From c814d3983fc3f04fdedcdc3f359d369f7d877cbd Mon Sep 17 00:00:00 2001
From: Rob Davies <rmd+git@sanger.ac.uk>
Date: Tue, 28 Jan 2025 10:27:23 +0000
Subject: [PATCH] Reset variant types after updating alleles

Variant type calls produced by bcf_set_variant_types() may be
stale after updating alleles via bcf_update_alleles() or
bcf_update_alleles_str(), so set d.var_type to -1 to force
a recalculation.

Fixes an out of bounds access in bcftools consensus that occurred
when it added a new allele to a record.
---
 vcf.c | 1 +
 1 file changed, 1 insertion(+)

diff --git a/vcf.c b/vcf.c
index 549fcb710..ba68825df 100644
--- a/vcf.c
+++ b/vcf.c
@@ -5495,6 +5495,7 @@ int bcf_has_filter(const bcf_hdr_t *hdr, bcf1_t *line, char *filter)
 static inline int _bcf1_sync_alleles(const bcf_hdr_t *hdr, bcf1_t *line, int nals)
 {
     line->d.shared_dirty |= BCF1_DIRTY_ALS;
+    line->d.var_type = -1;
 
     line->n_allele = nals;
     hts_expand(char*, line->n_allele, line->d.m_allele, line->d.allele);