How severe is CVE-2026-31969?

CVE-2026-31969 has a CVSS 3.x base score of 8.1, rated high severity. It is exploitable over network with low attack complexity, requires no privileges and user interaction. Impact on confidentiality is none, integrity high, and availability high.

Is CVE-2026-31969 being actively exploited?

It is not currently listed in CISA's KEV catalog. Its EPSS exploit-prediction score is 0% (26th percentile), an estimate of the probability of exploitation in the next 30 days.

What products are affected by CVE-2026-31969?

CVE-2026-31969 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-2026-31969?

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-2026-31969 have an EU (EUVD) identifier?

Yes. CVE-2026-31969 is tracked in the ENISA EU Vulnerability Database (EUVD) as EUVD-2026-12944.

When was CVE-2026-31969 published?

CVE-2026-31969 was published on 2026-03-18 and last updated on 2026-06-17.

CVE-2026-31969

CVE-2026-31969 is a high-severity vulnerability in Htslib with a CVSS 3.x base score of 8.1. 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-122.

Key facts

Severity: High (CVSS 3.x base score 8.1)
CVSS v4: 7.1
EPSS exploit prediction: 0% (26th percentile)
Actively exploited: Not listed in CISA KEV
EU (EUVD) id: EUVD-2026-12944
Weakness: CWE-122
Affected product: Htslib
Published: 2026-03-18
Last modified: 2026-06-17

Description

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. When reading data encoded using the `BYTE_ARRAY_STOP` method, an out-by-one error in the `cram_byte_array_stop_decode_char()` function check for a full output buffer could result in a single attacker-controlled byte being written beyond the end of a heap allocation. 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.

Frequently asked questions

What is CVE-2026-31969?: 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. When reading data encoded using the `BYTE_ARRAY_STOP` method, an out-by-one error in the `cram_byte_array_stop_decode_char()` function check for a full output buffer could result in a single attacker-controlled byte being written beyond the end of a heap allocation. 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.
How severe is CVE-2026-31969?: CVE-2026-31969 has a CVSS 3.x base score of 8.1, rated high severity. It is exploitable over network with low attack complexity, requires no privileges and user interaction. Impact on confidentiality is none, integrity high, and availability high.
Is CVE-2026-31969 being actively exploited?: It is not currently listed in CISA's KEV catalog. Its EPSS exploit-prediction score is 0% (26th percentile), an estimate of the probability of exploitation in the next 30 days.
What products are affected by CVE-2026-31969?: CVE-2026-31969 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-2026-31969?: 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-2026-31969 have an EU (EUVD) identifier?: Yes. CVE-2026-31969 is tracked in the ENISA EU Vulnerability Database (EUVD) as EUVD-2026-12944.
When was CVE-2026-31969 published?: CVE-2026-31969 was published on 2026-03-18 and last updated on 2026-06-17.

References

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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