#!/usr/bin/make -f

DH_VERBOSE := 1

export DEB_BUILD_MAINT_OPTIONS=hardening=+all

CMAKE_EXTRA_FLAGS += -DDEBIAN_BUILD=1 \
                     -DLINK=shared \
                     -DBUILD_FUNCTESTING=1 -DUSE_BAM=1

%:
	dh $@ --no-parallel

override_dh_auto_clean:
	dh_auto_clean
	rm -rf ext/bifrost/build ext/bifrost/tmp ext/bifrost/src/bifrost-build ext/bifrost/src/bifrost-stamp

override_dh_auto_configure:
	dh_auto_configure -- $(CMAKE_EXTRA_FLAGS)

override_dh_auto_test:
	dh_auto_test || true
	cd test && PATH=$$(find ../obj-* -name src):$(PATH) HOME=$$(mktemp --directory) XDG_CACHE_HOME=$(mktemp --directory) snakemake --cores 1 || true
	rm -rf test/.snakemake test/bus_out test/quant_out/run_info.json test/transcripts.kidx.gz \
	        test/quant_out test/transcripts.kidx
	# FIXME:
	# ./src/kallisto quant -o ./func_tests/quantbasic -i ./func_tests/basic7.idx --single -l 5 -s 2 ./func_tests/small.fastq.gz
	# ./func_tests/runtests.sh: line 12: 299146 Segmentation fault         (core dumped) ./src/kallisto quant -o ./func_tests/quantbasic -i ./func_tests/basic7.idx --single -l 5 -s 2 ./func_tests/small.fastq.gz 2> /dev/null > /dev/null
	#[Failed]
	#    This might leave a core file which should at least be removed to not make it into the final package
	find . -name 'core' -o -name 'core.[0-9]*' | xargs rm -f