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No exploitation reportedFix available

CVE-2026-31962

No exploitation reported by the sources we read.

  • Published2026-03-18
  • Fixed in1.22.2 · 1.21.1
  • WeaknessCWE-122 · CWE-125 · CWE-129

Am I affected?

With a domain, we read the version its public headers and pages expose. A distribution build can carry the fix under an older number.

Description

HTSlib is a library for reading and writing bioinformatics file formats. CRAM is a compressed format which stores DNA sequence alignment data. While most alignment records store DNA sequence and quality values, the format also allows them to omit this data in certain cases to save space. Due to some quirks of the CRAM format, it is necessary to handle these records carefully as they will actually store data that needs to be consumed and then discarded. Unfortunately the `cram_decode_seq()` did not handle this correctly in some cases. Where this happened it could result in reading a single byte from beyond the end of a heap allocation, followed by writing a single attacker-controlled byte to the same location. 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.

Timeline

dates in UTC
  1. 2026-03-1818:16CVE publishedNVD

Versions per branch

NVD
Htslib
BranchAffectedFixed in
1.22≥ 1.22, < 1.22.21.22.2
1.21< 1.21.11.21.1
1.23= 1.23no fix published

as publishedRanges as NVD and OSV publish them; a distribution’s build can be fixed under an older number.

Products declared by the CNA1 product

As GitHub_M, the CNA that assigned this CVE, declared them in the CVE record; versions as written.

  • samtools htslib
    Affected
    • = < 1.21.1no fix stated
    • = >= 1.22, < 1.22.2no fix stated
    • = = 1.23no fix stated

Source: the CNA record (CVE Program), © The MITRE Corporation,CVE Terms of UseCVE recordupdated 2026-03-18

Distribution builds and vendor advisories

Packages from OSV.dev and products from the vendors' CSAF advisories.

version not verifiedVersions not verified: read as OSV.dev and the vendors publish them, not checked against each vendor's release list.

Packages

  • htslibUbuntu:Pro:18.04:LTSall versions · no fixed version listed
  • htslibUbuntu:Pro:16.04:LTSall versions · no fixed version listed
  • htslibUbuntu:Pro:14.04:LTSall versions · no fixed version listed
  • htslibUbuntu:26.10all versions · no fixed version listed
  • htslibUbuntu:26.04:LTSall versions · no fixed version listed
  • htslibUbuntu:25.10all versions · no fixed version listed
  • htslibUbuntu:24.04:LTSall versions · no fixed version listed
  • htslibUbuntu:22.04:LTSall versions · no fixed version listed

7 more package ranges on OSV.dev

Full record on NVD

Fix

  1. Update Htslib to 1.22.2 · 1.21.1

Advisories and patches

Detection

Nuclei template
none so far
ProjectDiscovery
Exploit-DB
no entry
Exploit-DB
Proof of concept
Metasploit modules
none listed
Metasploit Framework

Sources

  • CISA-ADPSSVC decisionnone2026-03-18
  • CNACVSS 4.08.8known since 2026-10-23
  • NVDCVSS 3.18.8read 2026-10-23
  • CNAweakness (CWE)CWE-122, CWE-125, CWE-129, CWE-787known since 2026-10-23
  • FIRST EPSSEPSS score0.4 %2026-11-08
  • OSVaffected packages—

Identifiers

  • EUVD-2026-12923same flawENISA EUVD · LicenseRef-ENISA-legal-notice
  • OESA-2026-2547advisory covering several CVEsopenEuler · LicenseRef-unstated
  • OESA-2026-2757advisory covering several CVEsopenEuler · LicenseRef-unstated
  • OESA-2026-3491advisory covering several CVEsopenEuler · LicenseRef-unstated

Technical details

CVSS v3 Vector
CVSS:3.1/AV:N/AC:L/PR:N/UI:R/S:U/C:H/I:H/A:H
CVSS 4.0 vector
CVSS:4.0/AV:N/AC:L/AT:N/PR:N/UI:N/VC:L/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
Published
2026-03-18
Last Modified
2026-06-17
NVD status
Analyzed

Frequently asked questions

What is CVE-2026-31962?

HTSlib is a library for reading and writing bioinformatics file formats. CRAM is a compressed format which stores DNA sequence alignment data. While most alignment records store DNA sequence and quality values, the format also allows them to omit this data in certain cases to save space. Due to some quirks of the CRAM format, it is necessary to handle these records carefully as they will actually store data that needs to be consumed and then discarded. Unfortunately the `cram_decode_seq()` did not handle this correctly in some cases. Where this happened it could result in reading a single byte from beyond the end of a heap allocation, followed by writing a single attacker-controlled byte to the same location. 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.

Is CVE-2026-31962 actively exploited?

Active exploitation of CVE-2026-31962 has not been confirmed. Its EPSS score was 0.4% on 2026-11-08, the estimated probability of exploitation in the next 30 days.

What is the CVSS score for CVE-2026-31962?

CVE-2026-31962 has a CVSS v3 base score of 8.8 (HIGH severity), with vector string CVSS:3.1/AV:N/AC:L/PR:N/UI:R/S:U/C:H/I:H/A:H.

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