CVE-2026-31962 | HTSlib CRAM reader has heap buffer overflow due to improper validation of input

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.

Published: 2026-03-18 Last update: 2026-03-19 Assigner: [email protected] Source: [email protected]
NVD Status：Analyzed，CVE State: published
View at NVD, CVE.org, EUVD

CVE-2026-31962 is rated Moderate Risk (43.1/100): CVSS High severity, with low exploitation likelihood (EPSS 0.08%). Review affected assets and schedule remediation.

Risk is dynamic; we continuously reassess and refresh what is shown on this page as upstream context changes.

Exploit prediction scoring system (EPSS) score for CVE-2026-31962

EPSS lead: Daily EPSS estimates relative likelihood of exploitation; percentile ranks this CVE among scored vulnerabilities (higher = more severe relative rank).

# Date Old EPSS score New EPSS score Delta (New - Old)
1 2026-03-19 — 0.08% —

Full EPSS history (1 record total)

Common vulnerability scoring system (CVSS) metrics for CVE-2026-31962

CVSS metrics for this CVE.

Base score Version Severity Vector Exploitability Impact Score source
8.8 4.0 HIGH
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 Click to expand
Attack vector (AV:N)
Could be attacked over the internet or any normal routed network.
Attack complexity (AC:L)
Exploitation conditions are straightforward and stable.
Attack requirements (AT:N)
No additional preconditions are required beyond normal reachability.
Privileges required (PR:N)
No privileges are required.
User interaction (UI:N)
No user interaction is required.
Vulnerable system confidentiality impact (VC:L)
Limited confidentiality impact on the vulnerable system.
Vulnerable system integrity impact (VI:H)
High integrity impact on the vulnerable system.
Vulnerable system availability impact (VA:L)
Limited availability impact on the vulnerable system.
Subsequent system confidentiality impact (SC:N)
No confidentiality impact on subsequent systems.
Subsequent system integrity impact (SI:N)
No integrity impact on subsequent systems.
Subsequent system availability impact (SA:N)
No availability impact on subsequent systems.
Exploit maturity (threat) (E:X)
Not defined: no reliable threat intelligence; scoring assumes the worst case (equivalent to Attacked).
Confidentiality requirement (CR:X)
Not defined: insufficient information; scoring treats this like High (worst case).
Integrity requirement (IR:X)
Not defined: insufficient information; scoring treats this like High (worst case).
Availability requirement (AR:X)
Not defined: insufficient information; scoring treats this like High (worst case).
Modified attack vector (MAV:X)
Not defined: scoring uses the Base Attack Vector (AV).
Modified attack complexity (MAC:X)
Not defined: scoring uses the Base Attack Complexity (AC).
Modified attack requirements (MAT:X)
Not defined: scoring uses the Base Attack Requirements (AT).
Modified privileges required (MPR:X)
Not defined: scoring uses the Base Privileges Required (PR).
Modified user interaction (MUI:X)
Not defined: scoring uses the Base User Interaction (UI).
Modified vulnerable system confidentiality impact (MVC:X)
Not defined: scoring uses the Base VC metric.
Modified vulnerable system integrity impact (MVI:X)
Not defined: scoring uses the Base VI metric.
Modified vulnerable system availability impact (MVA:X)
Not defined: scoring uses the Base VA metric.
Modified subsequent system confidentiality impact (MSC:X)
Not defined: scoring uses the Base SC metric.
Modified subsequent system integrity impact (MSI:X)
Not defined: scoring uses the Base SI metric.
Modified subsequent system availability impact (MSA:X)
Not defined: scoring uses the Base SA metric.
Safety (supplemental) (S:X)
Not evaluated.
Automatable (supplemental) (AU:X)
Not evaluated.
Recovery (supplemental) (R:X)
Not evaluated.
Value density (supplemental) (V:X)
Not evaluated.
Vulnerability response effort (supplemental) (RE:X)
Not evaluated.
Provider urgency (supplemental) (U:X)
Not evaluated.
 — — [email protected]
8.8 3.1 HIGH
CVSS:3.1/AV:N/AC:L/PR:N/UI:R/S:U/C:H/I:H/A:H Click to expand
Attack vector (AV:N)
Could be attacked over the internet or any normal routed network—not just someone sitting at the machine.
Attack complexity (AC:L)
Once they can reach the bug, pulling it off is straightforward—no weird race conditions or rare setup.
Privileges required (PR:N)
No account or special rights needed—anonymous or random user is enough.
User interaction (UI:R)
A real person has to do something—click, install, enable—otherwise it doesn’t land.
Scope (S:U)
Damage stays in the same “trust bubble” as the broken component—no big spill into unrelated systems.
Confidentiality (C:H)
Serious risk that confidential data gets exposed in a big way.
Integrity (I:H)
They could widely tamper with or forge data—trust in the data is badly hurt.
Availability (A:H)
Could take the service down hard or make it unusable for people who depend on it.
 2.8 5.9 [email protected]

Weakness enumeration for CVE-2026-31962

OS Trackers for CVE-2026-31962

vendor priority summary link
debian not yet assigned CVE-2026-31962 not yet assigned priority: Debian including 1 source packages (htslib), 5 status rows across 5 suites (bookworm, bullseye, forky, sid, trixie): open 5. https://security-tracker.debian.org/tracker/CVE-2026-31962
redhat high — https://access.redhat.com/security/cve/CVE-2026-31962
ubuntu medium CVE-2026-31962 medium priority: Ubuntu including 1 source packages (htslib), 8 status rows across 8 suites (bionic, focal, jammy, noble, questing, trusty, upstream, xenial): needs-triage 8. https://ubuntu.com/security/CVE-2026-31962

Affected software / configurations for CVE-2026-31962

Vendor Product Version Raw CPE
htslib htslib < 1.21.1 cpe:2.3:a:htslib:htslib:*:*:*:*:*:*:*:*
htslib htslib >= 1.22, < 1.22.2 cpe:2.3:a:htslib:htslib:*:*:*:*:*:*:*:*
htslib htslib 1.23 cpe:2.3:a:htslib:htslib:1.23:*:*:*:*:*:*:*

References for CVE-2026-31962

cvelogic Threat Intelligence