for json output in bamtools convert

[bamtools.git] / Makefile

diff --git a/Makefile b/Makefile
index 7abd53b5d31e9c8f14472924b8717f3ea4c710b4..b3d285b6027df0d7155075cab97200d53787c7f6 100644 (file)
--- a/Makefile
+++ b/Makefile
@@ -1,21 +1,33 @@
 CXX=           g++\r
-CXXFLAGS=      -Wall -O3\r
-PROG=          BamConversion BamDump BamTrim BamMultiMerge\r
-LIBS=          -lz\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
-BamConversion:  BGZF.o BamReader.o BamWriter.o BamConversionMain.o\r
-       $(CXX) $(CXXFLAGS) -o $@  BGZF.o BamReader.o BamWriter.o BamConversionMain.o $(LIBS)\r
-\r
-BamDump:  BGZF.o BamReader.o BamDumpMain.o\r
-       $(CXX) $(CXXFLAGS) -o $@  BGZF.o BamReader.o BamDumpMain.o $(LIBS)\r
-\r
-BamTrim:  BGZF.o BamReader.o BamWriter.o BamTrimMain.o\r
-       $(CXX) $(CXXFLAGS) -o $@  BGZF.o BamReader.o BamWriter.o BamTrimMain.o $(LIBS)\r
-\r
-BamMultiMerge: BGZF.o BamMultiReader.o BamReader.o BamWriter.o BamMultiMergeMain.o\r
-       $(CXX) $(CXXFLAGS) -o $@ BGZF.o BamMultiReader.o BamReader.o BamWriter.o BamMultiMergeMain.o $(LIBS)\r
+bamtools: $(OBJS)\r
+       $(CXX) $(CXXFLAGS) -o $@ $(OBJS) $(LIBS)
 \r
 clean:\r
        rm -fr gmon.out *.o *.a a.out *~\r