CVE-2026-31963 | 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. 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.

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-2026-31963 is rated Moderate Risk (40.9/100): CVSS High severity, with low exploitation likelihood (EPSS 0.05%). 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-2026-31963

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 2026-04-19 0.04% 0.05% +0.01%
2 2026-03-20 0.08% 0.04% -0.03%
3 2026-03-19 — 0.08% —

Full EPSS history (3 records total)

Common vulnerability scoring system (CVSS) metrics for CVE-2026-31963

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: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 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:N)
No 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]
8.1 3.1 HIGH
CVSS:3.1/AV:N/AC:L/PR:N/UI:R/S:U/C:N/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:N)
Doesn’t really leak secrets in a meaningful 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 5.2 [email protected]

Weakness enumeration for CVE-2026-31963

OS Trackers for CVE-2026-31963

vendor priority summary link
debian not yet assigned CVE-2026-31963 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-2026-31963
redhat high — https://access.redhat.com/security/cve/CVE-2026-31963
ubuntu medium CVE-2026-31963 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-2026-31963

Affected software / configurations for CVE-2026-31963

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-2026-31963

cvelogic Threat Intelligence