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Fix literal string matching for external annotation filter values#2526

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sirus20x6 wants to merge 1 commit into
samtools:developfrom
sirus20x6:fix/annotate-pipe-literal
Open

Fix literal string matching for external annotation filter values#2526
sirus20x6 wants to merge 1 commit into
samtools:developfrom
sirus20x6:fix/annotate-pipe-literal

Fix literal string matching for external filter values in annotate (f…

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Cirrus CI / macosx + clang USE_CONFIG:yes failed Mar 26, 2026 in 1m 7s

Task Summary

Instruction test failed in 00:30

Details

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ℹ️ Scheduling was delayed due to a concurrency limit on community tasks

✅ 00:02 clone
✅ 00:05 package_install
✅ 00:03 htslib_clone
✅ 00:20 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/N2UVpYKJli/gtcheck.1.vcf.gz -g /var/folders/q_/v_6k8zks62lb0q_8f10mvn8h0000gn/T/N2UVpYKJli/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/N2UVpYKJli/gtcheck.1.vcf.gz -g /var/folders/q_/v_6k8zks62lb0q_8f10mvn8h0000gn/T/N2UVpYKJli/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/N2UVpYKJli/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/N2UVpYKJli/gtcheck.ntop.vcf.gz -g /var/folders/q_/v_6k8zks62lb0q_8f10mvn8h0000gn/T/N2UVpYKJli/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/N2UVpYKJli/gtcheck.ntop.vcf.gz -g /var/folders/q_/v_6k8zks62lb0q_8f10mvn8h0000gn/T/N2UVpYKJli/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/N2UVpYKJli/gtcheck.5.vcf.gz -g /var/folders/q_/v_6k8zks62lb0q_8f10mvn8h0000gn/T/N2UVpYKJli/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/N2UVpYKJli/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/N2UVpYKJli/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/N2UVpYKJli/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/N2UVpYKJli/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/N2UVpYKJli/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/N2UVpYKJli/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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