Added notes on how the package is tested.

[samtools.git] / Makefile

diff --git a/Makefile b/Makefile
index f3fb7a01365ee567c6bda338899c178c15230d73..35d578ffe50ded7ff4eb81caa084dbb245b17e5a 100644 (file)
--- a/Makefile
+++ b/Makefile
@@ -1,9 +1,10 @@
 CC=                    gcc
 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 \
-                       bam_pileup.o bam_lpileup.o bam_md.o glf.o razf.o faidx.o knetfile.o     \
-                       bam_sort.o sam_header.o
+                       bam_pileup.o bam_lpileup.o bam_md.o glf.o razf.o faidx.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
@@ -30,19 +31,22 @@ all-recur lib-recur clean-recur cleanlocal-recur install-recur:
 
 all:$(PROG)
 
+.PHONY:all lib clean cleanlocal
+.PHONY:all-recur lib-recur clean-recur cleanlocal-recur install-recur
+
 lib:libbam.a
 
 libbam.a:$(LOBJS)
                $(AR) -cru $@ $(LOBJS)
 
-samtools:lib $(AOBJS)
-               $(CC) $(CFLAGS) -o $@ $(AOBJS) -lm $(LIBPATH) $(LIBCURSES) -lz -L. -lbam
+samtools:$(AOBJS) libbam.a
+               $(CC) $(CFLAGS) -o $@ $(AOBJS) libbam.a -lm $(LIBPATH) $(LIBCURSES) -lz
 
-razip:razip.o razf.o knetfile.o
-               $(CC) $(CFLAGS) -o $@ razf.o razip.o knetfile.o -lz
+razip:razip.o razf.o $(KNETFILE_O)
+               $(CC) $(CFLAGS) -o $@ razf.o razip.o $(KNETFILE_O) -lz
 
-bgzip:bgzip.o bgzf.o
-               $(CC) $(CFLAGS) -o $@ bgzf.o bgzip.o -lz
+bgzip:bgzip.o bgzf.o $(KNETFILE_O)
+               $(CC) $(CFLAGS) -o $@ bgzf.o bgzip.o $(KNETFILE_O) -lz
 
 razip.o:razf.h
 bam.o:bam.h razf.h bam_endian.h kstring.h sam_header.h
@@ -62,7 +66,23 @@ sam_header.o:sam_header.h khash.h
 faidx.o:faidx.h razf.h khash.h
 faidx_main.o:faidx.h razf.h
 
+
+libbam.1.dylib-local:$(LOBJS)
+               libtool -dynamic $(LOBJS) -o libbam.1.dylib -lc -lz
+
+libbam.so.1-local:$(LOBJS)
+               $(CC) -shared -Wl,-soname,libbam.so -o libbam.so.1 $(LOBJS) -lc -lz
+
+dylib:
+               @$(MAKE) cleanlocal; \
+               case `uname` in \
+                       Linux) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" libbam.so.1-local;; \
+                       Darwin) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" libbam.1.dylib-local;; \
+                       *) echo 'Unknown OS';; \
+               esac
+
+
 cleanlocal:
-               rm -fr gmon.out *.o a.out *.dSYM razip $(PROG) *~ *.a
+               rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip $(PROG) *~ *.a *.so.* *.so *.dylib
 
 clean:cleanlocal-recur