Fix missing declaration for getopt on Mac OS X

[samtools.git] / misc / Makefile

diff --git a/misc/Makefile b/misc/Makefile
index 9434399bdc6a08245a013d19c8a598b9151ce644..e1a5add06a0fb6bc475ec6658d7c8d94e468411e 100644 (file)
--- a/misc/Makefile
+++ b/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 ace2sam wgsim seqtk bamcheck
+PROG=          md5sum-lite md5fa maq2sam-short maq2sam-long ace2sam wgsim bamcheck
 INCLUDES=      -I..
 SUBDIRS=       .
 
@@ -28,14 +28,14 @@ lib-recur all-recur clean-recur cleanlocal-recur install-recur:
 lib:
 
 bamcheck:bamcheck.o
-               $(CC) $(CFLAGS) -o $@ bamcheck.o -lm -lz -L.. -lbam
+               $(CC) $(CFLAGS) -o $@ bamcheck.o -lm -lz -L.. -lbam -lpthread
+
+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
 
-seqtk:seqtk.o
-               $(CC) $(CFLAGS) -o $@ seqtk.o -lm -lz
-
 wgsim:wgsim.o
                $(CC) $(CFLAGS) -o $@ wgsim.o -lm -lz
 
@@ -57,9 +57,6 @@ 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