X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=Makefile;h=0a2791e8810435f244e310ec8e64aaa46331269a;hb=3ddb3942053df00fdae714e77cbc2f5618db617e;hp=77523d93a80f9f5fa0c984f1506f47e38cf413fa;hpb=13f55c1789c59ae9a376ffa817e112b24be30069;p=samtools.git

diff --git a/Makefile b/Makefile
index 77523d9..0a2791e 100644
--- a/Makefile
+++ b/Makefile
@@ -2,13 +2,13 @@ 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
+DFLAGS=		-D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE #-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 knetfile.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
 INCLUDES=	
 SUBDIRS=	. misc
 
@@ -31,12 +31,12 @@ all:$(PROG)
 
 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
+### 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 -lz