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Single breakends not recognised by bcf_set_variant_type()

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Assessment

Difficulty
3/5
Estimated time
Half a day
Newbie friendliness
55/100
Issue type
Bug
Clarity
Mostly clear
Activity status
Active
Tech stack
c
Domain
data

Research direction

The bug is in bcf_set_variant_type(), which needs to classify the single-breakend ALT forms .A and A. from VCF spec section 5.4.9. Start by reading that function in the htslib sources and how it currently handles breakend ALT strings. Done means both forms are classified as breakends and a test or reproducer with those REF/ALT pairs gives the expected type. The issue does not say which variant type is expected, so confirm that with a maintainer first.

Written by the indexing model from the issue text.

Description

The single breakend notation is currently not recognized by htslib

REF=A  ALT=.A
REF=A  ALT=A.

See section 5.4.9 on Single breakends in VCF specification

Dominant language
C
Stars
954
Forks
475
Avg merge
5d 12h
Merged PRs (30d)
9

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