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Vulnerability record · CVE-2026-31968 · published 18 March 2026

CVE-2026-31968: Htslib stack-based buffer overflow vulnerability

HHtslib · Htslib

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.

8.8 CVSS 4.0 High EPSS 0.52% · top 58.2% CWE-121 · Stack-based buffer overflowCWE-122 · Heap-based buffer overflow
8.8CVSS 4.0 base score
0.52%EPSS exploitation probability, 30 days
NoNot in CISA KEV
1Affected product versions listed by NVD
2References
17 Jun 2026Last modified by NVD

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.

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/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:

Affected products

1 vulnerable configurations from NVD's CPE data, grouped by vendor and product.

References

LinkTags
https://github.com/samtools/htslib/commit/0ec436796eca7b4ce7fcc9b77270c102da29bb2e Patch
https://github.com/samtools/htslib/security/advisories/GHSA-cgcm-c9r2-p57j PatchVendor Advisory

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Related vulnerabilities

Same products first, then exploited flaws of the same weakness class.

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Source: NIST National Vulnerability Database (record CVE-2026-31968), CISA KEV, FIRST EPSS (scores of 2026-09-27). This page is refreshed as NVD updates the record.