CC= gcc
-CFLAGS= -g -Wall #-O2 #-m64 #-arch ppc
+CFLAGS= -g -Wall -O2 #-m64 #-arch ppc
DFLAGS= -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1
KNETFILE_O= knetfile.o
LOBJS= bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o \
$(KNETFILE_O) bam_sort.o sam_header.o bam_reheader.o
AOBJS= bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o \
bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o \
- bamtk.o kaln.o bam_mcns.o bam2bcf.o bcf.o
+ bamtk.o kaln.o bam_mcns.o bam2bcf.o
PROG= samtools
-INCLUDES=
-SUBDIRS= . misc
+INCLUDES= -Ibcftools
+SUBDIRS= . bcftools misc
LIBPATH=
LIBCURSES= -lcurses # -lXCurses
list='$(SUBDIRS)'; for subdir in $$list; do \
cd $$subdir; \
$(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
- INCLUDES="$(INCLUDES)" LIBPATH="$(LIBPATH)" $$target || exit 1; \
+ LIBPATH="$(LIBPATH)" $$target || exit 1; \
cd $$wdir; \
done;
libbam.a:$(LOBJS)
$(AR) -cru $@ $(LOBJS)
-samtools:$(AOBJS) libbam.a
- $(CC) $(CFLAGS) -o $@ $(AOBJS) libbam.a -lm $(LIBPATH) $(LIBCURSES) -lz
+samtools:lib-recur $(AOBJS)
+ $(CC) $(CFLAGS) -o $@ $(AOBJS) libbam.a -lm $(LIBPATH) $(LIBCURSES) -lz -Lbcftools -lbcf
razip:razip.o razf.o $(KNETFILE_O)
$(CC) $(CFLAGS) -o $@ razf.o razip.o $(KNETFILE_O) -lz