Collate input reads before alignment #26

	name: CI
	on:
	push:
	pull_request:

	jobs:
	ci:
	strategy:
	fail-fast: true
	matrix:
	python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
	poetry-version: ["1.5.1"]
	os: [ubuntu-22.04] #, macos-latest, windows-latest]
	runs-on: ${{ matrix.os }}
	steps:
	- uses: actions/checkout@v3
	- uses: actions/setup-python@v4
	with:
	python-version: ${{ matrix.python-version }}
	- name: Run image
	uses: abatilo/actions-poetry@v2
	with:
	poetry-version: ${{ matrix.poetry-version }}
	- name: Test build
	run: \|
	poetry config virtualenvs.in-project true
	poetry install
	. .venv/bin/activate
	sentieon-cli -h
	formatting:
	strategy:
	fail-fast: true
	runs-on: ubuntu-22.04
	steps:
	- uses: actions/checkout@v3
	- uses: actions/setup-python@v4
	with:
	python-version: "3.11"
	- name: Run image
	uses: abatilo/actions-poetry@v2
	with:
	poetry-version: "1.5.1"
	- name: Install the project dependencies
	run: poetry install
	- name: Run black formatter
	run: poetry run black --check --exclude '__pycache__\|scripts' --line-length 79 sentieon_cli
	- name: Run mypy
	run: poetry run mypy .
	- name: Run flake8
	run: poetry run flake8 . --extend-ignore E231,E221, --exclude .github/scripts/license_message.py,sentieon_cli/scripts/gvcf_combine.py,sentieon_cli/scripts/vcf_mod.py # false+ from python 3.12
	- name: Run the automated tests (for example)
	run: poetry run pytest -v
	- name: Run doct tests
	run: poetry run pytest --doctest-modules

Provide feedback