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Diffstat (limited to 'sci-biology/bwa/files/bwa-0.7.17-Makefile.patch')
-rw-r--r--sci-biology/bwa/files/bwa-0.7.17-Makefile.patch42
1 files changed, 42 insertions, 0 deletions
diff --git a/sci-biology/bwa/files/bwa-0.7.17-Makefile.patch b/sci-biology/bwa/files/bwa-0.7.17-Makefile.patch
new file mode 100644
index 000000000000..944369cb75e2
--- /dev/null
+++ b/sci-biology/bwa/files/bwa-0.7.17-Makefile.patch
@@ -0,0 +1,42 @@
+--- a/Makefile
++++ b/Makefile
+@@ -1,9 +1,7 @@
+-CC= gcc
+ #CC= clang --analyze
+-CFLAGS= -g -Wall -Wno-unused-function -O2
++CFLAGS+= -Wall -Wno-unused-function
+ WRAP_MALLOC=-DUSE_MALLOC_WRAPPERS
+-AR= ar
+-DFLAGS= -DHAVE_PTHREAD $(WRAP_MALLOC)
++CPPFLAGS+= -DHAVE_PTHREAD $(WRAP_MALLOC)
+ LOBJS= utils.o kthread.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o \
+ QSufSort.o bwt_gen.o rope.o rle.o is.o bwtindex.o
+ AOBJS= bwashm.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o \
+@@ -21,16 +19,13 @@
+
+ .SUFFIXES:.c .o .cc
+
+-.c.o:
+- $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
+-
+ all:$(PROG)
+
+ bwa:libbwa.a $(AOBJS) main.o
+- $(CC) $(CFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS)
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS)
+
+ bwamem-lite:libbwa.a example.o
+- $(CC) $(CFLAGS) $(DFLAGS) example.o -o $@ -L. -lbwa $(LIBS)
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) example.o -o $@ -L. -lbwa $(LIBS)
+
+ libbwa.a:$(LOBJS)
+ $(AR) -csru $@ $(LOBJS)
+@@ -39,7 +34,7 @@
+ rm -f gmon.out *.o a.out $(PROG) *~ *.a
+
+ depend:
+- ( LC_ALL=C ; export LC_ALL; makedepend -Y -- $(CFLAGS) $(DFLAGS) -- *.c )
++ ( LC_ALL=C ; export LC_ALL; makedepend -Y -- $(CFLAGS) $(CPPFLAGS) -- *.c )
+
+ # DO NOT DELETE THIS LINE -- make depend depends on it.
+