all: README.html

README.html: README.md
	pandoc  $< -o $@

%.count: %.csv.gz
	zcat $< | wc -l > $@

%.nodes.csv.gz: %.edges.csv.gz
	zcat $< | tr ' ' '\n' | sort $(SORT_FLAGS) -u | gzip -c > $@

# (loosely) top-down sorted
EDGE_FILES =
EDGE_FILES += $(sort $(wildcard snp_to_*.edges.csv.gz))
EDGE_FILES += $(sort $(wildcard rel_to_*.edges.csv.gz))
EDGE_FILES += $(sort $(wildcard rev_to_*.edges.csv.gz))
EDGE_FILES += $(sort $(wildcard dir_to_*.edges.csv.gz))

all.edges.csv.gz: $(EDGE_FILES) merge-edges.sh
	./merge-edges.sh $(EDGE_FILES) | pigz -c > $@