* Merge from branches/dev/

[samtools.git] / Makefile.lite

diff --git a/Makefile.lite b/Makefile.lite
new file mode 100644 (file)
index 0000000..2abb0ab
--- /dev/null
+++ b/Makefile.lite
@@ -0,0 +1,63 @@
+CC=                    gcc
+CXX=           g++
+CFLAGS=                -g -Wall -O2 -m64 #-arch ppc
+CXXFLAGS=      $(CFLAGS)
+DFLAGS=                -D_IOLIB=2 -D_FILE_OFFSET_BITS=64 -D_NO_CURSES -D_NO_RAZF
+OBJS=          bam.o bam_import.o bam_pileup.o bam_lpileup.o bam_sort.o bam_index.o \
+                       bgzf.o faidx.o bam_tview.o bam_maqcns.o bam_aux.o bam_plcmd.o \
+                       bam_mate.o bam_rmdup.o glf.o
+PROG=          samtools
+INCLUDES=      
+LIBS=          -lm -lz
+SUBDIRS=       .
+
+.SUFFIXES:.c .o
+
+.c.o:
+               $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
+
+all-recur lib-recur clean-recur cleanlocal-recur install-recur:
+               @target=`echo $@ | sed s/-recur//`; \
+               wdir=`pwd`; \
+               list='$(SUBDIRS)'; for subdir in $$list; do \
+                       cd $$subdir; \
+                       $(MAKE) -f Makefile.lite CC="$(CC)" CXX="$(CXX)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
+                               INCLUDES="$(INCLUDES)" $$target || exit 1; \
+                       cd $$wdir; \
+               done;
+
+all:$(PROG)
+
+lib:libbam.a
+
+libbam.a:$(OBJS)
+               $(AR) -cru $@ $(OBJS)
+
+samtools:lib bamtk.o
+               $(CC) $(CFLAGS) -o $@ bamtk.o $(LIBS) -L. -lbam
+
+razip:razip.o razf.o
+               $(CC) $(CFLAGS) -o $@ razf.o razip.o $(LIBS)
+
+bgzip:bgzip.o bgzf.o
+               $(CC) $(CFLAGS) -o $@ bgzf.o bgzip.o $(LIBS)
+
+razip.o:razf.h
+bam.o:bam.h razf.h bam_endian.h
+bam_import.o:bam.h kseq.h khash.h razf.h
+bam_pileup.o:bam.h razf.h ksort.h
+bam_plcmd.o:bam.h faidx.h bam_maqcns.h
+bam_index.o:bam.h khash.h ksort.h razf.h bam_endian.h
+bam_lpileup.o:bam.h ksort.h
+bam_tview.o:bam.h faidx.h bam_maqcns.h
+bam_maqcns.o:bam.h ksort.h bam_maqcns.h
+bam_sort.o:bam.h ksort.h razf.h
+razf.o:razf.h
+
+faidx.o:faidx.h razf.h khash.h
+faidx_main.o:faidx.h razf.h
+
+cleanlocal:
+               rm -fr gmon.out *.o a.out *.dSYM $(PROG) *~ *.a
+
+clean:cleanlocal-recur