move bcftools to samtools

[samtools.git] / Makefile

diff --git a/Makefile b/Makefile
index 7d98b247a79341885d518bcad46d51b08e9cba57..8a7418e3bcfd961c31810fee6faf86713a6433d6 100644 (file)
--- a/Makefile
+++ b/Makefile
@@ -7,10 +7,10 @@ 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
 
@@ -25,7 +25,7 @@ all-recur lib-recur clean-recur cleanlocal-recur install-recur:
                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;
 
@@ -39,8 +39,8 @@ lib:libbam.a
 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