fix parsing reads with 'X' or '=' instead of 'M' in cigar #108

	name: CI

	on:
	push:
	branches: [ main, master ]
	pull_request:
	branches: [ main, master ]

	# Allows you to run this workflow manually from the Actions tab
	workflow_dispatch:

	jobs:
	test-all:
	runs-on: ubuntu-latest
	env:
	GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

	# Steps represent a sequence of tasks that will be executed as part of the job
	steps:
	# Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
	- uses: actions/checkout@v2
	with:
	submodules: recursive

	- name: Manually install dependency
	run: \|
	sudo apt-get update -y
	sudo apt-get install -y libdeflate-dev libdeflate-tools
	sudo ln -sf /usr/lib/x86_64-linux-gnu/libdeflate.so /usr/local/lib/libdeflate.so
	ls -lth /usr/local/
	ls -lth /usr/local/lib/
	ls -lth /usr/local/lib/libdeflate.so
	sudo apt-get install -y libcurl4-openssl-dev
	sudo apt-get install -y libharfbuzz-dev
	sudo apt-get install -y libfribidi-dev
	which pkg-config

	- uses: r-lib/actions/setup-r@v2
	with:
	use-public-rspm: true

	- name: Install dependencies
	run: ./scripts/install-dependencies.sh

	- name: Unit tests
	run: ./scripts/test-unit.sh

	- name: Acceptance tests
	run: ./scripts/test-acceptance.sh

	- name: Test the build
	run: ./scripts/build-and-install.R

	- name: Test the CLI
	run: ./scripts/test-cli.R

	- name: Example test
	run: ./scripts/test-compare-vcf.sh

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