mendelian2 plugin

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Assessment

Difficulty
3/5
Estimated time
1-2 days
Newbie friendliness
38/100
Issue type
Bug
Clarity
Mostly clear
Activity status
Stale
Tech stack
c
Domain
bioinformatics, cli

Research direction

Start by reproducing the command with the mendelian2 plugin and the listed sample order against the provided VCF. Trace how mendelian2 reads the --pfm sample list, then verify that changing the order no longer causes the final sample to be reported as absent.

Written by the indexing model from the issue text.

Description

requires-test-case

Hi,
I am using mendelian2 bcftools plugin with this command :

bcftools +mendelian2 Input.vcf.gz --pfm 0705_WHOLE_BODY.CEL,F01_FOOT.CEL,M10_FOOT.CEL -m c

and I get this error: The sample is not present: M10_FOOT.CEL

but I'm sure the sample is present in the vcf file. if I move the order of the samples the last one in the list is always absent regardless of which one it is.
Any suggestions on how to fix this problem?

Thanks a lot

Dominant language
C
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Forks
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Avg merge
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Merged PRs (30d)
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