--- last-852/makefile.ori	2016-12-13 07:22:11.000000000 +0100
+++ last-852/makefile	2017-05-10 11:04:14.610665834 +0200
@@ -1,6 +1,7 @@
-CXXFLAGS = -O3 -std=c++11 -pthread -DHAS_CXX_THREADS
+CXXFLAGS ?= -O3
+CXXFLAGS += -std=c++11 -pthread -DHAS_CXX_THREADS
 all:
-	@cd src && $(MAKE) CXXFLAGS="$(CXXFLAGS)"
+	$(MAKE) -C src
 
 progs = src/lastdb src/lastal src/last-split src/last-merge-batches	\
 src/last-pair-probs src/lastdb8 src/lastal8 src/last-split8
@@ -13,17 +14,17 @@
 	cp $(progs) scripts/* $(bindir)
 
 clean:
-	@cd src && $(MAKE) clean
+	$(MAKE) -C src clean
 
 html:
-	@cd doc && $(MAKE)
+	$(MAKE) -C doc
 
 distdir = last-`hg id -n`
 
 RSYNCFLAGS = -aC --exclude '*8' --exclude 'last??' --exclude last-split --exclude last-merge-batches --exclude last-pair-probs
 
 dist: log html
-	@cd src && $(MAKE) version.hh CyclicSubsetSeedData.hh ScoreMatrixData.hh
+	$(MAKE) -C src version.hh CyclicSubsetSeedData.hh ScoreMatrixData.hh
 	rsync $(RSYNCFLAGS) build doc examples makefile scripts src data *.txt $(distdir)
 	zip -qrm $(distdir) $(distdir)
 
--- last-852/src/makefile.ori	2016-12-13 06:53:24.000000000 +0100
+++ last-852/src/makefile	2017-05-10 11:05:22.792501835 +0200
@@ -1,12 +1,13 @@
-CXX = g++
-CC  = gcc
+CXX ?= g++
+CC  ?= gcc
 
-CXXFLAGS = -O3 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef	\
--Wcast-align -pedantic -g -std=c++11 -pthread -DHAS_CXX_THREADS
+CXXFLAGS ?= -O3 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef	\
+-Wcast-align -pedantic -g
+CXXFLAGS += -std=c++11 -pthread -DHAS_CXX_THREADS
 # -Wconversion
 # -fomit-frame-pointer ?
 
-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	\