Merge branch 'master' into public #19

	name: GitHub Actions CI

	on:
	push:
	branches: [ master ]
	paths-ignore:
	- '**.md'
	pull_request:
	branches: [ master ]
	workflow_dispatch:

	jobs:


	linux-remote:
	name: Linux test (remote)
	runs-on: ubuntu-latest
	env:
	EXE: ./bin/kmc
	EXE_DUMP: ./bin/kmc_dump
	KMC_SINGLE_READ: ./tests/kmc_CLI/data/single_read.fq
	DATA_DIR: ./tests/kmc_CLI/data/
	steps:
	- uses: actions/checkout@v3
	with:
	submodules: recursive
	- name: make
	run: \|
	g++ -v
	make -j12 kmc kmc_tools kmc_dump

	- name: KMC single read, k=28, ci=1
	run: \|
	$EXE -k28 -ci1 -jstats.json $KMC_SINGLE_READ 28mers .
	cmp <(cat stats.json \| grep '#Total no. of k-mers' \| cut -f 2 -d ':' \| cut -f 2 -d ' ' \| cut -f 1 -d ',') <(echo "70")

	- name: small k, no counters
	run: \|
	$EXE -k4 -cs1 -v $KMC_SINGLE_READ 4mers .

	- name: count k-mers from KMC1 database when small-k-opt may be applied
	run: \|
	$EXE -k10 -v $KMC_SINGLE_READ 10mers .
	$EXE -k9 -v -fkmc 10mers 9mers .
	- name: issue 180
	run: \|
	$EXE -v -k5 -fa -ci1 -t1 $DATA_DIR/issue-180/input.fa bug-report.kmc .
	$EXE_DUMP bug-report.kmc issue-180.kmers
	cmp issue-180.kmers $DATA_DIR/issue-180/pattern.dump

	macos-remote:
	name: macOS build (remote)
	runs-on: macOS-latest

	steps:
	- uses: actions/checkout@v3
	with:
	submodules: recursive
	- uses: maxim-lobanov/setup-xcode@v1
	with:
	xcode-version: '14.1'
	- name: make
	run: make -j12 kmc

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