Skip to content

Fix vcfconvert ALT parsing, null deref, and sample compression #2528

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
pd3 merged 1 commit into from
Mar 31, 2026
+7 −7

Fix three bugs in vcfconvert.c

b23579b
Select commit
Loading
Failed to load commit list.
Merged

Fix vcfconvert ALT parsing, null deref, and sample compression #2528

Fix three bugs in vcfconvert.c
b23579b
Select commit
Loading
Failed to load commit list.
Cirrus CI / debian-gcc failed Mar 26, 2026 in 6m 39s

Task Summary

Instruction test failed in 04:36

Details

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

✅ 00:04 clone
✅ 00:04 install
✅ 00:01 htslib_clone
✅ 01:50 compile
❌ 04:36 test

	/tmp/cirrus-ci-build/bcftools gtcheck -u GT -e 30 -p s1,s1 /tmp/8tFlO1McXz/gtcheck.1.vcf.gz -g /tmp/8tFlO1McXz/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
.. ok

test_gtcheck:
	/tmp/cirrus-ci-build/bcftools gtcheck -u GT -e 300 /tmp/8tFlO1McXz/gtcheck.1.vcf.gz -g /tmp/8tFlO1McXz/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
.. ok

test_gtcheck:
	/tmp/cirrus-ci-build/bcftools gtcheck -u PL -e 30 /tmp/8tFlO1McXz/gtcheck.3.vcf.gz  | grep -v ^# | grep -v ^INFO 
.. ok

test_gtcheck:
	/tmp/cirrus-ci-build/bcftools gtcheck  /tmp/8tFlO1McXz/gtcheck.ntop.vcf.gz -g /tmp/8tFlO1McXz/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
.. ok

test_gtcheck:
	/tmp/cirrus-ci-build/bcftools gtcheck --n-matches 2 /tmp/8tFlO1McXz/gtcheck.ntop.vcf.gz -g /tmp/8tFlO1McXz/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
.. ok

test_gtcheck:
	/tmp/cirrus-ci-build/bcftools gtcheck  /tmp/8tFlO1McXz/gtcheck.5.vcf.gz -g /tmp/8tFlO1McXz/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/8tFlO1McXz/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/8tFlO1McXz/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/8tFlO1McXz/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/8tFlO1McXz/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/8tFlO1McXz/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/8tFlO1McXz/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