Adds optional arguments to report k-best alignments with a NH tag #78

	name: Simple Tests
	on:
	push:
	branches:
	- 'bug_fixes'
	- 'master'
	paths:
	- '**.h'
	- '**.cpp'
	- 'bowtie2'
	- 'bowtie2-build'
	- 'bowtie2-inspect'
	- 'Makefile'
	- 'scripts/sim/**'
	- 'scripts/test/**'
	pull_request:
	branches:
	- 'master'
	paths:
	- '**.h'
	- '**.cpp'
	- 'bowtie2'
	- 'bowtie2-build'
	- 'bowtie2-inspect'
	- 'Makefile'
	- 'scripts/sim/**'
	- 'scripts/test/**'
	jobs:
	setup:
	runs-on: ubuntu-latest
	steps:
	- name: Check out repository code
	uses: actions/checkout@v2
	- name: Install zlib development files
	run: \|
	sudo apt-get update
	sudo apt-get install zlib1g-dev
	linux:
	runs-on: ubuntu-latest
	needs: setup
	steps:
	- uses: actions/checkout@v2
	- name: Run simple tests
	run: \|
	make clean; make -j4 allall
	make simple-test
	linux-avx2:
	runs-on: ubuntu-latest
	needs: linux
	steps:
	- uses: actions/checkout@v2
	- name: Run simple tests using AVX2
	run: \|
	export SSE_AVX2=1
	make clean; make -j4 allall
	make simple-test
	macos:
	runs-on: macos-latest
	steps:
	- uses: actions/checkout@v2
	- name: Pull submodules
	run: \|
	git submodule init
	git submodule update
	- name: Run simple tests
	run: \|
	make clean; make -j4 allall
	make simple-test

Provide feedback