Add v4 variant QC annotation HT creation and true positive VCF export #1201

	name: CI
	on:
	push:
	branches:
	- main
	pull_request:
	jobs:
	pylint:
	name: Pylint
	runs-on: ubuntu-latest
	steps:
	- name: Checkout
	uses: actions/checkout@v3
	with:
	submodules: recursive
	- name: Setup Python 3.11
	uses: actions/setup-python@v4
	with:
	python-version: 3.11
	- name: Use pip cache
	uses: actions/cache@v3
	with:
	path: ~/.cache/pip
	key: pip-${{ hashFiles('*/requirements.txt') }}
	restore-keys: \|
	pip-
	- name: Install dependencies
	run: \|
	pip install wheel
	pip install -r requirements.txt
	pip install -r requirements-dev.txt
	- name: Check formatting
	run: black --check gnomad_qc
	- name: Check imports
	run: isort --check-only gnomad_qc
	- name: Check comment formatting
	run: autopep8 --exit-code --diff gnomad_qc
	- name: Run Pylint
	run: ./lint --disable=W
	- name: Check docstrings
	run: pydocstyle --match-dir='(?!v2\|cuKING).*' gnomad_qc

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