X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=Makefile;h=35d578ffe50ded7ff4eb81caa084dbb245b17e5a;hp=7bb44694e0ab26f8266bdadddb25075159b8b365;hb=049705238f6c2d4cdd79022e7bcf2cc7d83ba9c7;hpb=b27e00385f41769d03a8cca4dbd71275fc9fa906

diff --git a/Makefile b/Makefile
index 7bb4469..35d578f 100644
--- a/Makefile
+++ b/Makefile
@@ -1,18 +1,18 @@
 CC=			gcc
-CXX=		g++
 CFLAGS=		-g -Wall -O2 #-m64 #-arch ppc
-CXXFLAGS=	$(CFLAGS)
-DFLAGS=		-D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE #-D_NO_CURSES
+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
+			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
+			bamtk.o kaln.o
 PROG=		samtools
-INCLUDES=	
+INCLUDES=
 SUBDIRS=	. misc
-LIBPATH=	
+LIBPATH=
+LIBCURSES=	-lcurses # -lXCurses
 
 .SUFFIXES:.c .o
 
@@ -31,23 +31,25 @@ 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)
 
-### For the curses library: comment out `-lcurses' if you do not have curses installed
-samtools:lib $(AOBJS)
-		$(CC) $(CFLAGS) -o $@ $(AOBJS) $(LIBPATH) -lm -lcurses -lz -L. -lbam
+samtools:$(AOBJS) libbam.a
+		$(CC) $(CFLAGS) -o $@ $(AOBJS) libbam.a -lm $(LIBPATH) $(LIBCURSES) -lz
 
-razip:razip.o razf.o
-		$(CC) $(CFLAGS) -o $@ razf.o razip.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
+bam.o:bam.h razf.h bam_endian.h kstring.h sam_header.h
 sam.o:sam.h bam.h
 bam_import.o:bam.h kseq.h khash.h razf.h
 bam_pileup.o:bam.h razf.h ksort.h
@@ -59,11 +61,28 @@ bam_maqcns.o:bam.h ksort.h bam_maqcns.h
 bam_sort.o:bam.h ksort.h razf.h
 bam_md.o:bam.h faidx.h
 glf.o:glf.h
+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