-CC= gcc
-CXX= g++
-CFLAGS= -Wall -O3
-CXXFLAGS= $(CFLAGS)
-DFLAGS= -D_IOLIB=2 #-D_NDEBUG
-OBJS= BamReader.o bgzf.o
-PROG= BamReaderTest
-INCLUDES=
-ARFLAGS= -crs
+CXX= g++\r
+CXXFLAGS= -Wall -O3 -D_FILE_OFFSET_BITS=64\r
+PROG= bamtools\r
+API= BGZF.o \
+ BamIndex.o \
+ BamReader.o \
+ BamWriter.o \
+ BamMultiReader.o
+UTILS= bamtools_fasta.o \
+ bamtools_options.o \
+ bamtools_pileup.o \
+ bamtools_utilities.o
+TOOLKIT= bamtools_convert.o \
+ bamtools_count.o \
+ bamtools_coverage.o \
+ bamtools_filter.o \
+ bamtools_header.o \
+ bamtools_index.o \
+ bamtools_merge.o \
+ bamtools_random.o \
+ bamtools_sam.o \
+ bamtools_sort.o \
+ bamtools_stats.o
+MAIN= bamtools.o
+OBJS= $(API) $(UTILS) $(TOOLKIT) $(MAIN)
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) BamConversion *~
+\r
+all: $(PROG)\r
+\r
+bamtools: $(OBJS)\r
+ $(CXX) $(CXXFLAGS) -o $@ $(OBJS) $(LIBS)
+\r
+clean:\r
+ rm -fr gmon.out *.o *.a a.out *~\r