U.S. flag   An official website of the United States government
Dot gov

Official websites use .gov
A .gov website belongs to an official government organization in the United States.

Https

Secure .gov websites use HTTPS
A lock (Dot gov) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.

National Vulnerability Database

National Vulnerability Database

NVD

National Vulnerability Database
  1. Vulnerabilities

CVE-2026-31962 Detail

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.


Metrics

 
NVD enrichment efforts reference publicly available information to associate vector strings. CVSS information contributed by other sources is also displayed.
CVSS 4.0 Severity and Vector Strings:

NIST CVSS score
NIST: NVD
N/A
NVD assessment not yet provided.

Nist CVSS score does not match with CNA score
CNA:  GitHub, Inc.
CVSS-B 8.8 HIGH
Vector:  CVSS:4.0/AV:N/AC:L/AT:N/PR:N/UI:N/VC:L/VI:H/VA:L/SC:N/SI:N/SA:N

References to Advisories, Solutions, and Tools

By selecting these links, you will be leaving NIST webspace. We have provided these links to other web sites because they may have information that would be of interest to you. No inferences should be drawn on account of other sites being referenced, or not, from this page. There may be other web sites that are more appropriate for your purpose. NIST does not necessarily endorse the views expressed, or concur with the facts presented on these sites. Further, NIST does not endorse any commercial products that may be mentioned on these sites. Please address comments about this page to [email protected].

URL Source(s) Tag(s)
https://github.com/samtools/htslib/commit/d799b54c6401879187bba4741be83ff590ac73e3 GitHub, Inc.
https://github.com/samtools/htslib/security/advisories/GHSA-xxmp-v7h3-gpwp GitHub, Inc.

Weakness Enumeration

CWE-ID CWE Name Source
CWE-122 Heap-based Buffer Overflow GitHub, Inc.  
CWE-125 Out-of-bounds Read GitHub, Inc.  
CWE-129 Improper Validation of Array Index GitHub, Inc.  
CWE-787 Out-of-bounds Write GitHub, Inc.  

Change History

1 change records found show changes

Quick Info

CVE Dictionary Entry:
CVE-2026-31962
NVD Published Date:
03/18/2026
NVD Last Modified:
03/18/2026
Source:
GitHub, Inc.