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CVE-2026-31969

HTSlib CRAM decoder has a heap buffer overflow

High7.1EPSS 0.36%
Published
Updated
Reserved
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.

Scores

CVSS scores of CVE-2026-31969, by who scored it
Scored byCVSSScoreVector
GitHub_MCNA (assigner)4.0High7.1CVSS:4.0/AV:N/AC:L/AT:N/PR:N/UI:P/VC:N/VI:H/VA:L/SC:N/SI:N/SA:N
NVDNVD · Analyzed4.0High7.1CVSS:4.0/AV:N/AC:L/AT:N/PR:N/UI:P/VC:N/VI:H/VA:L/SC:N/SI:N/SA:N/E:X/CR:X/IR:X/AR:X/MAV:X/MAC:X/MAT:X/MPR:X/MUI:X/MVC:X/MVI:X/MVA:X/MSC:X/MSI:X/MSA:X/S:X/AU:X/R:X/V:X/RE:X/U:X
EPSS (exploitation in 30 days)
0.36% · top 70% of all CVEs (6 Nov 2026)
CISA SSVC
Exploitation: none · Automatable: no · Technical impact: partial
Loading the EPSS history…

The list uses the assigner's score when there is one, then CISA's, then NVD's: High 7.1.

Weakness

Affected products

  • samtools · htslib

    • affected < 1.21.1
    • affected >= 1.22, < 1.22.2
    • affected = 1.23

References (2)

Sources

The same CVE in the primary databases and aggregators, to check against.

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Record last updated .