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Author: Steffen Moeller,
Nilesh Patra
Last-Update: 2021-04-19 17:37:27 +0530
Description: Propagate variables to Makefile
--- a/src/makefile
+++ b/src/makefile
@@ -1,4 +1,7 @@
-CXXFLAGS = -msse4 -O3 -Wall -g -std=c++11 -pthread
+CXXFLAGS = -O3 -Wall -Wextra -g
+CXXFLAGS += -msse4
+CXXFLAGS += -std=c++11
+CXXFLAGS += -pthread -DHAS_CXX_THREAD
# -fomit-frame-pointer ?
# The number of symbol types that we can keep in sequences (e.g. 20
@@ -7,7 +10,7 @@
ALPHABET_CAPACITY = 66
CPPF = -DALPHABET_CAPACITY=$(ALPHABET_CAPACITY) -DHAS_CXX_THREADS $(CPPFLAGS)
-CFLAGS = -Wall -O2
+CFLAGS ?= -Wall -O2
alpObj = alp/sls_alignment_evaluer.o alp/sls_pvalues.o \
alp/sls_alp_sim.o alp/sls_alp_regression.o alp/sls_alp_data.o \
@@ -56,19 +59,19 @@
all: $(ALL)
../bin/lastdb: $(indexObj)
- $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $(indexObj) -lz
+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(indexObj) -lz
../bin/lastal: $(alignObj)
- $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $(alignObj) -lz
+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(alignObj) -lz
../bin/last-split: $(splitObj)
- $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $(splitObj)
+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(splitObj)
../bin/last-pair-probs: $(PPOBJ)
- $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $(PPOBJ) -lz
+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(PPOBJ) -lz
../bin/last-merge-batches: $(MBOBJ)
- $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(MBOBJ)
+ $(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ $(MBOBJ)
.SUFFIXES:
.SUFFIXES: .o .c .cc .cpp
@@ -106,10 +109,10 @@
depend:
sed '/[m][v]/q' makefile > m
- $(CXX) -MM -I. -std=c++11 *.cc >> m
- $(CC) -MM *.c >> m
- $(CXX) -MM alp/*.cpp | sed 's|.*:|alp/&|' >> m
- $(CXX) -MM -I. split/*.cc | sed 's|.*:|split/&|' >> m
+ $(CXX) $(CPPFLAGS) -MM -I. -std=c++11 *.cc >> m
+ $(CC) $(CPPFLAGS) -MM *.c >> m
+ $(CXX) $(CPPFLAGS) -MM alp/*.cpp | sed 's|.*:|alp/&|' >> m
+ $(CXX) $(CPPFLAGS) -MM -I. split/*.cc | sed 's|.*:|split/&|' >> m
mv m makefile
Alignment.o: Alignment.cc Alignment.hh Centroid.hh GappedXdropAligner.hh \
mcf_big_seq.hh mcf_contiguous_queue.hh mcf_reverse_queue.hh \
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