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 \