include Makefile

Author: pkalbers

Makefile

@@ -0,0 +1,29 @@
+CC := g++
+
+CFLAGS := -std=c++11 -Wno-unused-command-line-argument -O2 -march=native
+CCLIBS  := -lz -lpthread
+
+TARGET := geva_v1beta
+
+SUBDIRS := $(shell find ./src/ -type d)
+INCDIRS := $(addprefix -I, $(SUBDIRS))
+
+SOURCES := $(shell find . -name '*.cpp')
+OBJECTS := $(patsubst %.cpp, %.o, $(SOURCES))
+
+
+all: $(TARGET)
+
+%.o: %.cpp
+	$(CC) $(CFLAGS) -flto $(INCDIRS) -c $< -o $@ $(CCLIBS)
+
+$(TARGET): $(OBJECTS)
+	$(CC) -o $(TARGET) -flto $(CFLAGS) $(OBJECTS) $(CCLIBS)
+
+
+.PHONY: clean
+
+clean:
+	@rm -f $(OBJECTS) $(TARGET)
+
+

src/age/AgeInfer.cpp

@@ -42,7 +42,7 @@ void Pair::print_header(std::ostream & stream, const Param::Data param, const bo
 	else
 	{
 //		stream << " Fk SampleID0 Chr0 SampleID1 Chr1 Shared Missing Pass SegmentLHS SegmentRHS S_LHS S_RHS Shape Rate q25 q50 q75";
-		stream << " Fk SampleID0 Chr0 SampleID1 Chr1 Shared Pass SegmentLHS SegmentRHS Shape Rate";
+		stream << " SampleID0 Chr0 SampleID1 Chr1 Shared Pass SegmentLHS SegmentRHS Shape Rate";
 	}
 
 	stream << std::endl;
@@ -87,7 +87,7 @@ void Pair::print(std::ostream & stream, const Param::Data param, const bool full
 			const ChrType chr0 = this->pair.first.chromosome;
 			const ChrType chr1 = this->pair.second.chromosome;
 
-			stream << site_ptr->fk << ' ';
+//			stream << site_ptr->fk << ' ';
 
 			stream << this->pair.first.individual.value << ' ';
 
@@ -111,7 +111,7 @@ void Pair::print(std::ostream & stream, const Param::Data param, const bool full
 
 			stream << ((this->sharing) ? '1': '0') << ' ';
 
-			stream << std::fixed << std::setprecision(8) << this->missing << ' ';
+//			stream << std::fixed << std::setprecision(8) << this->missing << ' ';
 
 			stream << ((this->ccf[c].pass) ? '1': '0') << ' ';
 
@@ -1115,7 +1115,7 @@ void Site::print_header(std::ostream & stream, const Param::Data param, const bo
 	else
 	{
 //		stream << " Fk N_Shared N_Others PostMean PostMode PostMedian PostCI025 PostCI975 Robust Lower Upper";
-		stream << " N_Shared N_Others PostMean PostMode PostMedian";
+		stream << " N_Concordant N_Discordant PostMean PostMode PostMedian";
 	}
 
 	stream << std::endl;

src/gen/GenShare.cpp

@@ -180,7 +180,7 @@ size_t Share::select(const std::set<size_t> & position, const Grid::Data grid)
 		}
 	}
 
-	printf("\n %lu \n", count);
+//	printf("\n %lu \n", count);
 
 	if (count > 0)
 	{
@@ -206,7 +206,7 @@ size_t Share::select(const std::set<size_t> & position, const Grid::Data grid)
 		{
 			count += index->second.sites.size();
 		}
-		printf("\n %lu \n", count);
+//		printf("\n %lu \n", count);
 		count = 0;
 
 
@@ -225,7 +225,7 @@ size_t Share::select(const std::set<size_t> & position, const Grid::Data grid)
 		}
 	}
 
-	printf("\n %lu \n", count);
+//	printf("\n %lu \n", count);
 
 	this->clean_table();