refactor

.gitignore

@@ -30,3 +30,8 @@
 *.exe
 *.out
 *.app
+
+#
+bench
+utility
+generate

Makefile

@@ -19,14 +19,14 @@
 OPTFLAGS  := -O3 -march=native
 CFLAGS     = -std=c99 $(OPTFLAGS) $(DEBUG_FLAGS)
 CPPFLAGS   = -std=c++0x $(OPTFLAGS) $(DEBUG_FLAGS)
-CPP_SOURCE = flagstats.cpp utility.cpp
+CPP_SOURCE = benchmark/flagstats.cpp benchmark/utility.cpp benchmark/generate.cpp
 C_SOURCE   = 
 OBJECTS    = $(CPP_SOURCE:.cpp=.o) $(C_SOURCE:.c=.o)
 
-POSPOPCNT_PATH  := libalgebra
+POSPOPCNT_PATH  := ../libalgebra
 LZ4_PATH :=
 ZSTD_PATH :=
-INCLUDE_PATHS :=
+INCLUDE_PATHS := -I$(PWD)
 LIBRARY_PATHS :=
 ifneq ($(LZ4_PATH),)
 	INCLUDE_PATHS += -I$(LZ4_PATH)/include
@@ -42,23 +42,23 @@ INCLUDE_PATHS := $(sort $(INCLUDE_PATHS))
 LIBRARY_PATHS := $(sort $(LIBRARY_PATHS))
 
 # Default target
-all: flagstats utility
+all: benchmark utility generate
 
 # Generic rules
-utility.o: utility.cpp
-	$(CXX) $(CPPFLAGS) -c -o $@ $<
+utility: benchmark/utility.cpp
+	$(CXX) $(CPPFLAGS) -o $@ $<
 
-flagstats.o: flagstats.cpp
-	$(CXX) $(CPPFLAGS) -I$(POSPOPCNT_PATH) $(INCLUDE_PATHS) -c -o $@ $<
+generate: benchmark/generate.cpp
+	$(CXX) $(CPPFLAGS) -o $@ $<
 
-flagstats: flagstats.o
-	$(CXX) $(CPPFLAGS) flagstats.o -I$(POSPOPCNT_PATH) $(INCLUDE_PATHS) $(LIBRARY_PATHS) -o flagstats -llz4 -lzstd
+bench.o: benchmark/flagstats.cpp
+	$(CXX) $(CPPFLAGS) -I$(POSPOPCNT_PATH) $(INCLUDE_PATHS) -c -o $@ $<
 
-utility: utility.o
-	$(CXX) $(CPPFLAGS) utility.o -o utility
+benchmark: bench.o
+	$(CXX) $(CPPFLAGS) bench.o -I$(POSPOPCNT_PATH) $(INCLUDE_PATHS) $(LIBRARY_PATHS) -o bench -llz4 -lzstd
 
 clean:
 	rm -f $(OBJECTS)
-	rm -f flagstats utility
+	rm -f bench bench.o utility generate
 
 .PHONY: all clean

generate.cpp → benchmark/generate.cpp

@@ -8,8 +8,6 @@ int main(int argc, char** argv) {
     std::random_device rd; // obtain a random number from hardware
     std::mt19937 eng(rd()); // seed the generator
 
-    std::cerr << strtoull( argv[1], NULL, 10 ) << std::endl;
-
     std::uniform_int_distribution<uint16_t> distr(0, 4096-1); // right inclusive
     for (int i = 0; i < strtoull( argv[1], NULL, 10 ); ++i) {
         uint16_t x = distr(eng);

utility.cpp → benchmark/utility.cpp

@@ -1,7 +1,12 @@
 #include <string>
 #include <iostream>
 #include <fstream>
+#include <cstring>
 
+// Utility function accepting data from cin stream and converting
+// text-based FLAG values into uint16_t words.
+// Intended use:
+// samtools view FILE | cut -f 2 | utility > DEST_FILE.bin
 int main(int argc, char** argv) {
     std::string str;
     while (std::getline(std::cin, str)) {