Updated samtools to 0.1.19

[rsem.git] / sam / misc / Makefile

diff --git a/sam/misc/Makefile b/sam/misc/Makefile
index d2f8bd8ea56c74709f4f0d426787db3cd6c52dd9..d36e7acb4a4c68956f3fed6dbcc16d9c042dc729 100644 (file)
--- a/sam/misc/Makefile
+++ b/sam/misc/Makefile
@@ -4,7 +4,7 @@ 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 seqtk
+PROG=          md5sum-lite md5fa maq2sam-short maq2sam-long ace2sam wgsim bamcheck
 INCLUDES=      -I..
 SUBDIRS=       .
 
@@ -27,8 +27,14 @@ lib-recur all-recur clean-recur cleanlocal-recur install-recur:
 
 lib:
 
-seqtk:seqtk.o
-               $(CC) $(CFLAGS) -o $@ seqtk.o -lm -lz
+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
+
+ace2sam:ace2sam.o
+               $(CC) $(CFLAGS) -o $@ ace2sam.o -lz
 
 wgsim:wgsim.o
                $(CC) $(CFLAGS) -o $@ wgsim.o -lm -lz
@@ -51,12 +57,12 @@ maq2sam-long:maq2sam.c
 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 *.exe *.dSYM $(PROG) *~ *.a