* added zlib-1.2.3 as razip requires that

[samtools.git] / Makefile

diff --git a/Makefile b/Makefile
index 69ed702331f825cd17c6f8530de2a232d1abcf26..6bf4227753c1e29844701fa897d631fa6f3b39d8 100644 (file)
--- a/Makefile
+++ b/Makefile
@@ -1,11 +1,12 @@
 CC=                    gcc
 CXX=           g++
-CFLAGS=                -g -Wall -O2 -m64 #-arch ppc
+CFLAGS=                -g -Wall #-O2 -m64 #-arch ppc
 CXXFLAGS=      $(CFLAGS)
-DFLAGS=                -D_IOLIB=2 -D_FILE_OFFSET_BITS=64 #-D_NO_RAZF #-D_NO_CURSES
+DFLAGS=                -D_IOLIB=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 #-D_NO_RAZF #-D_NO_CURSES
 OBJS=          bam.o bam_import.o bam_pileup.o bam_lpileup.o bam_sort.o bam_index.o \
                        razf.o bgzf.o faidx.o bam_tview.o bam_maqcns.o bam_aux.o bam_plcmd.o \
-                       bam_mate.o bam_rmdup.o glf.o bam_stat.o
+                       bam_mate.o bam_rmdup.o glf.o bam_stat.o kstring.o bam_md.o sam.o sam_view.o \
+                       bam_rmdupse.o
 PROG=          razip bgzip samtools
 INCLUDES=      
 LIBS=          -lm -lz
@@ -21,8 +22,8 @@ all-recur lib-recur clean-recur cleanlocal-recur install-recur:
                wdir=`pwd`; \
                list='$(SUBDIRS)'; for subdir in $$list; do \
                        cd $$subdir; \
-                       $(MAKE) CC="$(CC)" CXX="$(CXX)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
-                               INCLUDES="$(INCLUDES)" $$target || exit 1; \
+                       $(MAKE) -f Makefile.generic CC="$(CC)" CXX="$(CXX)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
+                               INCLUDES="$(INCLUDES)" LIBS="$(LIBS)" $$target || exit 1; \
                        cd $$wdir; \
                done;
 
@@ -43,16 +44,19 @@ bgzip:bgzip.o bgzf.o
                $(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
+bam_plcmd.o:bam.h faidx.h bam_maqcns.h glf.h
 bam_index.o:bam.h khash.h ksort.h razf.h bam_endian.h
 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
+bam_md.o:bam.h faidx.h
 razf.o:razf.h
+glf.o:glf.h
 
 faidx.o:faidx.h razf.h khash.h
 faidx_main.o:faidx.h razf.h