Modified handling of BamAlignmentSupportData. This fix should allow BamWriter::SaveA...

[bamtools.git] / Makefile

diff --git a/Makefile b/Makefile
index 280ab48895870ce8be5c399142673ceb4177413a..be28287303aa2d0694f389dc5801ac64903fc816 100644 (file)
--- a/Makefile
+++ b/Makefile
@@ -1,16 +1,33 @@
 CXX=           g++\r
-CXXFLAGS=      -Wall -O3\r
+CXXFLAGS=      -Wall -O3 -D_FILE_OFFSET_BITS=64\r
 PROG=          bamtools\r
-API=           BGZF.o BamReader.o BamWriter.o BamMultiReader.o
-UTILS=         bamtools_options.o bamtools_utilities.o
-TOOLKIT=       bamtools_count.o bamtools_coverage.o bamtools_header.o bamtools_index.o bamtools_merge.o bamtools_sam.o bamtools_sort.o bamtools_stats.o
+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_sam.o \
+               bamtools_sort.o \
+               bamtools_stats.o
 MAIN=          bamtools.o
+OBJS=          $(API) $(UTILS) $(TOOLKIT) $(MAIN)
 LIBS=          -lz
 \r
 all: $(PROG)\r
 \r
-bamtools: $(API) $(UTILS) $(TOOLKIT) $(MAIN)\r
-       $(CXX) $(CXXFLAGS) -o $@ $(API) $(UTILS) $(TOOLKIT) $(MAIN) $(LIBS)\r
+bamtools: $(OBJS)\r
+       $(CXX) $(CXXFLAGS) -o $@ $(OBJS) $(LIBS)
 \r
 clean:\r
        rm -fr gmon.out *.o *.a a.out *~\r