CVE-2026-31965
CVE-2026-31965 is a high-severity vulnerability in Htslib with a CVSS 3.x base score of 8.2. It is not currently listed as actively exploited by CISA, and its EPSS exploit-prediction score is low. The underlying weakness is classified as CWE-125.
Key facts
- Severity: High (CVSS 3.x base score 8.2)
- CVSS v4: 6.9
- EPSS exploit prediction: 0% (29th percentile)
- Actively exploited: Not listed in CISA KEV
- EU (EUVD) id: EUVD-2026-12934
- Weakness: CWE-125
- Affected product: Htslib
- Published:
- Last modified:
Description
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.
Frequently asked questions
- What is CVE-2026-31965?
- 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.
- How severe is CVE-2026-31965?
- CVE-2026-31965 has a CVSS 3.x base score of 8.2, rated high severity. It is exploitable over network with low attack complexity, requires no privileges and no user interaction. Impact on confidentiality is low, integrity none, and availability high.
- Is CVE-2026-31965 being actively exploited?
- It is not currently listed in CISA's KEV catalog. Its EPSS exploit-prediction score is 0% (29th percentile), an estimate of the probability of exploitation in the next 30 days.
- What products are affected by CVE-2026-31965?
- CVE-2026-31965 primarily affects Htslib. In total, 2 product configurations (CPEs) are listed as vulnerable; see the affected-products list for the exact versions.
- How do I fix CVE-2026-31965?
- Review the linked vendor and NVD advisories for patched versions and mitigations, then upgrade or apply the recommended workaround. Given its high severity, prioritise patching exposed systems.
- Does CVE-2026-31965 have an EU (EUVD) identifier?
- Yes. CVE-2026-31965 is tracked in the ENISA EU Vulnerability Database (EUVD) as EUVD-2026-12934.
- When was CVE-2026-31965 published?
- CVE-2026-31965 was published on 2026-03-18 and last updated on 2026-06-17.
References
- https://github.com/samtools/htslib/commit/9cefb46453ad471e933b8212d4f45920524d3357
- https://github.com/samtools/htslib/security/advisories/GHSA-mqm2-v645-3qhr
Affected products (2)
- cpe:2.3:a:htslib:htslib:*:*:*:*:*:*:*:*
- cpe:2.3:a:htslib:htslib:1.23:*:*:*:*:*:*:*
More vulnerabilities in Htslib
- CVE-2018-13845 — Critical (CVSS 9.8): An issue has been found in HTSlib 1.8. It is a buffer over-read in sam_parse1 in sam.c.
- CVE-2017-1000206 — Critical (CVSS 9.8): samtools htslib library version 1.4.0 and earlier is vulnerable to buffer overflow in the CRAM rANS codec resulting in…
- CVE-2026-31967 — Critical (CVSS 9.1): HTSlib is a library for reading and writing bioinformatics file formats. CRAM is a compressed format which stores DNA…
- CVE-2026-31966 — Critical (CVSS 9.1): HTSlib is a library for reading and writing bioinformatics file formats. CRAM is a compressed format which stores DNA…
- CVE-2026-31962 — High (CVSS 8.8): HTSlib is a library for reading and writing bioinformatics file formats. CRAM is a compressed format which stores DNA…
- CVE-2020-36403 — High (CVSS 8.8): HTSlib through 1.10.2 allows out-of-bounds write access in vcf_parse_format (called from vcf_parse and vcf_read).
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