CVE-2026-31971 HTSlib CRAM decoder vulnerable to buffer overflow
A buffer overflow in HTSlib's CRAM decoder allows attackers to execute arbitrary code or crash applications by tricking users into opening malicious files.
- Exploited in the wild
- Not known
- Login needed
- Not needed
- Attackable
- Over the internet
- Victim action needed
- A user has to click or open something
- Fix
- Available
What is CVE-2026-31971?
CVE-2026-31971 is a high-severity memory corruption vulnerability in samtools htslib, published on 18 Mar 2026. An attacker can exploit it over the internet without logging in, and only if a user opens a file or follows a link.
Official 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.
Which versions are affected by CVE-2026-31971?
It affects 1 product.
Products include Htslib Htslib.
How do I fix CVE-2026-31971?
Upgrade to a fixed version.
Upgrade to the fixed version. Memory-safe languages, compiler hardening and fuzzing prevent most new cases. More about Memory corruption.
Is CVE-2026-31971 being exploited?
There is no known exploitation of CVE-2026-31971 in the wild and no public exploit code.
Other vulnerabilities in samtools htslib
- CVE-2018-13845 Memory corruption in n/a
- CVE-2017-1000206 Memory corruption in n/a
- CVE-2026-31962 HTSlib CRAM reader has heap buffer overflow due to improper validation of input
- CVE-2026-31963 HTSlib CRAM reader has heap buffer overflow due to improper validation of input
- CVE-2026-31968 HTSlib CRAM decoder vulnerable to buffer overflow
Sources
Also known as DEBIAN-CVE-2026-31971, GHSA-jvx4-4wq7-6fmh, UBUNTU-CVE-2026-31971.