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Fix missing header finalization and unchecked faidx return #2536

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sirus20x6 wants to merge 1 commit into from
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Fix missing header finalization and unchecked faidx_fetch_seq return

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Fix missing header finalization and unchecked faidx return #2536

Fix missing header finalization and unchecked faidx_fetch_seq return
119ffec
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Cirrus CI / debian-gcc failed Mar 26, 2026 in 6m 56s

Task Summary

Instruction test failed in 04:39

Details

⚠️ Not enough compute credits to prioritize tasks!
ℹ️ Scheduling was delayed due to a concurrency limit on community tasks

✅ 00:06 clone
✅ 00:06 install
✅ 00:02 htslib_clone
✅ 01:59 compile
❌ 04:39 test

	/tmp/cirrus-ci-build/bcftools gtcheck -u GT -e 30 -p s1,s1 /tmp/Ggrurc9OO8/gtcheck.1.vcf.gz -g /tmp/Ggrurc9OO8/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
.. ok

test_gtcheck:
	/tmp/cirrus-ci-build/bcftools gtcheck -u GT -e 300 /tmp/Ggrurc9OO8/gtcheck.1.vcf.gz -g /tmp/Ggrurc9OO8/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
.. ok

test_gtcheck:
	/tmp/cirrus-ci-build/bcftools gtcheck -u PL -e 30 /tmp/Ggrurc9OO8/gtcheck.3.vcf.gz  | grep -v ^# | grep -v ^INFO 
.. ok

test_gtcheck:
	/tmp/cirrus-ci-build/bcftools gtcheck  /tmp/Ggrurc9OO8/gtcheck.ntop.vcf.gz -g /tmp/Ggrurc9OO8/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
.. ok

test_gtcheck:
	/tmp/cirrus-ci-build/bcftools gtcheck --n-matches 2 /tmp/Ggrurc9OO8/gtcheck.ntop.vcf.gz -g /tmp/Ggrurc9OO8/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
.. ok

test_gtcheck:
	/tmp/cirrus-ci-build/bcftools gtcheck  /tmp/Ggrurc9OO8/gtcheck.5.vcf.gz -g /tmp/Ggrurc9OO8/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/Ggrurc9OO8/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/Ggrurc9OO8/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/Ggrurc9OO8/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/Ggrurc9OO8/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/Ggrurc9OO8/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/Ggrurc9OO8/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
View more details on Cirrus CI