change merger to use GetNextAlignmentCore

[bamtools.git] / Makefile

diff --git a/Makefile b/Makefile
index a61b64bcabd286df25f604e61c6b98189ab4cec8..ee9be979bc288de3d54a3f6571543ef833bcd51c 100644 (file)
--- a/Makefile
+++ b/Makefile
@@ -1,35 +1,17 @@
-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\r
+PROG=          bamtools\r
+API=           BGZF.o BamReader.o BamWriter.o BamMultiReader.o
+UTILS=         bamtools_options.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_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
+\r
+clean:\r
+       rm -fr gmon.out *.o *.a a.out *~\r