for json output in bamtools convert

[bamtools.git] / Makefile

diff --git a/Makefile b/Makefile
index 8862226d50cf01812083549ca1d71f41dc29cde0..b3d285b6027df0d7155075cab97200d53787c7f6 100644 (file)
--- a/Makefile
+++ b/Makefile
@@ -1,39 +1,33 @@
-CC=            gcc\r
 CXX=           g++\r
-CFLAGS=                -Wall -O3\r
-CXXFLAGS=      $(CFLAGS)\r
-DFLAGS=                -D_IOLIB=2 #-D_NDEBUG\r
-OBJS=          BamReader.o bgzf.o\r
-PROG=          BamReaderTest\r
-INCLUDES=       \r
-ARFLAGS=       -crs\r
-LIBS=          -lz\r
-SUBDIRS=       .\r
-\r
-.SUFFIXES:.c .cpp .o\r
-\r
-.c.o:\r
-               $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@\r
-\r
-.cpp.o:\r
-               $(CXX) -c $(CXXFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@\r
-\r
-all: $(PROG) BamConversion\r
-\r
-lib:libbambc.a\r
-\r
-libbambc.a:$(OBJS)\r
-               $(AR) $(ARFLAGS) $@ $(OBJS)\r
-\r
-BamReaderTest:lib BamReaderMain.o\r
-               $(CXX) $(CXXFLAGS) -o $@ BamReaderMain.o $(LIBS) -L. -lbambc\r
-\r
-BamConversion: lib BamWriter.o BamConversionMain.o\r
-       $(CXX) $(CXXFLAGS) -o $@ BamWriter.o BamConversionMain.o $(LIBS) -L. -lbambc\r
-\r
-BamMerge: lib BamMerge.o\r
-               $(CXX) $(CXXFLAGS) -o $@ BamWriter.o BamMerge.o $(LIBS) -L. -lbambc\r
-\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_sort.o \
+               bamtools_stats.o
+MAIN=          bamtools.o
+OBJS=          $(API) $(UTILS) $(TOOLKIT) $(MAIN)
+LIBS=          -lz
+\r
+all: $(PROG)\r
+\r
+bamtools: $(OBJS)\r
+       $(CXX) $(CXXFLAGS) -o $@ $(OBJS) $(LIBS)
 \r
 clean:\r
-               rm -fr gmon.out *.o *.a a.out $(PROG) BamConversion *~\r
+       rm -fr gmon.out *.o *.a a.out *~\r