`bcftools csq` crashes on a minimal 2-variant reverse-strand CDS

[Wytamma]

bcftools csq crashes with an error This should not happen... when two homozygous variants are in the same reverse-strand coding transcript. I've attached files to reproduce the bug. I checked version 1.21 on osx-arm64 with the same data and it did not crash.

Version

• bcftools 1.23.1

Commands

samtools faidx mini.fa
bcftools csq -f mini.fa -g mini.gff --phase m -Ov -o out.vcf mini.vcf

Actual result

Parsing mini.gff ...
Indexed 1 transcripts, 0 exons, 1 CDSs, 0 UTRs
Calling...
This should not happen... mini:2216  (null)

Controls

1. The insertion alone does not crash:

bcftools csq -f mini.fa -g mini.gff --phase m -Ov -o single.out.vcf mini.single.vcf

2. Localized mode also succeeds:

bcftools csq -l -f mini.fa -g mini.gff --phase m -Ov -o local.out.vcf mini.vcf

bcftools-csq-compound-bug.tar.gz