misc/Makefile, on behalf of ghuls: changed the order of bamcheck rules with -lz last

[samtools.git] / misc / Makefile

diff --git a/misc/Makefile b/misc/Makefile
index 792cbbbeb67e335ba65f4f93b920a31b4133f632..d36e7acb4a4c68956f3fed6dbcc16d9c042dc729 100644 (file)
--- a/misc/Makefile
+++ b/misc/Makefile
@@ -1,12 +1,11 @@
 CC=                    gcc
 CXX=           g++
-CFLAGS=                -g -Wall -O2 -m64 #-arch ppc
+CFLAGS=                -g -Wall -O2 #-m64 #-arch ppc
 CXXFLAGS=      $(CFLAGS)
-DFLAGS=                #-D_FILE_OFFSET_BITS=64
+DFLAGS=                -D_FILE_OFFSET_BITS=64
 OBJS=          
-PROG=          faidx md5sum-lite md5fa maq2sam-short maq2sam-long wgsim fa2csfa
+PROG=          md5sum-lite md5fa maq2sam-short maq2sam-long ace2sam wgsim bamcheck
 INCLUDES=      -I..
-LIBS=          -lm -lz
 SUBDIRS=       .
 
 .SUFFIXES:.c .o
@@ -21,21 +20,24 @@ lib-recur all-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)" \
+                       $(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
                                INCLUDES="$(INCLUDES)" $$target || exit 1; \
                        cd $$wdir; \
                done;
 
 lib:
 
-wgsim:wgsim.o
-               $(CC) $(CFLAGS) -o $@ wgsim.o -lm
+bamcheck:bamcheck.o
+               $(CC) $(CFLAGS) -o $@ bamcheck.o -L.. -lm -lbam -lpthread -lz
+
+bamcheck.o:bamcheck.c ../faidx.h ../khash.h ../sam.h ../razf.h
+               $(CC) $(CFLAGS) -c -I.. -o $@ bamcheck.c
 
-faidx:../faidx.c ../faidx.h
-               $(CC) $(CFLAGS) -D_NO_RAZF -DFAIDX_MAIN -o $@ ../faidx.c
+ace2sam:ace2sam.o
+               $(CC) $(CFLAGS) -o $@ ace2sam.o -lz
 
-fa2csfa:fa2csfa.o
-               $(CC) $(CFLAGS) -o $@ fa2csfa.o -lz
+wgsim:wgsim.o
+               $(CC) $(CFLAGS) -o $@ wgsim.o -lm -lz
 
 md5fa:md5.o md5fa.o md5.h ../kseq.h
                $(CC) $(CFLAGS) -o $@ md5.o md5fa.o -lz
@@ -46,8 +48,6 @@ md5sum-lite:md5sum-lite.o
 md5sum-lite.o:md5.c md5.h
                $(CC) -c $(CFLAGS) -DMD5SUM_MAIN -o $@ md5.c
 
-fa2csfa:fa2csfa.c ../kseq.h
-
 maq2sam-short:maq2sam.c
                $(CC) $(CFLAGS) -o $@ maq2sam.c -lz
 
@@ -57,7 +57,13 @@ maq2sam-long:maq2sam.c
 md5fa.o:md5.h md5fa.c
                $(CC) $(CFLAGS) -c -I.. -o $@ md5fa.c
 
+wgsim.o:wgsim.c ../kseq.h
+               $(CC) $(CFLAGS) -c -I.. -o $@ wgsim.c
+
+ace2sam.o:ace2sam.c ../kstring.h ../kseq.h
+               $(CC) $(CFLAGS) -c -I.. -o $@ ace2sam.c
+
 cleanlocal:
-               rm -fr gmon.out *.o a.out *.dSYM $(PROG) *~ *.a
+               rm -fr gmon.out *.o a.out *.exe *.dSYM $(PROG) *~ *.a
 
 clean:cleanlocal-recur