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diff --git a/Makefile b/Makefile
index fbbbe79..a1d449b 100644
--- a/Makefile
+++ b/Makefile
@@ -1,5 +1,5 @@
all:
- (cd src; $(MAKE))
+ $(MAKE) -C src
clean:
rm -f chaos anchors order glocal utils/bin2bl mlagan utils/cstat utils/bin2mf utils/rc *~ utils/contigorder utils/getbounds utils/cextract utils/seqmerge utils/getlength utils/getoverlap utils/*~ utils/scorealign utils/scorecontigs mlagan.purify utils/getcontigpos utils/fa2xfa utils/Glue utils/dotplot utils/overlay
(cd src; $(MAKE) clean)
diff --git a/src/Makefile b/src/Makefile
index 7f6b6fd..dd6309b 100644
--- a/src/Makefile
+++ b/src/Makefile
@@ -4,51 +4,51 @@ CFLAGS = -O3 # -Wall -W
TRGT_DIR = ..
all: ../anchors ../chaos ../order ../mlagan ../prolagan ../utils/bin2mf ../utils/bin2bl ../utils/cextract ../utils/cstat ../utils/contigorder ../utils/getbounds ../utils/getlength ../utils/getoverlap ../utils/rc ../utils/seqmerge ../utils/scorealign ../utils/scorecontigs ../utils/getcontigpos ../utils/fa2xfa ../utils/Glue ../utils/dotplot ../utils/overlay
- (cd glocal; $(MAKE))
+ $(MAKE) -C glocal
clean:
rm -f *.o *~ utils/*~ mlagan.purify core
(cd glocal; $(MAKE) clean)
../anchors: anchors.c skiplist.c
- $(CC) -o $(TRGT_DIR)/anchors anchors.c skiplist.c
+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/anchors anchors.c skiplist.c
../chaos: fchaos.c thrtrie.c skiplist.c global.c translate.c mempage.c filebuffer.c
- $(CC) -o $(TRGT_DIR)/chaos fchaos.c thrtrie.c skiplist.c global.c translate.c filebuffer.c -lm -DCHAOS__FLAG
+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/chaos fchaos.c thrtrie.c skiplist.c global.c translate.c filebuffer.c -lm -DCHAOS__FLAG
../order: order.c diagmatrix.c filebuffer.c
- $(CC) -o $(TRGT_DIR)/order order.c diagmatrix.c filebuffer.c
+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/order order.c diagmatrix.c filebuffer.c
../mlagan: mlagan.c diagmatrix.c multial.c skiplist.c filebuffer.c
- $(CC) -o $(TRGT_DIR)/mlagan mlagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG
+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/mlagan mlagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG
../prolagan: prolagan.c diagmatrix.c multial.c skiplist.c filebuffer.c
- $(CC) -o $(TRGT_DIR)/prolagan prolagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG
+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/prolagan prolagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG
../utils/bin2mf: utils/bin2mf.c
- $(CC) -o $(TRGT_DIR)/utils/bin2mf utils/bin2mf.c
+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/bin2mf utils/bin2mf.c
../utils/bin2bl: utils/bin2bl.c
- $(CC) -o $(TRGT_DIR)/utils/bin2bl utils/bin2bl.c
+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/bin2bl utils/bin2bl.c
../utils/cextract: utils/cextract.c
- $(CC) -o $(TRGT_DIR)/utils/cextract utils/cextract.c
+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/cextract utils/cextract.c
../utils/cstat: utils/cstat.c
- $(CC) -o $(TRGT_DIR)/utils/cstat utils/cstat.c
+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/cstat utils/cstat.c
../utils/contigorder: utils/contigorder.c
- $(CC) -o $(TRGT_DIR)/utils/contigorder utils/contigorder.c
+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/contigorder utils/contigorder.c
../utils/getbounds: utils/getbounds.c
- $(CC) -o $(TRGT_DIR)/utils/getbounds utils/getbounds.c
+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/getbounds utils/getbounds.c
../utils/getcontigpos: utils/getcontigpos.c
- $(CC) -o $(TRGT_DIR)/utils/getcontigpos utils/getcontigpos.c
+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/getcontigpos utils/getcontigpos.c
../utils/getlength: utils/getlength.c
- $(CC) -o $(TRGT_DIR)/utils/getlength utils/getlength.c
+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/getlength utils/getlength.c
../utils/getoverlap: utils/getoverlap.c
- $(CC) -o $(TRGT_DIR)/utils/getoverlap utils/getoverlap.c
+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/getoverlap utils/getoverlap.c
../utils/rc: utils/rc.c
- $(CC) -o $(TRGT_DIR)/utils/rc utils/rc.c
+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/rc utils/rc.c
../utils/seqmerge: utils/seqmerge.c
- $(CC) -o $(TRGT_DIR)/utils/seqmerge utils/seqmerge.c
+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/seqmerge utils/seqmerge.c
../utils/scorealign: utils/scorealign.c
- $(CC) -o $(TRGT_DIR)/utils/scorealign utils/scorealign.c -lm
+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/scorealign utils/scorealign.c -lm
../utils/scorecontigs: utils/scorecontigs.c
- $(CC) -o $(TRGT_DIR)/utils/scorecontigs utils/scorecontigs.c -lm
+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/scorecontigs utils/scorecontigs.c -lm
../utils/fa2xfa: utils/fa2xfa.c
- $(CC) -o $(TRGT_DIR)/utils/fa2xfa utils/fa2xfa.c
+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/fa2xfa utils/fa2xfa.c
../utils/overlay: utils/overlay.c
- $(CC) -o $(TRGT_DIR)/utils/overlay utils/overlay.c
+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/overlay utils/overlay.c
../utils/Glue: utils/Glue.cpp
- $(CPP) -o $(TRGT_DIR)/utils/Glue utils/Glue.cpp
+ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/Glue utils/Glue.cpp
../utils/dotplot: utils/dotplot.cpp
- $(CPP) -o $(TRGT_DIR)/utils/dotplot utils/dotplot.cpp
+ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/dotplot utils/dotplot.cpp
diff --git a/src/glocal/Makefile b/src/glocal/Makefile
index ce1421a..b82507f 100755
--- a/src/glocal/Makefile
+++ b/src/glocal/Makefile
@@ -10,10 +10,10 @@ TRGT = glocal
OBJECTS = glocal.o io.o rightinfluence.o leftinfluence.o score.o
.cpp.o:
- $(CC) -Wno-deprecated $(CFLAGS) $(INCDIR) -c $*.cpp
+ $(CXX) $(CXXFLAGS) $(INCDIR) -c $*.cpp
$(TRGT): $(OBJECTS)
- $(CLINKER) $(OPTFLAGS) $(OBJECTS) -o $(TRGT_DIR)/$(TRGT) $(MLIB)
+ $(CXX) $(LDFLAGS) $(OBJECTS) -o $(TRGT_DIR)/$(TRGT) $(MLIB)
clean :
rm -f *.o ./*~ *~ core
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