What’s Vulnerable › Vulnerabilities

CVE-2026-116742: HTSlib through 1.24 Heap Out-of-Bounds Write via Truncated .gzi Index Count

• Severity: medium (CVSS 4.4 v3.1)
• Exploited in the wild: not listed in CISA KEV
• EPSS: 0.1% probability of exploitation in the next 30 days
• Public exploit or detection template: none known
• Published: 2026-10-26 · updated 2026-10-27
• Weakness: CWE-197

Description

HTSlib through 1.24 contains a heap out-of-bounds write and read vulnerability in bgzf_index_load_hfile() in bgzf.c that allows attackers to corrupt heap memory by supplying a crafted .gzi index entry count. A count of 0xFFFFFFFF truncates noffs to zero, causing writes past a malloc(0) buffer and an offs[-1] read in bgzf_useek(), resulting in heap corruption or crashes in tools like samtools and bcftools.

Affected products

• samtools htslib: through 1.24

References

• https://github.com/samtools/htslib
• https://github.com/samtools/htslib/blob/1.24/bgzf.c#L2504
• https://github.com/samtools/htslib/commit/18dddf02bb2c0053b32acec427723555a24b2873
• https://github.com/samtools/htslib/issues/2113
• https://github.com/samtools/htslib/pull/2057
• https://hackmd.io/@haindpwn/htslib-bgzf-gzi-int-truncation-oob
• https://www.vulncheck.com/advisories/htslib-through-1.24-heap-out-of-bounds-write-via-truncated-gzi-index-count

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