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Vulnerability record · CVE-2026-31963 · published 18 March 2026

CVE-2026-31963: 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. 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.

8.8 CVSS 4.0 High EPSS 0.52% · top 58.2% CWE-122 · Heap-based buffer overflowCWE-129 · CWE-129
8.8CVSS 4.0 base score
0.52%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. 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.

CVSS:4.0/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:

Affected products

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

References

LinkTags
https://github.com/samtools/htslib/commit/8bcc9907be0f945ddc31796d64f078fa05456acd Patch
https://github.com/samtools/htslib/security/advisories/GHSA-qgqh-h2q9-7w3c PatchVendor Advisory

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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-2026-31962Htslib 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. While …EPSS 0.59%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-2026-31963), CISA KEV, FIRST EPSS (scores of 2026-09-27). This page is refreshed as NVD updates the record.