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SHELL = /bin/sh
LEX = @LEX@ -I
YACC = @YACC@
YFLAGS = -d
CC = @CC@
MY_CFLAGS = @CFLAGS@ @extra_cflags@
LDFLAGS = @LDFLAGS@
LIBS = @LIBS@
CP = @CP@
MV = @MV@
RANLIB = @RANLIB@
AR = @AR@
CHMOD = @CHMOD@
COMPRESS = \"@COMPRESS@\"
prefix = @prefix@
exec_prefix = @exec_prefix@
bindir = @bindir@
INSTALL_PERM = 755
#MONITOR_SRC = loki_monitor.c count_dbr.c
#MONITOR_FLAGS = -DUSE_MONITOR
#DMALLOC_INC = @DMALLOC_INC@
#DMALLOC_LIB = @DMALLOC_LIB@
#DMALLOC_FLAGS = @DMALLOC_FLAGS@
INCLUDES = -I../include
CFLAGS += $(MY_CFLAGS) $(INCLUDES) $(DMALLOC_FLAGS) $(MONITOR_FLAGS)
ALL_LIBS = $(DMALLOC_LIB) -L. -L../libsrc -lloki -lgen $(LIBS)
LKLIB_SRC = param_parse.c param_lex.c read_binfiles.c loki_utils.c kinship.c \
genedrop.c mat_utils.c output_recomb.c seg_pen.c gen_pen.c loki_ibd.c \
get_founders.c pass_founder_genes.c
LOKI_SRC = loki.c loki_peel.c loki_init.c alloc_loki.c \
loki_sample.c loki_pen.c loki_tlmoves.c meiosis_scan.c \
loki_identity.c sample_rand.c sample_effects.c loki_setup.c \
loki_dump.c sample_cens.c handle_res.c print_data.c calc_var_locus.c \
loki_output.c sample_nu.c loki_complex_peel.c loki_npl.c \
loki_simple_sample.c loki_simple_peel.c loki_trait_simple_peel.c \
loki_trait_simple_sample.c get_par_probs.c read_solar_idfile.c \
peel_to_par.c update_segs.c $(MONITOR_SRC)
LKLIB_OBJ = ${LKLIB_SRC:.c=.o}
LOKI_OBJ = ${LOKI_SRC:.c=.o}
PROGS = loki
all: $(PROGS)
.y.c:
$(YACC) $(YFLAGS) $<
$(MV) $(MVFLAGS) y.tab.c $@
$(MV) $(MVFLAGS) y.tab.h ${@:.c=.h}
param_parse.h: param_parse.c
param_lex.o: param_lex.c
$(CC) -c $(CFLAGS) -DYY_NO_UNPUT $<
loki_ibd.o: loki_ibd.c
$(CC) -c $(CFLAGS) -DIBD_COMPRESS_PROG=$(COMPRESS) $<
libloki.a: $(LKLIB_OBJ) ../include/config.h
$(AR) cr $@ $(LKLIB_OBJ)
$(RANLIB) $@
loki: libloki.a $(LOKI_OBJ) ../libsrc/libgen.a ../include/config.h
$(CC) $(CFLAGS) -o $@ $(LOKI_OBJ) $(LDFLAGS) $(ALL_LIBS)
../bin:
mkdir ../bin
install: $(PROGS) ../bin
for file in $(PROGS); do \
$(CP) $$file $(bindir)/; \
$(CHMOD) $(INSTALL_PERM) $(bindir)/$$file ; \
done
clean:
rm -f *~ *.o *.a *.bak a.out core seedfile depend
distclean: clean
rm -f $(PROGS) Makefile
depend: $(LOKI_SRC) $(LKLIB_SRC) $(MONITOR_SRC)
@MAKEDEPEND@ $(INCLUDES) $(DMALLOC_FLAGS) $(LOKI_SRC) $(LKLIB_SRC) $(MONITOR_SRC)
touch depend
# DO NOT DELETE THIS LINE -- make depend depends on it.
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