Home/CVE/HTSlib is a library for reading and writing bioinformatics file formats. CRAM is a compressed format which stores DNA se
CVE

CVE-2026-31967

HTSlib is a library for reading and writing bioinformatics file formats. CRAM is a compressed format which stores DNA se

HTSlib is a library for reading and writing bioinformatics file formats. CRAM is a compressed format which stores DNA sequence alignment data. In the cram_decode_slice() function called while reading CRAM records, the value of the mate reference id field was not validated.

Later use of this value, for example when converting the data to SAM format, could result in the out of bounds array reads when looking up the corresponding reference name. If the array value obtained also happened to be a valid pointer, it would be interpreted as a string and an attempt would be made to write the data as part of the SAM record. This bug may allow information about program state to be leaked.

It may also cause a program crash through an attempt to access invalid memory. Versions 1.23.1, 1.22.2 and 1.21.1 include fixes for this issue. There is no workaround for this issue.

CRITICAL · CVSS 9.1 EPSS 0.00024
Schedule remediation
  • SSVC automatable: yes - attacks can be scripted at scale
  • CVSS base score ≥ 7.0
Sigma rules0 YARA rules0
⬡

Weakness Classification

CWE-125Out-of-bounds Read
CWE-129Improper Validation of Array Index
▤

Affected Products & Versions

3
htslib< 1.21.1
htslib>= 1.22 and < 1.22.2
htsliball versions
▣

Scoring & Timeline

9.1
CRITICAL · CVSS v3.1 · security-advisories@github.com
View on NVD
Attack Vector
Network Adjacent Local Physical
Attack Complexity
Low High
Privileges Required
None Low High
User Interaction
None Required
Scope
Unchanged Changed
Confidentiality
None Low High
Integrity
None Low High
Availability
None Low High
Published to NVD18 Mar 2026 · 08:16 PM
CVSS VectorCVSS:3.1/AV:N/AC:L/PR:N/UI:N/S:U/C:H/I:N/A:H
SSVC triage · cisa-vulnrichment
Exploitation
none
Automatable
yes
Technical impact
partial
SSVC asks the questions that actually drive patch urgency: is it being exploited, can attacks be automated, and how total is the impact.
🔗

References & Sources

2
Source URLs (vendor pages, mailing lists, write-ups). Exploit/PoC links are in their own section above to avoid duplication.
https://github.com/samtools/htslib/commit/9cefb46453ad471e933b8212d4f45920524d3357Patch
https://github.com/samtools/htslib/security/advisories/GHSA-33x5-c6vj-8f2wPatchVendor Advisory
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