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No exploitation reportedFix available

CVE-2026-31963

No exploitation reported by the sources we read.

  • Published2026-03-18
  • Fixed in1.22.2 · 1.21.1
  • WeaknessCWE-122 · CWE-129 · CWE-787

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. As one method of removing redundant data, CRAM uses reference-based compression so that instead of storing the full sequence for each alignment record it stores a location in an external reference sequence along with a list of differences to the reference at that location as a sequence of "features". When decoding these features, an out-by-one error in a test for CRAM features that appear beyond the extent of the CRAM record sequence could result in an invalid write of one attacker-controlled byte beyond the end of a heap buffer. 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. 2026-03-1819:16CVE 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

4 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 3.18.1read 2026-10-23
  • CNAweakness (CWE)CWE-122, CWE-129, CWE-787known since 2026-10-23
  • FIRST EPSSEPSS score0.4 %2026-11-08
  • OSVaffected packages—

Identifiers

Technical details

CVSS v3 Vector
CVSS:3.1/AV:N/AC:L/PR:N/UI:R/S:U/C:N/I:H/A:H
CVSS 4.0 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/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-2026-31963?

HTSlib is a library for reading and writing bioinformatics file formats. CRAM is a compressed format which stores DNA sequence alignment data. As one method of removing redundant data, CRAM uses reference-based compression so that instead of storing the full sequence for each alignment record it stores a location in an external reference sequence along with a list of differences to the reference at that location as a sequence of "features". When decoding these features, an out-by-one error in a test for CRAM features that appear beyond the extent of the CRAM record sequence could result in an invalid write of one attacker-controlled byte beyond the end of a heap buffer. 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-2026-31963 actively exploited?

Active exploitation of CVE-2026-31963 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-2026-31963?

CVE-2026-31963 has a CVSS v3 base score of 8.1 (HIGH severity), with vector string CVSS:3.1/AV:N/AC:L/PR:N/UI:R/S:U/C:N/I:H/A:H.

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