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. For the `VARINT` and `CONST` encodings, incomplete validation of the context in which the encodings were used could result in up to eight bytes being written beyond the end of a heap allocation, or up to eight bytes being written to the location of a one byte variable on the stack, possibly causing the values to adjacent variables to change unexpectedly. Depending on the data stream this could result either in a heap buffer overflow or a stack overflow. If a user opens a file crafted to exploit this issue it could lead to the program crashing, overwriting of data structures on the heap or stack in ways not expected by the program, or changing the control flow of 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.
Published: 2026-03-18
Score: 8.8 High
EPSS: < 1% Very Low
KEV: No
Impact: Heap/Stack Buffer Overflow with potential arbitrary code execution
Action: Patch Immediately
AI Analysis

Impact

The vulnerability occurs in HTSlib's CRAM decoder when processing VARINT and CONST encodings; missing validation can allow up to eight bytes to be written beyond the allocated buffer, causing a heap or stack overflow. Attack via a maliciously crafted CRAM file could crash the application, corrupt internal data structures, or modify control flow, potentially leading to arbitrary code execution.

Affected Systems

The issue affects the htslib library used by samtools. Versions earlier than 1.23.1, 1.22.2 and 1.21.1 are vulnerable. The fix is included in v1.23.1, v1.22.2, and v1.21.1.

Risk and Exploitability

The CVSS score is 8.8, indicating high severity, while the EPSS score is less than 1%, suggesting a low likelihood of exploitation. The vulnerability is not listed in the CISA KEV catalog. Exploitation requires an attacker to supply a maliciously crafted CRAM file that an application using HTSlib will parse; thus the primary vector is a file-based attack.

Generated by OpenCVE AI on March 19, 2026 at 18:25 UTC.

Remediation

No vendor fix or workaround currently provided.

OpenCVE Recommended Actions

  • Upgrade htslib to v1.23.1 or later (or v1.22.2/v1.21.1 if constrained).
  • Validate CRAM files and restrict processing to trusted sources; monitor for abnormal crashes or memory corruption.

Generated by OpenCVE AI on March 19, 2026 at 18:25 UTC.

Tracking

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Advisories

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History

Thu, 19 Mar 2026 17:45:00 +0000

Type Values Removed Values Added
First Time appeared Htslib
Htslib htslib
CPEs cpe:2.3:a:htslib:htslib:*:*:*:*:*:*:*:*
cpe:2.3:a:htslib:htslib:1.23:*:*:*:*:*:*:*
Vendors & Products Htslib
Htslib htslib
Metrics cvssV3_1

{'score': 8.1, 'vector': 'CVSS:3.1/AV:N/AC:L/PR:N/UI:R/S:U/C:N/I:H/A:H'}

Thu, 19 Mar 2026 09:45:00 +0000

Type Values Removed Values Added
First Time appeared Samtools
Samtools htslib
Vendors & Products Samtools
Samtools htslib

Wed, 18 Mar 2026 20:15:00 +0000

Type Values Removed Values Added
Metrics ssvc

{'options': {'Automatable': 'yes', 'Exploitation': 'none', 'Technical Impact': 'partial'}, 'version': '2.0.3'}

Wed, 18 Mar 2026 19:45:00 +0000

Type Values Removed Values Added
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. For the `VARINT` and `CONST` encodings, incomplete validation of the context in which the encodings were used could result in up to eight bytes being written beyond the end of a heap allocation, or up to eight bytes being written to the location of a one byte variable on the stack, possibly causing the values to adjacent variables to change unexpectedly. Depending on the data stream this could result either in a heap buffer overflow or a stack overflow. If a user opens a file crafted to exploit this issue it could lead to the program crashing, overwriting of data structures on the heap or stack in ways not expected by the program, or changing the control flow of 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.
Title HTSlib CRAM decoder vulnerable to buffer overflow
Weaknesses CWE-121
CWE-122
CWE-787
CWE-843
References
Metrics cvssV4_0

{'score': 8.8, 'vector': 'CVSS:4.0/AV:N/AC:L/AT:N/PR:N/UI:N/VC:N/VI:H/VA:L/SC:N/SI:N/SA:N'}

Subscriptions

Htslib Htslib
Samtools Htslib
cve-icon MITRE

Status: PUBLISHED

Assigner: GitHub_M

Published:

Updated: 2026-03-18T19:57:36.668Z

Reserved: 2026-03-10T15:40:10.485Z

Link: CVE-2026-31968

cve-icon Vulnrichment

Updated: 2026-03-18T19:57:27.324Z

cve-icon NVD

Status : Analyzed

Published: 2026-03-18T20:16:21.480

Modified: 2026-03-19T17:31:24.010

Link: CVE-2026-31968

cve-icon Redhat

No data.

cve-icon OpenCVE Enrichment

Updated: 2026-03-25T11:52:22Z

Weaknesses