Merge pull request #226 from tmaklin/gcc-13-headers-patch1 #22
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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 | |