X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=Makefile;h=db183330d1fb76ce4fa0d17d8dab65afdfbeb65a;hp=7bb44694e0ab26f8266bdadddb25075159b8b365;hb=e582623cf8c4778c7dc792318635821d3c494b0d;hpb=b27e00385f41769d03a8cca4dbd71275fc9fa906

diff --git a/Makefile b/Makefile
index 7bb4469..db18333 100644
--- a/Makefile
+++ b/Makefile
@@ -1,18 +1,19 @@
 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_LARGEFILE64_SOURCE -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
-AOBJS=		bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o	\
+			bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o \
+			$(KNETFILE_O) bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
+AOBJS=		bam_tview.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 bam2bcf.o bam2bcf_indel.o errmod.o sample.o \
+			cut_target.o phase.o bam2depth.o
 PROG=		samtools
-INCLUDES=	
-SUBDIRS=	. misc
-LIBPATH=	
+INCLUDES=	-I.
+SUBDIRS=	. bcftools misc
+LIBPATH=
+LIBCURSES=	-lcurses # -lXCurses
 
 .SUFFIXES:.c .o
 
@@ -31,39 +32,62 @@ 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)
+		$(AR) -csru $@ $(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:lib-recur $(AOBJS)
+		$(CC) $(CFLAGS) -o $@ $(AOBJS) -Lbcftools $(LIBPATH) libbam.a -lbcf $(LIBCURSES) -lm -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
-bam_plcmd.o:bam.h faidx.h bam_maqcns.h glf.h
+bam_plcmd.o:bam.h faidx.h bcftools/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
-bam_maqcns.o:bam.h ksort.h bam_maqcns.h
+bam_tview.o:bam.h faidx.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:bcftools/bcf.h
+bam2bcf.o:bam2bcf.h errmod.h bcftools/bcf.h
+bam2bcf_indel.o:bam2bcf.h
+errmod.o:errmod.h
+phase.o:bam.h khash.h ksort.h
+bamtk.o:bam.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