Updated atomic Makefiles to include "-Wall". Updated master Makefile to include closestBed

Makefile

@@ -19,7 +19,7 @@ export CXX ?= g++
 #include includes/$(BLD_PLATFORM).inc
 
 # define our source subdirectories
-SUBDIRS = $(SRC_DIR)/complementBed $(SRC_DIR)/coverageBed $(SRC_DIR)/intersectBed $(SRC_DIR)/mergeBed $(SRC_DIR)/genomeCoverageBed $(SRC_DIR)/fastaFromBed $(SRC_DIR)/sortBed $(SRC_DIR)/windowBed
+SUBDIRS = $(SRC_DIR)/closestBed $(SRC_DIR)/complementBed $(SRC_DIR)/coverageBed $(SRC_DIR)/intersectBed $(SRC_DIR)/mergeBed $(SRC_DIR)/genomeCoverageBed $(SRC_DIR)/fastaFromBed $(SRC_DIR)/sortBed $(SRC_DIR)/windowBed
 
 UTIL_SUBDIRS = $(SRC_DIR)/utils/bedFile $(SRC_DIR)/utils/sequenceUtilities
 all:

src/closestBed/Makefile

 CXX = g++
-CXXFLAGS = -O3
+CXXFLAGS = -O3 -Wall
 LDFLAGS = 
 
 UTILITIES_DIR = ../utils/

src/complementBed/Makefile

 CXX = g++
-CXXFLAGS = -O3
+CXXFLAGS = -O3  -Wall
 LDFLAGS = 
 LIBFLAGS = -lc
 

src/coverageBed/Makefile

 CXX = g++
-CXXFLAGS = -O3
-LDFLAGS = 
+CXXFLAGS = -O3  -Wall
+LDFLAGS =
 
 UTILITIES_DIR = ../utils/
 OBJ_DIR = ../../obj/

src/fastaFromBed/Makefile

 CXX = g++
-CXXFLAGS = -O3
+CXXFLAGS = -O3  -Wall
 LDFLAGS = 
 
 UTILITIES_DIR = ../utils/

src/genomeCoverageBed/Makefile

 CXX = g++
-CXXFLAGS = -O3
+CXXFLAGS = -O3  -Wall
 LDFLAGS =  
 
 UTILITIES_DIR = ../utils/

src/intersectBed/Makefile

 CXX = g++
-CXXFLAGS = -O3
+CXXFLAGS = -O3  -Wall
 LDFLAGS = 
 
 UTILITIES_DIR = ../utils/

src/mergeBed/Makefile

 CXX = g++
-CXXFLAGS = -O3
+CXXFLAGS = -O3  -Wall
 LDFLAGS = 
 
 UTILITIES_DIR = ../utils/

src/sortBed/Makefile

 CXX = g++
-CXXFLAGS = -O3
+CXXFLAGS = -O3  -Wall
 LDFLAGS = 
 
 UTILITIES_DIR = ../utils/

src/utils/bedFile/Makefile

 CXX = g++ -c
-CXXFLAGS = -O3
+CXXFLAGS = -O3  -Wall
 LDFLAGS = 
 OBJS = ../../../obj/
 

src/utils/sequenceUtilities/Makefile

 CXX = g++ -c
-CXXFLAGS = -O3
+CXXFLAGS = -O3  -Wall
 LDFLAGS = 
 OBJS = ../../../obj/
 

src/windowBed/Makefile

 CXX = g++
-CXXFLAGS = -O3
+CXXFLAGS = -O3  -Wall
 LDFLAGS = 
 
 UTILITIES_DIR = ../utils/