Reorganization of toolkit. Split subtools out to own headers. Added custom getopt...

[bamtools.git] / Makefile

diff --git a/Makefile b/Makefile
index 41ba8204439f25ede6492ac72f7a9eb7822e99d6..d3d8ad287ae2df95d1bd0cbee54122ca92771513 100644 (file)
--- a/Makefile
+++ b/Makefile
@@ -1,35 +1,13 @@
-CC=            gcc
-CXX=           g++
-CFLAGS=                -Wall -pg -O3 -m64
-CXXFLAGS=      $(CFLAGS)
-DFLAGS=                -D_IOLIB=2 #-D_NDEBUG
-OBJS=          BamReader.o bgzf.o
-PROG=          BamReaderTest
-INCLUDES=       
-ARFLAGS=       -crs
-LIBS=          -lz
-SUBDIRS=       .
-
-.SUFFIXES:.c .cpp .o
-
-.c.o:
-               $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
-
-.cpp.o:
-               $(CXX) -c $(CXXFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
-
-all: $(PROG) BamConversion
-
-lib:libbambc.a
-
-libbambc.a:$(OBJS)
-               $(AR) $(ARFLAGS) $@ $(OBJS)
-
-BamReaderTest:lib BamReaderMain.o
-               $(CXX) $(CXXFLAGS) -o $@ BamReaderMain.o $(LIBS) -L. -lbambc
-
-BamConversion: lib BamWriter.o BamConversionMain.o
-       $(CXX) $(CXXFLAGS) -o $@ BamWriter.o BamConversionMain.o $(LIBS) -L. -lbambc
-
-clean:
-               rm -fr gmon.out *.o *.a a.out $(PROG) *~
+CXX=           g++\r
+CXXFLAGS=      -Wall -O3\r
+PROG=          bamtools bamtools_test\r
+LIBS=          -lz\r
+OBJS=          BGZF.o BamReader.o BamWriter.o BamMultiReader.o bamtools.o
+\r
+all: $(PROG)\r
+\r
+bamtools: $(OBJS)\r
+       $(CXX) $(CXXFLAGS) -o $@ $(OBJS) $(LIBS)\r
+\r
+clean:\r
+       rm -fr gmon.out *.o *.a a.out *~\r