CVE-2026-31962
HTSlib CRAM reader has heap buffer overflow 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. While most alignment records store DNA sequence and quality values, the format also allows them to omit this data in certain cases to save space. Due to some quirks of the CRAM format, it is necessary to handle these records carefully as they will actually store data that needs to be consumed and then discarded. Unfortunately the `cram_decode_seq()` did not handle this correctly in some cases. Where this happened it could result in reading a single byte from beyond the end of a heap allocation, followed by writing a single attacker-controlled byte to the same location. 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.
INFO
Published Date :
March 18, 2026, 6:16 p.m.
Last Modified :
March 18, 2026, 6:16 p.m.
Remotely Exploit :
Yes !
Source :
[email protected]
Affected Products
The following products are affected by CVE-2026-31962
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 | HIGH | [email protected] |
Solution
- Update HTSlib to a version that includes the fix.
- Ensure CRAM files are handled securely.
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-2026-31962.
| URL | Resource |
|---|---|
| https://github.com/samtools/htslib/commit/d799b54c6401879187bba4741be83ff590ac73e3 | |
| https://github.com/samtools/htslib/security/advisories/GHSA-xxmp-v7h3-gpwp |
CWE - Common Weakness Enumeration
While CVE identifies
specific instances of vulnerabilities, CWE categorizes the common flaws or
weaknesses that can lead to vulnerabilities. CVE-2026-31962 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-2026-31962
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-2026-31962 vulnerability anywhere in the article.
The following table lists the changes that have been made to the
CVE-2026-31962 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. While most alignment records store DNA sequence and quality values, the format also allows them to omit this data in certain cases to save space. Due to some quirks of the CRAM format, it is necessary to handle these records carefully as they will actually store data that needs to be consumed and then discarded. Unfortunately the `cram_decode_seq()` did not handle this correctly in some cases. Where this happened it could result in reading a single byte from beyond the end of a heap allocation, followed by writing a single attacker-controlled byte to the same location. 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. Added CVSS V4.0 AV:N/AC:L/AT:N/PR:N/UI:N/VC:L/VI:H/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-787 Added CWE CWE-129 Added CWE CWE-122 Added Reference https://github.com/samtools/htslib/commit/d799b54c6401879187bba4741be83ff590ac73e3 Added Reference https://github.com/samtools/htslib/security/advisories/GHSA-xxmp-v7h3-gpwp