Makefile

CC = gcc
CFLAGS = -Wall -Wextra -Ofast -std=c99 -fopenmp
LIBS = -lz -lm

EXE = snp-dists
PREFIX = /usr/local
TESTDIR = test

.PHONY: all check clean format
.DEFAULT: all

all: $(EXE)

$(EXE): main.c kseq.h
	$(CC) $(CFLAGS) -o $(EXE) $< $(LIBS)

install: $(EXE)
	install -v -t $(PREFIX)/bin $(EXE)

clean:
	$(RM) *~ *.o $(EXE)

check: $(EXE)
	./$(EXE) -v
	./$(EXE) /dev/null || true
	./$(EXE) -qb $(TESTDIR)/singleton.aln | diff -bB - $(TESTDIR)/singleton.res
	./$(EXE) -qb $(TESTDIR)/good.aln | diff -bB - $(TESTDIR)/good.res
	./$(EXE) -qb $(TESTDIR)/gzip.aln.gz | diff -bB -  $(TESTDIR)/gzip.res
	./$(EXE) -qb -k $(TESTDIR)/lowercase.aln | diff -bB - $(TESTDIR)/lowercase-k.res
	./$(EXE) -qb    $(TESTDIR)/lowercase.aln | diff -bB - $(TESTDIR)/lowercase.res
	./$(EXE) -qb -c -q $(TESTDIR)/good.aln | diff -bB - $(TESTDIR)/good-c.res
	./$(EXE) -qb -a $(TESTDIR)/ambig.aln | diff -bB - $(TESTDIR)/ambig-a.res
	./$(EXE) -qbcm $(TESTDIR)/good.aln | diff -bB - $(TESTDIR)/good-c-m.res
	./$(EXE) -qb    $(TESTDIR)/ambig.aln | diff -bB - $(TESTDIR)/ambig.res
#	./$(EXE) $(TESTDIR)/huge.aln.gz > /dev/null

format:
	clang-format -i main.c