bcftools view -T with collapse option?

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#683 2 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
cli

Research direction

Start by reading how bcftools view handles -T and how the collapse option is implemented for the other commands mentioned in the issue. The change is complete when view can subset variants using chr, pos, ref, and alt, with the none behavior requested by the reporter, and its behavior is verified against the existing command checks.

Written by the indexing model from the issue text.

Description

Hi,

I like bcftools neat design and fast speed very much. Here is the feature I want but not sure whether there is another way to achieve this already.

I would like to subset variants with exactly the four fields: chr pos ref alt. When I use view -T, it does not consider alt. I know the collapse option is available for other commands, the option "none" is what I want. But it does not seem available for command view.

Could you help to add this feature?

Thanks,

W.C.

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

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