bcftools isec does not support stdin input

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#297 4 comments 0 reactions 0 assignees View on GitHub

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Assessment

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

Research direction

Start at the bcftools isec command entry point and trace how its two VCF inputs are opened. Check the existing input-handling behavior for stdin and process-substitution-style arguments, then identify where focused tests for isec inputs belong. Done means the example using bcftools view outputs is accepted by isec without breaking regular file inputs.

Written by the indexing model from the issue text.

Description

This is an enhancement request. It would be great, if bcftools isec could support stdin input like this:

bcftools isec -C <(bcftools view [OPTIONS] $vcf1) <(bcftools view [OPTIONS] $vcf2)

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

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