* samtools-0.1.5-9 (r405)

[samtools.git] / Makefile

diff --git a/Makefile b/Makefile
index 77523d93a80f9f5fa0c984f1506f47e38cf413fa..40b35ae5440b5a0521c7296f6dd2b2f9e9b3ae92 100644 (file)
--- a/Makefile
+++ b/Makefile
@@ -1,16 +1,17 @@
 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=      
+DFLAGS=                -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=2
+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_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o     \
+                       bamtk.o
+PROG=          samtools
+INCLUDES=
 SUBDIRS=       . misc
+LIBPATH=
+LIBCURSES=     -lXCurses # -lXCurses
 
 .SUFFIXES:.c .o
 
@@ -23,7 +24,7 @@ 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)" $$target || exit 1; \
+                               INCLUDES="$(INCLUDES)" LIBPATH="$(LIBPATH)" $$target || exit 1; \
                        cd $$wdir; \
                done;
 
@@ -31,12 +32,11 @@ 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
+samtools:lib $(AOBJS)
+               $(CC) $(CFLAGS) -o $@ $(AOBJS) -lm $(LIBPATH) $(LIBCURSES) -lz -L. -lbam
 
 razip:razip.o razf.o
                $(CC) $(CFLAGS) -o $@ razf.o razip.o -lz