CVE-2026-31963
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. As one method of removing redundant data, CRAM uses reference-based compression so that instead of storing the full sequence for each alignment record it stores a location in an external reference sequence along with a list of differences to the reference at that location as a sequence of "features". When decoding these features, an out-by-one error in a test for CRAM features that appear beyond the extent of the CRAM record sequence could result in an invalid write of one attacker-controlled byte beyond the end of a heap buffer. 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, 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-2026-31963
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 patched version.
- Apply fixes for CRAM feature decoding issues.
- Validate CRAM files for external reference data.
- Rebuild applications linked against HTSlib.
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-2026-31963.
| URL | Resource |
|---|---|
| https://github.com/samtools/htslib/commit/8bcc9907be0f945ddc31796d64f078fa05456acd | |
| https://github.com/samtools/htslib/security/advisories/GHSA-qgqh-h2q9-7w3c |
CWE - Common Weakness Enumeration
While CVE identifies
specific instances of vulnerabilities, CWE categorizes the common flaws or
weaknesses that can lead to vulnerabilities. CVE-2026-31963 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-2026-31963
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-2026-31963 vulnerability anywhere in the article.
The following table lists the changes that have been made to the
CVE-2026-31963 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. As one method of removing redundant data, CRAM uses reference-based compression so that instead of storing the full sequence for each alignment record it stores a location in an external reference sequence along with a list of differences to the reference at that location as a sequence of "features". When decoding these features, an out-by-one error in a test for CRAM features that appear beyond the extent of the CRAM record sequence could result in an invalid write of one attacker-controlled byte beyond the end of a heap buffer. 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:N/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-787 Added CWE CWE-129 Added CWE CWE-122 Added Reference https://github.com/samtools/htslib/commit/8bcc9907be0f945ddc31796d64f078fa05456acd Added Reference https://github.com/samtools/htslib/security/advisories/GHSA-qgqh-h2q9-7w3c