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High · 7.1 CVE-2026-31969 EUVD-2026-12944

HTSlib CRAM decoder has a heap buffer overflow

Published Mar 18, 2026 · Updated Mar 18, 2026 · Assigned by GitHub_M

Description

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.

Affected products

VendorProductAffectedFixed
samtools htslib < 1.21.1, >= 1.22, < 1.22.2, = 1.23 —

Fixed in Linux distributions

Distributions backport fixes, so the version that fixes this vulnerability differs per release — upgrade to at least the version shown. From the distributions' security trackers and advisories.

ReleasePackageFixed inAdvisory
Debian 14 htslib 1.24-2 —
Debian 13 htslib No fix yet —
Debian 12 htslib No fix yet —
ReleasePackageFixed inAdvisory
Ubuntu 26.10 htslib No fix yet —
Ubuntu 26.04 LTS htslib No fix yet —
Ubuntu 25.10 htslib No fix yet —
Ubuntu 24.04 LTS htslib No fix yet —
Ubuntu 22.04 LTS htslib No fix yet —
Show 4 more (older releases, extended support, other products)
ReleasePackageFixed inAdvisory
Ubuntu 20.04 LTS htslib No fix yet —
Ubuntu Pro 18.04 LTS htslib No fix yet —
Ubuntu Pro 16.04 LTS htslib No fix yet —
Ubuntu Pro 14.04 LTS htslib No fix yet —

References