Change default to no initial mapping filter and add coverage analysis #19

	name: CI

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

	env:
	CARGO_TERM_COLOR: always

	jobs:
	test:
	name: Test Suite
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v3

	- name: Install Rust
	uses: actions-rs/toolchain@v1
	with:
	profile: minimal
	toolchain: stable
	override: true
	components: rustfmt, clippy

	- name: Check formatting
	run: cargo fmt -- --check

	- name: Run clippy
	run: cargo clippy -- -D warnings

	- name: Build
	run: cargo build --verbose --all-targets

	- name: Run tests
	run: cargo test --verbose

	- name: Run tests (release mode)
	run: cargo test --release --verbose

	- name: Check for forbidden files
	run: \|
	# Check for files that should never be committed
	if git ls-tree -r HEAD --name-only \| grep -E '\.(fa\|fasta\|paf\|gdb\|ktab\|bps)$' \| grep -v 'data/scerevisiae8.fa.gz'; then
	echo "ERROR: Found forbidden data files in repository!"
	echo "Only data/scerevisiae8.fa.gz is allowed"
	exit 1
	fi

	build:
	name: Build Check
	runs-on: ubuntu-latest
	strategy:
	matrix:
	rust:
	- stable
	- beta
	- nightly
	steps:
	- uses: actions/checkout@v3

	- name: Install Rust
	uses: actions-rs/toolchain@v1
	with:
	profile: minimal
	toolchain: ${{ matrix.rust }}
	override: true

	- name: Build
	run: cargo build --verbose

	- name: Build (all features)
	run: cargo build --verbose --all-features

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