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CVE-2026-31965— HTSlib CRAM reader has out-of-bounds reads due to improper validation of input

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之前版本存在输入验证错误漏洞，该漏洞源于cram_decode_slice函数中参考ID字段验证过晚，可能导致越界读取。

AI Predicted 5.3 Difficulty: Moderate EPSS 0.39% · P33
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I. Basic Information for CVE-2026-31965

Vulnerability Information
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Vulnerability Title
HTSlib CRAM reader has out-of-bounds reads due to improper validation of input
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. In the `cram_decode_slice()` function called while reading CRAM records, validation of the reference id field occurred too late, allowing two out of bounds reads to occur before the invalid data was detected. The bug does allow two values to be leaked to the caller, however as the function reports an error it may be difficult to exploit them. It is also possible that the program will crash due to trying to access invalid memory. 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:L/VI:N/VA:L/SC:N/SI:N/SA:N
Source: CVE Program / CVE List V5
Vulnerability Type
跨界内存读
Source: CVE Program / CVE List V5
Vulnerability Title
HTSlib 输入验证错误漏洞
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之前版本存在输入验证错误漏洞，该漏洞源于cram_decode_slice函数中参考ID字段验证过晚，可能导致越界读取。
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-2026-31965

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III. Intelligence Information for CVE-2026-31965

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Patches & Fixes for CVE-2026-31965 (1)

Vendor Advisories for CVE-2026-31965 (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-2026-31966 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-125