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CVE-2026-31969— HTSlib CRAM decoder has a heap buffer overflow

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之前版本存在缓冲区错误漏洞，该漏洞源于cram_byte_array_stop_decode_char函数存在差一错误，可能导致堆缓冲区溢出。

AI Predicted 8.6 Difficulty: Moderate EPSS 0.34% · P27
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I. Basic Information for CVE-2026-31969

Vulnerability Information
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Vulnerability Title
HTSlib CRAM decoder has a heap buffer overflow
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. When reading data encoded using the `BYTE_ARRAY_STOP` method, an out-by-one error in the `cram_byte_array_stop_decode_char()` function check for a full output buffer could result in a single attacker-controlled byte being written beyond the end of a heap allocation. 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.
Source: CVE Program / CVE List V5
CVSS Information
CVSS:4.0/AV:N/AC:L/AT:N/PR:N/UI:P/VC:N/VI:H/VA:L/SC:N/SI:N/SA:N
Source: CVE Program / CVE List V5
Vulnerability Type
堆缓冲区溢出
Source: CVE Program / CVE List V5
Vulnerability Title
HTSlib 缓冲区错误漏洞
Source: CNNVD (China National Vulnerability Database)
Vulnerability Description
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之前版本存在缓冲区错误漏洞，该漏洞源于cram_byte_array_stop_decode_char函数存在差一错误，可能导致堆缓冲区溢出。
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-2026-31969

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III. Intelligence Information for CVE-2026-31969

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Patches & Fixes for CVE-2026-31969 (1)

Vendor Advisories for CVE-2026-31969 (1)

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-2026-31964 HTSlib CRAM decoder has a NULL Pointer Dereference
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-2026-31970 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-122

V. Comments for CVE-2026-31969

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