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Vulnerability record · CVE-2026-31964 · published 18 March 2026

CVE-2026-31964: Htslib null pointer dereference 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 using a variety of encodings and compression methods. 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 `CONST`, `XPACK` and `XRLE` encodings did not properly implement the interface needed to do this. Trying to decode records with omitted sequence or quality data using these encodings would result in an attempt to write to a NULL pointer. Exploiting this bug causes a NULL pointer dereference. Typically this will cause the program to crash. Versions 1.23.1, 1.22.2 and 1.21.1 include fixes for this issue. There is no workaround for this issue.

6.9 CVSS 4.0 Medium EPSS 0.49% · top 60.5% CWE-476 · NULL pointer dereference
6.9CVSS 4.0 base score
0.49%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 using a variety of encodings and compression methods. 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 `CONST`, `XPACK` and `XRLE` encodings did not properly implement the interface needed to do this. Trying to decode records with omitted sequence or quality data using these encodings would result in an attempt to write to a NULL pointer. Exploiting this bug causes a NULL pointer dereference. Typically this will cause the program to crash. 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:L/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/e64e68da567d2309509d059ace016d5d7fc7514f Patch
https://github.com/samtools/htslib/security/advisories/GHSA-5w97-85gf-86rm 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-2026-31963Htslib 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-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%

Source: NIST National Vulnerability Database (record CVE-2026-31964), CISA KEV, FIRST EPSS (scores of 2026-09-28). This page is refreshed as NVD updates the record.