbb-2020_U2.tgz
+  SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/oneTBB-2020.2
   INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
   PATCH_COMMAND "${TBB_PATCH_STEP}"
   CONFIGURE_COMMAND ""

external/twopaco/common/junctionapi/junctionapi.h

@@ -49,14 +49,6 @@ namespace TwoPaCo
 			}
 		}
 
-		void RestoreReader() {
-			/*if (!in_) {
-				throw std::runtime_error("No input file exists");
-			}*/
-			in_.clear();
-			in_.seekg(0, in_.beg);
-			nowChr_=0;
-		}
 		void RestoreVector(std::vector<bool> & mark, size_t chr)
 		{
 			JunctionPosition pos;

external/twopaco/common/streamfastaparser.h

@@ -148,10 +148,6 @@ namespace TwoPaCo
 			}
 		}
 
-		void reset() {
-			parser_.reset(new TwoPaCo::StreamFastaParser(fileName_[0]));
-		}
-
 		bool NextChr(std::string & buf)
 		{
 			buf.clear();

external/twopaco/graphconstructor/CMakeLists.txt

@@ -2,6 +2,9 @@ project(twopaco CXX)
 cmake_minimum_required(VERSION 3.9)
 
 set(CMAKE_PROJECT_NAME twopaco)
+#if(CMAKE_COMPILER_IS_GNUCXX)
+#	list(APPEND "CMAKE_CXX_FLAGS" "-std=c++0x")
+#endif()
 
 include_directories(${twopaco_SOURCE_DIR} ${TBB_INCLUDE_DIRS} "../common")
 link_directories(${TBB_LIB_DIR})

external/twopaco/graphconstructor/bifurcationstorage.h

@@ -1,7 +1,6 @@
 #ifndef _BIFURCATION_STORAGE_H_
 #define _BIFURCATION_STORAGE_H_
 
-#include <algorithm>
 #include "common.h"
 #include "compressedstring.h"
 
@@ -35,7 +34,7 @@ namespace TwoPaCo
 			}
 
 			size_t hashFunctionNumber = 3;
-			bitsPower = std::max(static_cast<size_t>(bitsPower), size_t(24));
+			bitsPower = max(bitsPower, size_t(24));
 			bifurcationFilter_.assign(uint64_t(1) << bitsPower, false);
 			hashFunction_.resize(hashFunctionNumber);
 			for (HashFunctionPtr & ptr : hashFunction_)
@@ -162,4 +161,4 @@ namespace TwoPaCo
 	};
 }
 
-#endif
+#endif

external/twopaco/graphconstructor/constructor.cpp

@@ -50,7 +50,7 @@ class OddConstraint : public TCLAP::Constraint <unsigned int>
 	}
 };
 
-int buildGraphMain(std::vector<std::string>& args)  //}int argc, char * argv[])
+int buildGraphMain(std::vector<std::string>& args)//main(int argc, char * argv[])
 {
 	OddConstraint constraint;
 	try
@@ -124,7 +124,7 @@ int buildGraphMain(std::vector<std::string>& args)  //}int argc, char * argv[])
 			"file name",
 			cmd);
 
-		cmd.parse(args);//argc, argv);		
+		cmd.parse(args);//(argc, argv);		
 		using TwoPaCo::Range;
 		if (runTests.getValue())
 		{

external/twopaco/graphdump/CMakeLists.txt

@@ -2,6 +2,9 @@ project(graphdump CXX)
 cmake_minimum_required(VERSION 3.9)
 
 set(CMAKE_PROJECT_NAME graphdump)
+#if(CMAKE_COMPILER_IS_GNUCXX)
+#	list(APPEND "CMAKE_CXX_FLAGS" "-std=c++0x")
+#endif()
 
 include_directories(${twopaco_SOURCE_DIR} ${TBB_INCLUDE_DIRS} "../common" "./" )
 link_directories(${TBB_LIB_DIR})
@@ -14,7 +17,6 @@ install(TARGETS graphdump DESTINATION lib EXPORT graphdump-targets)
 install(EXPORT graphdump-targets DESTINATION lib/graphdump)
 
 
-
 set(CPACK_PACKAGE_VERSION_MAJOR "0")
 set(CPACK_PACKAGE_VERSION_MINOR "9")
 set(CPACK_PACKAGE_VERSION_PATCH "3")