Bug 2448750 (CVE-2026-31962)

Summary: CVE-2026-31962 htslib: htslib: Heap buffer overflow leading to arbitrary code execution via crafted CRAM file
Product: [Other] Security Response Reporter: OSIDB Bzimport <bzimport>
Component: vulnerabilityAssignee: Product Security DevOps Team <prodsec-dev>
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Priority: high    
Version: unspecifiedKeywords: Security
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Hardware: All   
OS: Linux   
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A flaw was found in htslib, a library for reading and writing bioinformatics file formats. A local user could exploit a heap buffer overflow vulnerability by opening a specially crafted CRAM file. This flaw occurs due to incorrect handling of certain CRAM format records, leading to reading and writing a single byte beyond a heap allocation. Successful exploitation could result in a program crash, data corruption, or potentially arbitrary code execution.
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Bug Depends On: 2448852, 2448850, 2448851, 2448853, 2448854, 2448855    
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Description OSIDB Bzimport 2026-03-18 19:03:14 UTC 
HTSlib is a library for reading and writing bioinformatics file formats. CRAM is a compressed format which stores DNA sequence alignment data. 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 `cram_decode_seq()` did not handle this correctly in some cases. Where this happened it could result in reading a single byte from beyond the end of a heap allocation, followed by writing a single attacker-controlled byte to the same location. 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.