← Vulnerability feed

Vulnerability record · CVE-2026-31962 · published 18 March 2026

CVE-2026-31962: Htslib heap-based buffer overflow vulnerability

HHtslib · Htslib

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.

8.8 CVSS 4.0 High EPSS 0.59% · top 54.0% CWE-122 · Heap-based buffer overflowCWE-125 · Out-of-bounds read
8.8CVSS 4.0 base score
0.59%EPSS exploitation probability, 30 days
NoNot in CISA KEV
1Affected product versions listed by NVD
2References
17 Jun 2026Last modified by NVD

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.

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/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:

Affected products

1 vulnerable configurations from NVD's CPE data, grouped by vendor and product.

References

LinkTags
https://github.com/samtools/htslib/commit/d799b54c6401879187bba4741be83ff590ac73e3 Patch
https://github.com/samtools/htslib/security/advisories/GHSA-xxmp-v7h3-gpwp PatchVendor Advisory

Track CVE-2026-31962 inside VULONE

Watch it alongside the ransomware crews, C2 infrastructure and forum chatter that reference it, query it through the API and pull it into your SIEM over TAXII.

Start free Open in platform

Related vulnerabilities

Same products first, then exploited flaws of the same weakness class.

9.8CVE-2018-13845Htslib out-of-bounds read vulnerabilityAn issue has been found in HTSlib 1.8. It is a buffer over-read in sam_parse1 in sam.c.EPSS 1.6%9.8CVE-2017-1000206Htslib memory buffer overflow vulnerabilitysamtools htslib library version 1.4.0 and earlier is vulnerable to buffer overflow in the CRAM rANS codec resulting in potential arbitrary code execu…EPSS 2.0%8.8CVE-2026-31968Htslib stack-based buffer overflow vulnerabilityHTSlib is a library for reading and writing bioinformatics file formats. CRAM is a compressed format which stores DNA sequence alignment data using a…EPSS 0.52%8.8CVE-2026-31963Htslib heap-based buffer overflow vulnerabilityHTSlib is a library for reading and writing bioinformatics file formats. CRAM is a compressed format which stores DNA sequence alignment data. As one…EPSS 0.52%8.8CVE-2020-36403Htslib out-of-bounds write vulnerabilityHTSlib through 1.10.2 allows out-of-bounds write access in vcf_parse_format (called from vcf_parse and vcf_read).EPSS 1.6%7.5CVE-2018-13843Htslib vulnerabilityAn issue has been found in HTSlib 1.8. It is a memory leak in bgzf_getline in bgzf.c. NOTE: the software maintainer's position is that the "failure t…EPSS 1.5%7.5CVE-2018-13844Htslib memory leak vulnerabilityAn issue has been found in HTSlib 1.8. It is a memory leak in fai_read in faidx.c. NOTE: This has been disputed with the assertion that this vulnerab…EPSS 1.4%7.1CVE-2026-31971Htslib stack-based buffer overflow vulnerabilityHTSlib is a library for reading and writing bioinformatics file formats. CRAM is a compressed format which stores DNA sequence alignment data using a…EPSS 0.52%

Source: NIST National Vulnerability Database (record CVE-2026-31962), CISA KEV, FIRST EPSS (scores of 2026-09-27). This page is refreshed as NVD updates the record.