CVE-2026-31971

CVE-2026-31971 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-121.

Key facts

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_LEN` method, the `cram_byte_array_len_decode()` failed to validate that the amount of data being unpacked matched the size of the output buffer where it was to be stored. Depending on the data series being read, this could result either in a heap or a stack overflow with attacker-controlled bytes. Depending on the data stream this could result either in a heap buffer overflow or a stack overflow. If a user opens a file crafted to exploit this issue it could lead to the program crashing, overwriting of data structures on the heap or stack in ways not expected by the program, or changing the control flow of 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-2026-31971?
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_LEN` method, the `cram_byte_array_len_decode()` failed to validate that the amount of data being unpacked matched the size of the output buffer where it was to be stored. Depending on the data series being read, this could result either in a heap or a stack overflow with attacker-controlled bytes. Depending on the data stream this could result either in a heap buffer overflow or a stack overflow. If a user opens a file crafted to exploit this issue it could lead to the program crashing, overwriting of data structures on the heap or stack in ways not expected by the program, or changing the control flow of 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-2026-31971?
CVE-2026-31971 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-2026-31971 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-2026-31971?
CVE-2026-31971 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-2026-31971?
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-2026-31971 have an EU (EUVD) identifier?
Yes. CVE-2026-31971 is tracked in the ENISA EU Vulnerability Database (EUVD) as EUVD-2026-12948.
When was CVE-2026-31971 published?
CVE-2026-31971 was published on 2026-03-18 and last updated on 2026-06-17.

References

Affected products (2)

More vulnerabilities in Htslib

All CVEs affecting Htslib →

Other CWE-121 (Stack-based Buffer Overflow) vulnerabilities

Browse all CWE-121 (Stack-based Buffer Overflow) vulnerabilities →