Added rule for bamcheck creation

[samtools.git] / misc / Makefile

diff --git a/misc/Makefile b/misc/Makefile
index 1008e91cd10f13fd89ddb1ccaa5dac092ab3a337..9434399bdc6a08245a013d19c8a598b9151ce644 100644 (file)
--- a/misc/Makefile
+++ b/misc/Makefile
@@ -1,10 +1,10 @@
 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
 OBJS=          
-PROG=          md5sum-lite md5fa maq2sam-short maq2sam-long wgsim
+PROG=          md5sum-lite md5fa maq2sam-short maq2sam-long ace2sam wgsim seqtk bamcheck
 INCLUDES=      -I..
 SUBDIRS=       .
 
@@ -27,11 +27,20 @@ lib-recur all-recur clean-recur cleanlocal-recur install-recur:
 
 lib:
 
+bamcheck:bamcheck.o
+               $(CC) $(CFLAGS) -o $@ bamcheck.o -lm -lz -L.. -lbam
+
+ace2sam:ace2sam.o
+               $(CC) $(CFLAGS) -o $@ ace2sam.o -lz
+
+seqtk:seqtk.o
+               $(CC) $(CFLAGS) -o $@ seqtk.o -lm -lz
+
 wgsim:wgsim.o
-               $(CC) $(CFLAGS) -o $@ wgsim.o -lm
+               $(CC) $(CFLAGS) -o $@ wgsim.o -lm -lz
 
 md5fa:md5.o md5fa.o md5.h ../kseq.h
-               $(CC) $(CFLAGS) -o $@ md5.o md5fa.o -L../zlib -lz
+               $(CC) $(CFLAGS) -o $@ md5.o md5fa.o -lz
 
 md5sum-lite:md5sum-lite.o
                $(CC) $(CFLAGS) -o $@ md5sum-lite.o
@@ -40,15 +49,24 @@ md5sum-lite.o:md5.c md5.h
                $(CC) -c $(CFLAGS) -DMD5SUM_MAIN -o $@ md5.c
 
 maq2sam-short:maq2sam.c
-               $(CC) $(CFLAGS) -I../zlib -o $@ maq2sam.c -L../zlib -lz
+               $(CC) $(CFLAGS) -o $@ maq2sam.c -lz
 
 maq2sam-long:maq2sam.c
-               $(CC) $(CFLAGS) -I../zlib -DMAQ_LONGREADS -o $@ maq2sam.c -L../zlib -lz
+               $(CC) $(CFLAGS) -DMAQ_LONGREADS -o $@ maq2sam.c -lz
 
 md5fa.o:md5.h md5fa.c
                $(CC) $(CFLAGS) -c -I.. -o $@ md5fa.c
 
+seqtk.o:seqtk.c ../khash.h ../kseq.h
+               $(CC) $(CFLAGS) -c -I.. -o $@ seqtk.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