X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=Makefile;h=0d3eb4cde7ca8c894dc2bbe01c70284d09ede3e1;hb=d46afb500a437323dda82920f9fb18324b2dbec0;hp=4699878859358647cfe05946214d68f2f841d8c5;hpb=e50413dd979a616b604914afd2488a308359ec6a;p=samtools.git

diff --git a/Makefile b/Makefile
index 4699878..0d3eb4c 100644
--- a/Makefile
+++ b/Makefile
@@ -1,7 +1,7 @@
 CC=			gcc
 CFLAGS=		-g -Wall -O2
 #LDFLAGS=		-Wl,-rpath,\$$ORIGIN/../lib
-DFLAGS=		-D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -DBGZF_CACHE -D_CURSES_LIB=1
+DFLAGS=		-D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1
 KNETFILE_O=	knetfile.o
 LOBJS=		bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o	\
 			bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o \
@@ -43,13 +43,16 @@ libbam.a:$(LOBJS)
 		$(AR) -csru $@ $(LOBJS)
 
 samtools:lib-recur $(AOBJS)
-		$(CC) $(CFLAGS) -o $@ $(AOBJS) $(LDFLAGS) libbam.a -Lbcftools -lbcf $(LIBPATH) $(LIBCURSES) -lm -lz
+		$(CC) $(CFLAGS) -o $@ $(AOBJS) $(LDFLAGS) libbam.a -Lbcftools -lbcf $(LIBPATH) $(LIBCURSES) -lm -lz -lpthread
 
 razip:razip.o razf.o $(KNETFILE_O)
 		$(CC) $(CFLAGS) -o $@ razf.o razip.o $(KNETFILE_O) -lz
 
 bgzip:bgzip.o bgzf.o $(KNETFILE_O)
-		$(CC) $(CFLAGS) -o $@ bgzf.o bgzip.o $(KNETFILE_O) -lz
+		$(CC) $(CFLAGS) -o $@ bgzf.o bgzip.o $(KNETFILE_O) -lz -lpthread
+
+bgzf.o:bgzf.h
+		$(CC) -c $(CFLAGS) $(DFLAGS) -DBGZF_CACHE $(INCLUDES) bgzf.c -o $@
 
 razip.o:razf.h
 bam.o:bam.h razf.h bam_endian.h kstring.h sam_header.h