HTSlib is a library for reading and writing bioinformatics file formats. CRAM is a compressed format which stores DNA sequence alignment data using a variety of encodings and compression methods. When reading data encoded using the BYTE_ARRAY_STOP method, an out-by-one error in the cram_byte_array_stop_decode_char() function check for a full output buffer could result in a single attacker-controlled byte being written beyond the end of a heap allocation. Exploiting this bug causes a heap buffer overflow. If a user opens a file crafted to exploit this issue, it could lead to the program crashing, or overwriting of data and heap structures in ways not expected by the program. It may be possible to use this to obtain arbitrary code execution. Versions 1.23.1, 1.22.2 and 1.21.1 include fixes for this issue. There is no workaround for this issue.
This page covers CVE-2026-31969 as tracked by Debian, for the package htslib. No fixed version has been recorded for this distribution yet.
This issue can be reached over the network, attack complexity is low, an attacker needs no privileges on the target. A user must be tricked into taking some action. The scope is unchanged, so the impact stays within the vulnerable component. Rated impact: confidentiality none, integrity high, availability high.
The score comes from this vector: CVSS:3.1/AV:N/AC:L/PR:N/UI:R/S:U/C:N/I:H/A:H
DEBIAN-CVE-2026-31969 is classified as CWE-122: Heap-based Buffer Overflow. A write past the end of a heap allocation corrupts allocator metadata or neighbouring objects.
DEBIAN-CVE-2026-31969 is recorded against 1 package.
Published on 18 March 2026 and last revised on 4 August 2026. No public exploit is currently recorded for this entry. Record sourced from OSV.
security-tracker.debian.org (Advisory)
htslib has other advisories on record. If you are patching this one, these are worth checking on the same host:
These advisories are the same class of weakness (CWE-122: Heap-based Buffer Overflow) in other software:
Each distribution ships its own build and its own fixed version. Pick the one you run:
Details
CVSS:3.1/AV:N/AC:L/PR:N/UI:R/S:U/C:N/I:H/A:H
Affected Packages
| Software | From version | Fixed in |
|---|---|---|
| htslib | — | — |
References
Similar Threats
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