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Fix a bug in breakend detection #1858

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Nov 19, 2024
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@pd3 pd3 commented Nov 17, 2024

it was incorrectly assumed that the ALT allele is
of equal length to REF allele, but the VCF specification allows breakend insertions, such as C > CAGTNNNNNCA[2:321682[

Resolves samtools/bcftools#2317

it was incorrectly assumed that the ALT allele is
of equal length to REF allele, but the VCF specification
allows breakend insertions, such as C > CAGTNNNNNCA[2:321682[

Resolves samtools/bcftools#2317
pd3 added a commit to samtools/bcftools that referenced this pull request Nov 17, 2024
@daviesrob daviesrob merged commit a662866 into samtools:develop Nov 19, 2024
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bcftools norm can not handle insertion-breakend entries with fasta reference (VCF4.3+)
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