Considering "NON-REF" as a literal during merge

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#819 1 comment 0 reactions 0 assignees View on GitHub

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Assessment

Difficulty
4/5
Estimated time
3-5 days
Newbie friendliness
25/100
Issue type
Bug
Clarity
Needs clarification
Activity status
Stale
Tech stack
c
Domain
bioinformatics

Research direction

No source file or test is identified. First reproduce a VCF/GVCF merge through BCF files and inspect how the ALT field handles "NON-REF"; done means it is treated as a symbolic reference rather than a literal and the resulting records no longer incorrectly list it as a literal.

Written by the indexing model from the issue text.

Description

invalid

When trying to merge VCF and GVCF files using BCF files, "NON-REF" under the ALT field is being considered as a literal instead of a symbolic reference. VCF tools list all "NON-REF" fields in the end and and thus it is easy to filter them out.

I've looked at the source code for the BCF tools and tried to make an alteration to the code but I haven't been able to do so successfully.

Any suggestions on how to rectify this problem?

Thank you!

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

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