add CI (#179)

Author: ankane

.github/workflows/ci.yml

@@ -0,0 +1,19 @@
+name: CI
+on: [push, pull_request]
+jobs:
+  ubuntu:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v5
+      - run: sudo apt-get update && sudo apt-get install libhts-dev bcftools
+      - run: echo /home/linuxbrew/.linuxbrew/bin >> $GITHUB_PATH
+      - run: brew install nim
+      - run: nimble test
+  mac:
+    runs-on: macos-latest
+    steps:
+      - uses: actions/checkout@v5
+      - run: brew install nim htslib bcftools
+      - run: sed -i "" -e "s/nim c/nim c --passL:-Wl,-rpath,\/opt\/homebrew\/opt\/htslib\/lib/" slivar.nimble
+      - run: sed -i "" -e "s/nim c/nim c --passL:-Wl,-rpath,\/opt\/homebrew\/opt\/htslib\/lib/" tests/functional-tests.sh
+      - run: nimble test

tests/functional-tests.sh

@@ -50,7 +50,7 @@ assert_exit_code 0
 run check_denovo $exe expr -v tests/ashk-trio.vcf.gz --js js/slivar-functions.js --pass-only --trio "denovo:kid.het && mom.hom_ref && dad.hom_ref && (mom.AD[1] + dad.AD[1]) < 2 && kid.GQ > 10 && mom.GQ > 10 && dad.GQ > 10 && kid.DP > 10 && mom.DP > 10 && dad.DP > 10" --ped tests/ashk-trio.ped -o xx.bcf
 assert_exit_code 0
 assert_equal 0 $(bcftools view -H -i 'FMT/GT[0] == "RR"' xx.bcf | wc -l)
-assert_equal "0" "$(bcftools view -H -i 'FMT/DP[0] <= 10 || FMT/DP[1] <= 10 || FMT/DP[2] <= 10' xx.bcf | wc -l)"
+assert_equal 0 $(bcftools view -H -i 'FMT/DP[0] <= 10 || FMT/DP[1] <= 10 || FMT/DP[2] <= 10' xx.bcf | wc -l)
 assert_equal 11 $(bcftools view -H xx.bcf | wc -l)