Symbolic alleles returned when --types ref requested

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Assessment

Difficulty
4/5
Estimated time
3-5 days
Newbie friendliness
35/100
Issue type
Bug
Clarity
Mostly clear
Activity status
Stale
Tech stack
c
Domain
bioinformatics, cli

Research direction

Start by reproducing the behavior with bcftools view --types ref and inspect how bcf_get_variant_types classifies symbolic alleles. Review the linked htslib discussion before choosing whether the change belongs in bcftools or the htslib API. Done means the star allele is distinguished from other symbolic alleles such as <CNV> and <INS>.

Written by the indexing model from the issue text.

Description

Because the unseen star allele is not supported by bcf_get_variant_types, the command bcftools view --types ref is unable to distinguish between the star allele and other symbolic alleles, such as , , etc. This could be fixed either in bcftools or in bcftools+extend htslib API.

See https://github.com/samtools/htslib/pull/1467#issuecomment-1186930979 and https://github.com/samtools/htslib/pull/1467#issuecomment-1190006133

Dominant language
C
Stars
891
Forks
277
Avg merge
2d 23h
Merged PRs (30d)
2

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