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bcftools isec: Segmentation fault when using filters #1632

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gabeng opened this issue Dec 29, 2021 · 1 comment
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bcftools isec: Segmentation fault when using filters #1632

gabeng opened this issue Dec 29, 2021 · 1 comment

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@gabeng
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gabeng commented Dec 29, 2021

bcftools 1.14

sites-a.vcf.gz contains a variant with AF = 0.0099
The following command creates a Segmentation fault:

bcftools isec -p test -i'AF>0.09' sites-a.vcf.gz sites-b.vcf.gz

This command does not create a Segmentation fault (note that all variants from the datasets are now included):

bcftools isec -p test -i'AF>0.009' sites-a.vcf.gz sites-b.vcf.gz

You can create other scenarios with -e instead of -i creating Segmentation faults. Similar filtering works with other commands like bcftools view etc. Attached are sample files.
I was able to work around the issue with merging and filtering files, but it would be nice if the filter option in the isec command would work.

filter.zip

@pd3 pd3 closed this as completed in 018607e Jan 4, 2022
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pd3 commented Jan 4, 2022

This is now fixed. Thank you for the bug report.

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