CVE-2026-31965 | HTSlib CRAM reader has out-of-bounds reads 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. In the `cram_decode_slice()` function called while reading CRAM records, validation of the reference id field occurred too late, allowing two out of bounds reads to occur before the invalid data was detected. The bug does allow two values to be leaked to the caller, however as the function reports an error it may be difficult to exploit them. It is also possible that the program will crash due to trying 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.

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-2026-31965 is rated Low Risk (29.3/100): CVSS Medium severity, with low exploitation likelihood (EPSS 0.02%). Monitor for updates and reassess as exploit intelligence or EPSS changes.

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-2026-31965

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 2026-04-21 0.05% 0.02% -0.03%
2 2026-03-24 0.04% 0.05% +0.01%
3 2026-03-19 — 0.04% —

Full EPSS history (3 records total)

Common vulnerability scoring system (CVSS) metrics for CVE-2026-31965

CVSS metrics for this CVE.

Base score Version Severity Vector Exploitability Impact Score source
6.9 4.0 MEDIUM
CVSS:4.0/AV:N/AC:L/AT:N/PR:N/UI:N/VC:L/VI:N/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:N)
No 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]
8.2 3.1 HIGH
CVSS:3.1/AV:N/AC:L/PR:N/UI:N/S:U/C:L/I:N/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:N)
Nobody has to click “OK” or open a trap file; it can work without a victim helping.
Scope (S:U)
Damage stays in the same “trust bubble” as the broken component—no big spill into unrelated systems.
Confidentiality (C:L)
Some sensitive info could get out, but not a total data dump.
Integrity (I:N)
Data isn’t meaningfully altered or forged.
Availability (A:H)
Could take the service down hard or make it unusable for people who depend on it.
 3.9 4.2 [email protected]

Weakness enumeration for CVE-2026-31965

OS Trackers for CVE-2026-31965

vendor priority summary link
debian not yet assigned CVE-2026-31965 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-2026-31965
redhat medium — https://access.redhat.com/security/cve/CVE-2026-31965
ubuntu medium CVE-2026-31965 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-2026-31965

Affected software / configurations for CVE-2026-31965

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-2026-31965

cvelogic Threat Intelligence