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Merge branch 'master' into public #19

Merge branch 'master' into public

Merge branch 'master' into public #19

Workflow file for this run

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