X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=Makefile;h=8a7418e3bcfd961c31810fee6faf86713a6433d6;hb=fd187467e3c5f026a4d934c5b0cb68a42939f6e1;hp=77523d93a80f9f5fa0c984f1506f47e38cf413fa;hpb=13f55c1789c59ae9a376ffa817e112b24be30069;p=samtools.git

diff --git a/Makefile b/Makefile
index 77523d9..8a7418e 100644
--- a/Makefile
+++ b/Makefile
@@ -1,16 +1,18 @@
 CC=			gcc
-CXX=		g++
 CFLAGS=		-g -Wall -O2 #-m64 #-arch ppc
-CXXFLAGS=	$(CFLAGS)
-### For ncurses: please apply `-D_NO_CURSES' if you do not have ncurses installed
-DFLAGS=		-D_IOLIB=2 -D_FILE_OFFSET_BITS=64 #-D_NO_CURSES
-OBJS=		bam.o bam_import.o bam_pileup.o bam_lpileup.o bam_sort.o bam_index.o \
-			razf.o bgzf.o faidx.o bam_tview.o bam_maqcns.o bam_aux.o bam_plcmd.o \
-			bam_mate.o bam_rmdup.o glf.o bam_stat.o kstring.o bam_md.o sam.o sam_view.o \
-			bam_rmdupse.o
-PROG=		bgzip samtools
-INCLUDES=	
-SUBDIRS=	. misc
+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_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
+PROG=		samtools
+INCLUDES=	-Ibcftools
+SUBDIRS=	. bcftools misc
+LIBPATH=
+LIBCURSES=	-lcurses # -lXCurses
 
 .SUFFIXES:.c .o
 
@@ -23,33 +25,35 @@ 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)" $$target || exit 1; \
+				LIBPATH="$(LIBPATH)" $$target || exit 1; \
 			cd $$wdir; \
 		done;
 
 all:$(PROG)
 
+.PHONY:all lib clean cleanlocal
+.PHONY:all-recur lib-recur clean-recur cleanlocal-recur install-recur
+
 lib:libbam.a
 
-libbam.a:$(OBJS)
-		$(AR) -cru $@ $(OBJS)
+libbam.a:$(LOBJS)
+		$(AR) -cru $@ $(LOBJS)
 
-### For ncurses: comment out `-lcurses' if you do not have ncurses installed
-samtools:lib bamtk.o
-		$(CC) $(CFLAGS) -o $@ bamtk.o -lm -L. -lbam -lcurses -lz
+samtools:lib-recur $(AOBJS)
+		$(CC) $(CFLAGS) -o $@ $(AOBJS) libbam.a -lm $(LIBPATH) $(LIBCURSES) -lz -Lbcftools -lbcf
 
-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
-bam_plcmd.o:bam.h faidx.h bam_maqcns.h glf.h
+bam_plcmd.o:bam.h faidx.h bam_maqcns.h glf.h bam_mcns.h bcf.h bam2bcf.h
 bam_index.o:bam.h khash.h ksort.h razf.h bam_endian.h
 bam_lpileup.o:bam.h ksort.h
 bam_tview.o:bam.h faidx.h bam_maqcns.h
@@ -57,11 +61,30 @@ 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
+bcf.o:bcf.h
+bam2bcf.o:bam2bcf.h bcf.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