* no changes to samtools itself

[samtools.git] / Makefile

diff --git a/Makefile b/Makefile
index 6b60a7b5ab4efaf326bcc8c8e7d5064790d3c8b8..77523d93a80f9f5fa0c984f1506f47e38cf413fa 100644 (file)
--- 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
+### 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
-PROG=          razip bgzip samtools
+                       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=      
-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;
 
@@ -33,17 +34,19 @@ 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
+               $(CC) $(CFLAGS) -o $@ bamtk.o -lm -L. -lbam -lcurses -lz
 
 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