Incoporated changes from Nils Homer.

[samtools.git] / Makefile

diff --git a/Makefile b/Makefile
index 99f7ecaf454c8bda2ee632d6529e6538e2608c31..fdcddd6f426893e9a0a221c1231bfdedd8200de7 100644 (file)
--- a/Makefile
+++ b/Makefile
@@ -1,12 +1,13 @@
 CC=                    gcc
-CFLAGS=                -g -Wall -O2 #-m64 #-arch ppc
+CFLAGS=                -g -Wall -O2
+#LDFLAGS=              -Wl,-rpath,\$$ORIGIN/../lib
 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 \
                        $(KNETFILE_O) bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-AOBJS=         bam_tview.o bam_plcmd.o sam_view.o      \
-                       bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o     \
+AOBJS=         bam_tview.o bam_plcmd.o sam_view.o \
+                       bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o \
                        bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o \
                        cut_target.o phase.o bam2depth.o padding.o
 PROG=          samtools
@@ -16,6 +17,7 @@ LIBPATH=
 LIBCURSES=     -lcurses # -lXCurses
 
 .SUFFIXES:.c .o
+.PHONY: all lib
 
 .c.o:
                $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
@@ -41,7 +43,7 @@ libbam.a:$(LOBJS)
                $(AR) -csru $@ $(LOBJS)
 
 samtools:lib-recur $(AOBJS)
-               $(CC) $(CFLAGS) -o $@ $(AOBJS) -Lbcftools $(LIBPATH) libbam.a -lbcf $(LIBCURSES) -lm -lz
+               $(CC) $(CFLAGS) -o $@ $(AOBJS) $(LDFLAGS) libbam.a -Lbcftools -lbcf $(LIBPATH) $(LIBCURSES) -lm -lz
 
 razip:razip.o razf.o $(KNETFILE_O)
                $(CC) $(CFLAGS) -o $@ razf.o razip.o $(KNETFILE_O) -lz