update to public

Makefile

@@ -1,5 +1,7 @@
 all: kmc kmc_dump kmc_tools py_kmc_api
 
+dummy := $(shell git submodule update --init --recursive)
+
 UNAME_S := $(shell uname -s)
 UNAME_M := $(shell uname -m)
 UNAME_P := $(shell uname -p)
@@ -169,15 +171,15 @@ $(LIB_KMC_CORE): $(KMC_CORE_OBJS) $(RADULS_OBJS) $(KMC_API_OBJS) $(KFF_OBJS)
 
 kmc: $(KMC_CLI_OBJS) $(LIB_KMC_CORE) $(LIB_ZLIB)
 	-mkdir -p $(OUT_BIN_DIR)
-	$(CC) $(CLINK) -o $(OUT_BIN_DIR)/$@ $^ $(LIB_ZLIB)
+	$(CC) $(CLINK) -o $(OUT_BIN_DIR)/$@ $^
 
 kmc_dump: $(KMC_DUMP_OBJS) $(KMC_API_OBJS)
 	-mkdir -p $(OUT_BIN_DIR)
 	$(CC) $(CLINK) -o $(OUT_BIN_DIR)/$@ $^
 
 kmc_tools: $(KMC_TOOLS_OBJS) $(KMC_API_OBJS) $(KFF_OBJS) $(LIB_ZLIB)
 	-mkdir -p $(OUT_BIN_DIR)
-	$(CC) $(CLINK) -I 3rd_party/cloudflare -o $(OUT_BIN_DIR)/$@ $^ $(LIB_ZLIB)
+	$(CC) $(CLINK) -I 3rd_party/cloudflare -o $(OUT_BIN_DIR)/$@ $^
 
 $(PY_KMC_API_DIR)/%.o: $(KMC_API_DIR)/%.cpp
 	$(CC) -c -fPIC -Wall -O3 $(CPU_FLAGS) -std=c++14 $^ -o $@

kmc_core/kff_writer.h

@@ -2,6 +2,7 @@
 
 #include <string>
 #include <vector>
+#include <cstdint>
 
 template<typename T>
 void StoreBigEndian(uint8_t* buff, const T& data)

kmc_core/kmc.h

@@ -1802,14 +1802,26 @@ template <unsigned SIZE> KMC::Stage2Results CKMC<SIZE>::ProcessStage2_impl()
 
 template <unsigned SIZE> KMC::Stage1Results CKMC<SIZE>::ProcessStage1()
 {
-	auto res = ProcessStage1_impl();
+	KMC::Stage1Results res;
+	//run on separate exception aware thread for proper exception handling
+	CExceptionAwareThread th([&res, this] {
+		res = this->ProcessStage1_impl();
+	});
+	th.join();
+
 	CThreadExceptionCollector::Inst().RethrowIfAnyException();
 	return res;
 }
 
 template <unsigned SIZE> KMC::Stage2Results CKMC<SIZE>::ProcessStage2()
 {
-	auto res = ProcessStage2_impl();
+	KMC::Stage2Results res;
+	//run on separate exception aware thread for proper exception handling if exception thrown in main thread
+	CExceptionAwareThread th([&res, this] {
+		res = this->ProcessStage2_impl();
+		});
+	th.join();
+
 	CThreadExceptionCollector::Inst().RethrowIfAnyException();
 	return res;
 }

kmc_core/small_sort.h

@@ -153,13 +153,25 @@ class CSmallSort {
 
 	static void Adjust(uint32 max_small_size = 256)
 	{
+		static bool is_adjusted = false;
+		if (is_adjusted)
+			return;
+
+		static std::mutex mtx;
+		std::lock_guard<std::mutex> lck(mtx);
+		if (is_adjusted)
+			return;
+
 		PrepareArray();
 		EvaluateAlgorithms(max_small_size);
 		SmoothTimes();
 		SelectBestSorters();
 		ReleaseArray();
+
+		is_adjusted = true;
 	}
 
+
 	static void Sort(CKmer<SIZE> *ptr, uint32 size)
 	{
 		sorters[size](ptr, size);

kmc_tools/kff_info_reader.cpp

@@ -6,6 +6,7 @@
 //#include <iostream>
 #include <algorithm>
 #include <cstring>
+#include <cstdint>
 
 std::string CKFFInfoReader::ReadVarName()
 {

kmc_tools/kff_info_reader.h

@@ -4,6 +4,7 @@
 #include <limits>
 #include <string>
 #include <map>
+#include <cstdint>
 
 
 template<typename T>

kmc_tools/parser.cpp

@@ -253,4 +253,4 @@ bool CParser::nextLine(std::string& line)
 	}
 }
 
-// ***** EOF
+// ***** EOF