CVE-2026-31965
HTSlib CRAM reader has out-of-bounds reads due to improper validation of input
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.
INFO
Published Date :
March 18, 2026, 7:16 p.m.
Last Modified :
March 18, 2026, 7:16 p.m.
Remotely Exploit :
Yes !
Source :
[email protected]
Affected Products
The following products are affected by CVE-2026-31965
vulnerability.
Even if cvefeed.io is aware of the exact versions of the
products
that
are
affected, the information is not represented in the table below.
No affected product recoded yet
CVSS Scores
| Score | Version | Severity | Vector | Exploitability Score | Impact Score | Source |
|---|---|---|---|---|---|---|
| CVSS 4.0 | MEDIUM | [email protected] |
Solution
- Update HTSlib to version 1.23.1 or later.
- Apply available patches for affected HTSlib versions.
- Recompile applications using the updated library.
- Test applications for stability after updating.
References to Advisories, Solutions, and Tools
Here, you will find a curated list of external links that provide in-depth
information, practical solutions, and valuable tools related to
CVE-2026-31965.
| URL | Resource |
|---|---|
| https://github.com/samtools/htslib/commit/9cefb46453ad471e933b8212d4f45920524d3357 | |
| https://github.com/samtools/htslib/security/advisories/GHSA-mqm2-v645-3qhr |
CWE - Common Weakness Enumeration
While CVE identifies
specific instances of vulnerabilities, CWE categorizes the common flaws or
weaknesses that can lead to vulnerabilities. CVE-2026-31965 is
associated with the following CWEs:
Common Attack Pattern Enumeration and Classification (CAPEC)
Common Attack Pattern Enumeration and Classification
(CAPEC)
stores attack patterns, which are descriptions of the common attributes and
approaches employed by adversaries to exploit the CVE-2026-31965
weaknesses.
We scan GitHub repositories to detect new proof-of-concept exploits. Following list is a collection of public exploits and proof-of-concepts, which have been published on GitHub (sorted by the most recently updated).
Results are limited to the first 15 repositories due to potential performance issues.
The following list is the news that have been mention
CVE-2026-31965 vulnerability anywhere in the article.
The following table lists the changes that have been made to the
CVE-2026-31965 vulnerability over time.
Vulnerability history details can be useful for understanding the evolution of a vulnerability, and for identifying the most recent changes that may impact the vulnerability's severity, exploitability, or other characteristics.
-
New CVE Received by [email protected]
Mar. 18, 2026
Action Type Old Value New Value Added 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. Added CVSS V4.0 AV:N/AC:L/AT:N/PR:N/UI:N/VC:L/VI:N/VA:L/SC:N/SI:N/SA:N/E:X/CR:X/IR:X/AR:X/MAV:X/MAC:X/MAT:X/MPR:X/MUI:X/MVC:X/MVI:X/MVA:X/MSC:X/MSI:X/MSA:X/S:X/AU:X/R:X/V:X/RE:X/U:X Added CWE CWE-125 Added CWE CWE-129 Added Reference https://github.com/samtools/htslib/commit/9cefb46453ad471e933b8212d4f45920524d3357 Added Reference https://github.com/samtools/htslib/security/advisories/GHSA-mqm2-v645-3qhr