preliminary

Makefile

@@ -9,6 +9,7 @@ SHELL := /bin/bash -e
 export OBJ_DIR	= obj
 export BIN_DIR	= bin
 export SRC_DIR	= src
+export UTIL_DIR	= src/utils
 export CXX		= g++
 export CXXFLAGS = -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC
 export LIBS		= -lz
@@ -59,6 +60,8 @@ UTIL_SUBDIRS =	$(SRC_DIR)/utils/lineFileUtilities \
 				$(SRC_DIR)/utils/Fasta \
 				$(SRC_DIR)/utils/genomeFile
 
+BUILT_OBJECTS = $(OBJ_DIR)/*.o
+
 all:
 	[ -d $(OBJ_DIR) ] || mkdir -p $(OBJ_DIR)
 	[ -d $(BIN_DIR) ] || mkdir -p $(BIN_DIR)
@@ -78,7 +81,8 @@ all:
 		echo ""; \
 	done
 
-	echo "- Building main bedtools binary."
+	@echo "- Building main bedtools binary."
+	@$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/bedtools $(BUILT_OBJECTS) -L$(UTIL_DIR)/BamTools/lib/ -lbamtools $(LIBS)
 	
 
 .PHONY: all

src/intersectBed/intersectMain.cpp

@@ -22,9 +22,9 @@ using namespace std;
 #define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen))== 0) && (actualLen == paramLen)
 
 // function declarations
-void ShowHelp(void);
+void intersect_help(void);
 
-int main(int argc, char* argv[]) {
+int intersect_main(int argc, char* argv[]) {
 
     // our configuration variables
     bool showHelp = false;
@@ -68,7 +68,7 @@ int main(int argc, char* argv[]) {
         }
     }
 
-    if(showHelp) ShowHelp();
+    if(showHelp) intersect_help();
 
     // do some parsing (all of these parameters require 2 strings)
     for(int i = 1; i < argc; i++) {
@@ -223,11 +223,11 @@ int main(int argc, char* argv[]) {
         return 0;
     }
     else {
-        ShowHelp();
+        intersect_help();
     }
 }
 
-void ShowHelp(void) {
+void intersect_help(void) {
 
     cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl;