Error while running bcftools view

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Assessment

Difficulty
3/5
Estimated time
1-2 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 bcftools view -r HLA-C*06:46N input.vcf.gz command and inspect how the region argument is parsed when the contig name contains a colon. Use the reported _regions_init_string error as the entry point, then verify that the intended region syntax works without breaking ordinary region queries.

Written by the indexing model from the issue text.

Description

Hi,

I'am trying to run the following:
bcftools view -r HLA-C*06:46N input.vcf.gz

And it did not work and I got the following:
[synced_bcf_reader.c:949 _regions_init_string] Could not parse the region(s): HLA-C06:46N
Failed to read the regions: HLA-C06:46N

Apparently the problem is in the colon that this contig has in its name. Is there a way of fixing this error?

Thanks,

ernesto

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