HTSlib is a library for reading and writing bioinformatics file formats. CRAM is a compressed format which stores DNA sequence alignment data using a variety of encodings and compression methods. 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 CONST, XPACK and XRLE encodings did not properly implement the interface needed to do this. Trying to decode records with omitted sequence or quality data using these encodings would result in an attempt to write to a NULL pointer. Exploiting this bug causes a NULL pointer dereference. Typically this will cause the program to crash. Versions 1.23.1, 1.22.2 and 1.21.1 include fixes for this issue. There is no workaround for this issue.
CVE-2026-31964
This high-severity CVE scores 7.5 under NVD CVSS v3. EPSS exploit-prediction score not yet available (the EPSS model rescores nightly; freshly-published CVEs typically appear within 48 hours). GitHub Security Advisory data not yet ingested — confidence will rise once GHSA publishes (typical lag: hours to days for open-source ecosystem CVEs; never for infrastructure-only CVEs).
- High severity, but no confirmed exploitation yet
No vendor fix yet — apply a workaround or compensating control (WAF / firewall / segmentation) and watch for a patch.
- CVSS v3
- 7.5
- EG Score
- 7.5(low)
- EG Risk
- 38(Track)EG Risk 38/100SSVC: Track
EG Risk is EchelonGraph's 0–100 priority score: it fuses intrinsic severity with real-world exploitation and automatability so you can rank equal-severity CVEs and fix the most dangerous first. Higher = act sooner. Distinct from the 0–10 EG Score (severity).
How it’s computedSeverity75% × 45%Exploitation0% × 40%Automatability30% × 15%Action: Routine — remediate on your standard cadence. - EPSS PROB
- 0%
- EPSS %ILE
- 25%
- KEV
- Not listed
Published
March 18, 2026
Last Modified
June 17, 2026
References (2)
- security-advisories@githubhttps://github.com/samtools/htslib/commit/e64e68da567d2309509d059ace016d5d7fc7514f
- security-advisories@githubhttps://github.com/samtools/htslib/security/advisories/GHSA-5w97-85gf-86rm
Weakness Classification(1)
MITRE Common Weakness Enumeration — the root-cause categories this CVE belongs to.
Data Freshness Timeline
(refreshed 5× in last 7d / 5× in last 30d)
Each row is a source pipeline that fetched or updated this CVE on that date, with what changed. For example, "NVD update" means NVD published or revised its analysis for this CVE; "MITRE cvelistV5" means we ingested or refreshed it from the CNA feed. Most recent first.
- 2026-07-30 16:28 UTCEPSS rescore
- 2026-07-30 01:30 UTCEPSS rescore
- 2026-07-28 15:36 UTCEPSS rescore
- 2026-07-27 14:41 UTCEG score recompute
- 2026-07-27 14:27 UTCOSV refresh
Related CVEs(same CWE)
Frequently asked(5)
What is CVE-2026-31964?
When was CVE-2026-31964 disclosed?
Is CVE-2026-31964 actively exploited?
What is the CVSS score of CVE-2026-31964?
How do I remediate CVE-2026-31964?
Dependency Blast Radius
Explore the affected products and dependency analysis for CVE-2026-31964
Is Your Infrastructure Affected by CVE-2026-31964?
EchelonGraph automatically scans your cloud infrastructure and maps CVE exposure using blast radius analysis.