* update Makefile

[samtools.git] / Makefile

diff --git a/Makefile b/Makefile
index 6bf4227753c1e29844701fa897d631fa6f3b39d8..86612c1b524b7185d9714b839067875b8bc85aa7 100644 (file)
--- a/Makefile
+++ b/Makefile
@@ -1,16 +1,17 @@
 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_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 #-D_NO_RAZF #-D_NO_CURSES
+### 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=          razip bgzip samtools
-INCLUDES=      
-LIBS=          -lm -lz
-SUBDIRS=       . misc
+INCLUDES=      -Izlib
+LIBS=          -lm -Lzlib -lz
+SUBDIRS=       zlib . misc
 
 .SUFFIXES:.c .o
 
@@ -22,7 +23,7 @@ all-recur lib-recur clean-recur cleanlocal-recur install-recur:
                wdir=`pwd`; \
                list='$(SUBDIRS)'; for subdir in $$list; do \
                        cd $$subdir; \
-                       $(MAKE) -f Makefile.generic CC="$(CC)" CXX="$(CXX)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
+                       $(MAKE) -f Makefile CC="$(CC)" CXX="$(CXX)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
                                INCLUDES="$(INCLUDES)" LIBS="$(LIBS)" $$target || exit 1; \
                        cd $$wdir; \
                done;
@@ -34,6 +35,7 @@ lib:libbam.a
 libbam.a:$(OBJS)
                $(AR) -cru $@ $(OBJS)
 
+### For ncurses: comment out `-lcurses' if you do not have ncurses installed
 samtools:lib bamtk.o
                $(CC) $(CFLAGS) -o $@ bamtk.o $(LIBS) -L. -lbam -lcurses