Fix literal string matching for external annotation filter values#2526
Open
sirus20x6 wants to merge 1 commit into
Open
Fix literal string matching for external annotation filter values#2526sirus20x6 wants to merge 1 commit into
sirus20x6 wants to merge 1 commit into
Cirrus CI / ubuntu-clang CFLAGS:-g -Wall -O3 CONFIG_OPTS:--enable-libgsl --enable-perl-filters LDFLAGS:-Wl,-rpath,`pwd`/inst/lib USE_CONFIG:yes
failed
Mar 26, 2026 in 3m 1s
Task Summary
Instruction test failed in 01:36
Details
ℹ️ Scheduling was delayed due to a concurrency limit on community tasks
✅ 00:03 clone
✅ 00:19 install
✅ 00:01 htslib_clone
✅ 00:57 compile
❌ 01:36 test
/tmp/cirrus-ci-build/bcftools gtcheck -u GT -e 30 -p s1,s1 /tmp/h0A6MEygHF/gtcheck.1.vcf.gz -g /tmp/h0A6MEygHF/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO
.. ok
test_gtcheck:
/tmp/cirrus-ci-build/bcftools gtcheck -u GT -e 300 /tmp/h0A6MEygHF/gtcheck.1.vcf.gz -g /tmp/h0A6MEygHF/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO
.. ok
test_gtcheck:
/tmp/cirrus-ci-build/bcftools gtcheck -u PL -e 30 /tmp/h0A6MEygHF/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO
.. ok
test_gtcheck:
/tmp/cirrus-ci-build/bcftools gtcheck /tmp/h0A6MEygHF/gtcheck.ntop.vcf.gz -g /tmp/h0A6MEygHF/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO
.. ok
test_gtcheck:
/tmp/cirrus-ci-build/bcftools gtcheck --n-matches 2 /tmp/h0A6MEygHF/gtcheck.ntop.vcf.gz -g /tmp/h0A6MEygHF/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO
.. ok
test_gtcheck:
/tmp/cirrus-ci-build/bcftools gtcheck /tmp/h0A6MEygHF/gtcheck.5.vcf.gz -g /tmp/h0A6MEygHF/gtcheck.5.gts.vcf.gz | grep -v ^# | grep -v Time
.. ok
test_gtcheck:
/tmp/cirrus-ci-build/bcftools gtcheck -p A,B,B,C /tmp/h0A6MEygHF/gtcheck.6.vcf.gz | grep -v ^# | grep -v ^INFO
.. ok
test_gtcheck:
/tmp/cirrus-ci-build/bcftools gtcheck -t 11:33 -p A,D,A,E,D,E -u GT -e 10 /tmp/h0A6MEygHF/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO
.. ok
test_vcf_plugin:
export BCFTOOLS_PLUGINS=/tmp/cirrus-ci-build/plugins; /tmp/cirrus-ci-build/bcftools +vcf2table /tmp/h0A6MEygHF/merge.4.b.vcf.gz | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
export BCFTOOLS_PLUGINS=/tmp/cirrus-ci-build/plugins; /tmp/cirrus-ci-build/bcftools +vcf2table /tmp/h0A6MEygHF/merge.4.b.bcf | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
export BCFTOOLS_PLUGINS=/tmp/cirrus-ci-build/plugins; /tmp/cirrus-ci-build/bcftools +vcf2table /tmp/h0A6MEygHF/split-vep.2.vcf.gz -- --hide 'INFO,URL' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
export BCFTOOLS_PLUGINS=/tmp/cirrus-ci-build/plugins; /tmp/cirrus-ci-build/bcftools +vcf2table /tmp/h0A6MEygHF/split-vep.2.bcf -- --hide 'INFO,URL' | grep -v ^##bcftools_
.. ok
Number of tests:
total .. 2430
passed .. 2428
failed .. 2
make: *** [Makefile:328: test-plugins] Error 1
Exit status: 2
Loading