build

--with-missing-fields: fill AD={DP},0 for non-variant genotypes #29

	name: build
	on: [push, pull_request]

	jobs:

	lint:
	runs-on: ubuntu-20.04
	steps:
	- uses: actions/checkout@v2
	- name: deps
	run: \|
	sudo apt-get -qq update
	sudo apt-get install -y clang-format cppcheck python3-pip
	sudo pip3 install --system pre-commit
	- name: pre-commit
	run: pre-commit run --all-files

	build:
	runs-on: ubuntu-20.04
	steps:
	- uses: actions/checkout@v2
	- name: build
	run: \|
	docker pull ubuntu:18.04
	docker pull ubuntu:20.04
	docker build --no-cache -t spvcf .
	- name: inspect
	run: \|
	docker run -v $(pwd):/mnt spvcf cp /usr/local/bin/spvcf /mnt
	ldd spvcf
	sha256sum spvcf
	- name: upload exe
	uses: actions/upload-artifact@v2
	with:
	name: spvcf
	path: spvcf
	- name: WDL test
	run: \|
	pip3 install --upgrade miniwdl
	miniwdl run test/test_spvcf.wdl vcf_gz=test/data/small.vcf.gz docker=spvcf:latest --verbose
	- name: docker login ghcr.io
	uses: docker/login-action@v1
	with:
	registry: ghcr.io
	username: ${{ github.repository_owner }}
	password: ${{ secrets.GITHUB_TOKEN }}
	- name: push image
	run: \|
	REPO="ghcr.io/mlin/spvcf"
	TAG="$(git describe --tags --always --dirty)"
	docker tag spvcf:latest "${REPO}:${TAG}"
	docker push "${REPO}:${TAG}"

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