Fix literal string matching for external annotation filter values #2526
+22
−2
Cirrus CI / macosx + clang USE_CONFIG:no
failed
Mar 26, 2026 in 1m 1s
Task Summary
Instruction test failed in 00:30
Details
ℹ️ Scheduling was delayed due to a concurrency limit on community tasks
✅ 00:02 clone
✅ 00:07 package_install
✅ 00:01 htslib_clone
✅ 00:14 compile
❌ 00:30 test
/private/var/folders/q_/v_6k8zks62lb0q_8f10mvn8h0000gn/T/cirrus-ci-build/bcftools gtcheck -u GT -e 30 -p s1,s1 /var/folders/q_/v_6k8zks62lb0q_8f10mvn8h0000gn/T/UPM3CoYAmz/gtcheck.1.vcf.gz -g /var/folders/q_/v_6k8zks62lb0q_8f10mvn8h0000gn/T/UPM3CoYAmz/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO
.. ok
test_gtcheck:
/private/var/folders/q_/v_6k8zks62lb0q_8f10mvn8h0000gn/T/cirrus-ci-build/bcftools gtcheck -u GT -e 300 /var/folders/q_/v_6k8zks62lb0q_8f10mvn8h0000gn/T/UPM3CoYAmz/gtcheck.1.vcf.gz -g /var/folders/q_/v_6k8zks62lb0q_8f10mvn8h0000gn/T/UPM3CoYAmz/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO
.. ok
test_gtcheck:
/private/var/folders/q_/v_6k8zks62lb0q_8f10mvn8h0000gn/T/cirrus-ci-build/bcftools gtcheck -u PL -e 30 /var/folders/q_/v_6k8zks62lb0q_8f10mvn8h0000gn/T/UPM3CoYAmz/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO
.. ok
test_gtcheck:
/private/var/folders/q_/v_6k8zks62lb0q_8f10mvn8h0000gn/T/cirrus-ci-build/bcftools gtcheck /var/folders/q_/v_6k8zks62lb0q_8f10mvn8h0000gn/T/UPM3CoYAmz/gtcheck.ntop.vcf.gz -g /var/folders/q_/v_6k8zks62lb0q_8f10mvn8h0000gn/T/UPM3CoYAmz/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO
.. ok
test_gtcheck:
/private/var/folders/q_/v_6k8zks62lb0q_8f10mvn8h0000gn/T/cirrus-ci-build/bcftools gtcheck --n-matches 2 /var/folders/q_/v_6k8zks62lb0q_8f10mvn8h0000gn/T/UPM3CoYAmz/gtcheck.ntop.vcf.gz -g /var/folders/q_/v_6k8zks62lb0q_8f10mvn8h0000gn/T/UPM3CoYAmz/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO
.. ok
test_gtcheck:
/private/var/folders/q_/v_6k8zks62lb0q_8f10mvn8h0000gn/T/cirrus-ci-build/bcftools gtcheck /var/folders/q_/v_6k8zks62lb0q_8f10mvn8h0000gn/T/UPM3CoYAmz/gtcheck.5.vcf.gz -g /var/folders/q_/v_6k8zks62lb0q_8f10mvn8h0000gn/T/UPM3CoYAmz/gtcheck.5.gts.vcf.gz | grep -v ^# | grep -v Time
.. ok
test_gtcheck:
/private/var/folders/q_/v_6k8zks62lb0q_8f10mvn8h0000gn/T/cirrus-ci-build/bcftools gtcheck -p A,B,B,C /var/folders/q_/v_6k8zks62lb0q_8f10mvn8h0000gn/T/UPM3CoYAmz/gtcheck.6.vcf.gz | grep -v ^# | grep -v ^INFO
.. ok
test_gtcheck:
/private/var/folders/q_/v_6k8zks62lb0q_8f10mvn8h0000gn/T/cirrus-ci-build/bcftools gtcheck -t 11:33 -p A,D,A,E,D,E -u GT -e 10 /var/folders/q_/v_6k8zks62lb0q_8f10mvn8h0000gn/T/UPM3CoYAmz/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO
.. ok
test_vcf_plugin:
export BCFTOOLS_PLUGINS=/private/var/folders/q_/v_6k8zks62lb0q_8f10mvn8h0000gn/T/cirrus-ci-build/plugins; /private/var/folders/q_/v_6k8zks62lb0q_8f10mvn8h0000gn/T/cirrus-ci-build/bcftools +vcf2table /var/folders/q_/v_6k8zks62lb0q_8f10mvn8h0000gn/T/UPM3CoYAmz/merge.4.b.vcf.gz | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
export BCFTOOLS_PLUGINS=/private/var/folders/q_/v_6k8zks62lb0q_8f10mvn8h0000gn/T/cirrus-ci-build/plugins; /private/var/folders/q_/v_6k8zks62lb0q_8f10mvn8h0000gn/T/cirrus-ci-build/bcftools +vcf2table /var/folders/q_/v_6k8zks62lb0q_8f10mvn8h0000gn/T/UPM3CoYAmz/merge.4.b.bcf | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
export BCFTOOLS_PLUGINS=/private/var/folders/q_/v_6k8zks62lb0q_8f10mvn8h0000gn/T/cirrus-ci-build/plugins; /private/var/folders/q_/v_6k8zks62lb0q_8f10mvn8h0000gn/T/cirrus-ci-build/bcftools +vcf2table /var/folders/q_/v_6k8zks62lb0q_8f10mvn8h0000gn/T/UPM3CoYAmz/split-vep.2.vcf.gz -- --hide 'INFO,URL' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
export BCFTOOLS_PLUGINS=/private/var/folders/q_/v_6k8zks62lb0q_8f10mvn8h0000gn/T/cirrus-ci-build/plugins; /private/var/folders/q_/v_6k8zks62lb0q_8f10mvn8h0000gn/T/cirrus-ci-build/bcftools +vcf2table /var/folders/q_/v_6k8zks62lb0q_8f10mvn8h0000gn/T/UPM3CoYAmz/split-vep.2.bcf -- --hide 'INFO,URL' | grep -v ^##bcftools_
.. ok
Number of tests:
total .. 2429
passed .. 2427
failed .. 2
make: *** [test-plugins] Error 1
Exit status: 2
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