CC= gcc
CXX= g++
-CFLAGS= -g -Wall -O2 -m64 #-arch ppc
+CFLAGS= -g -Wall -O2 #-m64 #-arch ppc
CXXFLAGS= $(CFLAGS)
-DFLAGS= -D_IOLIB=2 -D_FILE_OFFSET_BITS=64 #-D_NO_RAZF #-D_NO_CURSES
+### For ncurses: please apply `-D_NO_CURSES' if you do not have ncurses installed
+DFLAGS= -D_IOLIB=2 -D_FILE_OFFSET_BITS=64 #-D_NO_CURSES
OBJS= bam.o bam_import.o bam_pileup.o bam_lpileup.o bam_sort.o bam_index.o \
razf.o bgzf.o faidx.o bam_tview.o bam_maqcns.o bam_aux.o bam_plcmd.o \
- bam_mate.o bam_rmdup.o glf.o bam_stat.o kstring.o
+ bam_mate.o bam_rmdup.o glf.o bam_stat.o kstring.o bam_md.o sam.o sam_view.o \
+ bam_rmdupse.o
PROG= razip bgzip samtools
-INCLUDES=
-LIBS= -lm -lz
-SUBDIRS= . misc
+INCLUDES= -Izlib
+LIBS= -lm -Lzlib -lz
+SUBDIRS= zlib . misc
.SUFFIXES:.c .o
wdir=`pwd`; \
list='$(SUBDIRS)'; for subdir in $$list; do \
cd $$subdir; \
- $(MAKE) CC="$(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;
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
$(CC) $(CFLAGS) -o $@ bgzf.o bgzip.o $(LIBS)
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
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
+bam_md.o:bam.h faidx.h
razf.o:razf.h
glf.o:glf.h