X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=Makefile;h=9bf6d80cd8f32070a18a181f7507acb0066c37e3;hb=1a23a35867ee992dcffcf3d17df2b7d41732f33b;hp=d4a4101db733bf09dee97f237c74d3742b67d72c;hpb=42e756837f7acb91bfd1134ef16d423e71c913d7;p=samtools.git

diff --git a/Makefile b/Makefile
index d4a4101..9bf6d80 100644
--- a/Makefile
+++ b/Makefile
@@ -1,14 +1,15 @@
 CC=			gcc
 CXX=		g++
-CFLAGS=		-g -Wall -O2 -m64 #-arch ppc
+CFLAGS=		-g -Wall -O2 #-m64 #-arch ppc
 CXXFLAGS=	$(CFLAGS)
-DFLAGS=		-D_IOLIB=2 -D_FILE_OFFSET_BITS=64 #-D_NO_RAZF #-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
-PROG=		razip bgzip samtools
+DFLAGS=		-D_FILE_OFFSET_BITS=64 #-D_NO_CURSES
+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
+AOBJS=		bam_sort.o 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
+PROG=		samtools bgzip
 INCLUDES=	
-LIBS=		-lm -lz
 SUBDIRS=	. misc
 
 .SUFFIXES:.c .o
@@ -21,8 +22,8 @@ all-recur lib-recur clean-recur cleanlocal-recur install-recur:
 		wdir=`pwd`; \
 		list='$(SUBDIRS)'; for subdir in $$list; do \
 			cd $$subdir; \
-			$(MAKE) CC="$(CC)" CXX="$(CXX)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
-				INCLUDES="$(INCLUDES)" LIBS="$(LIBS)" $$target || exit 1; \
+			$(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
+				INCLUDES="$(INCLUDES)" $$target || exit 1; \
 			cd $$wdir; \
 		done;
 
@@ -30,20 +31,22 @@ all:$(PROG)
 
 lib:libbam.a
 
-libbam.a:$(OBJS)
-		$(AR) -cru $@ $(OBJS)
+libbam.a:$(LOBJS)
+		$(AR) -cru $@ $(LOBJS)
 
-samtools:lib bamtk.o
-		$(CC) $(CFLAGS) -o $@ bamtk.o $(LIBS) -L. -lbam -lcurses
+### For the curses library: comment out `-lcurses' if you do not have curses installed
+samtools:lib $(AOBJS)
+		$(CC) $(CFLAGS) -o $@ $(AOBJS) -lm -lcurses -lz -L. -lbam
 
 razip:razip.o razf.o
-		$(CC) $(CFLAGS) -o $@ razf.o razip.o $(LIBS)
+		$(CC) $(CFLAGS) -o $@ razf.o razip.o -lz
 
 bgzip:bgzip.o bgzf.o
-		$(CC) $(CFLAGS) -o $@ bgzf.o bgzip.o $(LIBS)
+		$(CC) $(CFLAGS) -o $@ bgzf.o bgzip.o -lz
 
 razip.o:razf.h
-bam.o:bam.h razf.h bam_endian.h
+bam.o:bam.h razf.h bam_endian.h kstring.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
@@ -52,13 +55,13 @@ 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_sort.o:bam.h ksort.h razf.h
-razf.o:razf.h
+bam_md.o:bam.h faidx.h
 glf.o:glf.h
 
 faidx.o:faidx.h razf.h khash.h
 faidx_main.o:faidx.h razf.h
 
 cleanlocal:
-		rm -fr gmon.out *.o a.out *.dSYM $(PROG) *~ *.a
+		rm -fr gmon.out *.o a.out *.dSYM razip $(PROG) *~ *.a
 
 clean:cleanlocal-recur