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CVE-2026-31964— HTSlib CRAM decoder has a NULL Pointer Dereference

Quick assessment

Affected

samtools htslib

Exploitation

No confirmed in-the-wild exploitation; assess based on exposure

Recommended action

Check the vendor advisory and references for a fixed version. If immediate upgrade is impossible, restrict exposure and increase monitoring.

HTSlib是samtools开源的一个C语言的库文件。 HTSlib 1.23.1之前版本、1.22.2之前版本和1.21.1之前版本存在代码问题漏洞，该漏洞源于CONST、XPACK和XRLE编码未正确处理接口，可能导致空指针取消引用。

AI Predicted 6.5 Difficulty: Easy EPSS 0.34% · P27 Updated Mar 19, 2026

Possible ATT&CK Techniques 1 AI

T1190 · Exploit Public-Facing Application

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I. Basic Information for CVE-2026-31964

Vulnerability Information

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Vulnerability Title

HTSlib CRAM decoder has a NULL Pointer Dereference

Source: CVE Program / CVE List V5

Vulnerability 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.

Source: CVE Program / CVE List V5

CVSS Information

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

Source: CVE Program / CVE List V5

Vulnerability Type

空指针解引用

Source: CVE Program / CVE List V5

Vulnerability Title

HTSlib 代码问题漏洞

Source: CNNVD (China National Vulnerability Database)

Vulnerability Description

Source: CNNVD (China National Vulnerability Database)

CVSS Information

N/A

Source: CNNVD (China National Vulnerability Database)

Vulnerability Type

N/A

Source: CNNVD (China National Vulnerability Database)

Affected Products

Vendor	Product	Affected Versions	CPE	Subscribe
samtools	htslib	< 1.21.1	-

II. Public POCs for CVE-2026-31964

#	POC Description	Source Link	Shenlong Link

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No public POC found.

III. Intelligence Information for CVE-2026-31964

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Patches & Fixes for CVE-2026-31964 (1)

Fix codecs that did not correctly handle out == NULL · samtools/htslib@e64e68d · GitHub x_refsource_MISC

Vendor Advisories for CVE-2026-31964 (1)

NULL Pointer Dereference in HTSlib CRAM decoder · Advisory · samtools/htslib · GitHub x_refsource_CONFIRM

https://www.cve.org/CVERecord?id=CVE-2026-31964

Same Patch Batch · samtools · 2026-03-18 · 12 CVEs total

CVE-2026-31962		HTSlib CRAM reader has heap buffer overflow due to improper validation of input
CVE-2026-31963		HTSlib CRAM reader has heap buffer overflow due to improper validation of input
CVE-2026-31965		HTSlib CRAM reader has out-of-bounds reads due to improper validation of input
CVE-2026-31966		HTSlib CRAM reader has out-of-bounds read due to improper validation of input
CVE-2026-31967		HTSlib CRAM reader has out-of-bounds read due to improper validation of input
CVE-2026-31968		HTSlib CRAM decoder vulnerable to buffer overflow
CVE-2026-31971		HTSlib CRAM decoder vulnerable to buffer overflow
CVE-2026-31969		HTSlib CRAM decoder has a heap buffer overflow
CVE-2026-31970		HTSlib BGZF index file reader has a heap buffer overflow
CVE-2026-31973		NULL pointer dereference in samtools cram-size
CVE-2026-31972		samtools mpileup has use-after-free leading to an invalid read

IV. Related Vulnerabilities

Same product: htslib

Same vendor: samtools

Same weakness: CWE-476