Bug 2448755 (CVE-2026-31963)

Summary: CVE-2026-31963 htslib: HTSlib: 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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OS: Linux   
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A flaw was found in HTSlib, a library for reading and writing bioinformatics file formats. When processing CRAM (Compressed Reference-oriented Alignment Map) files, an out-by-one error in feature decoding can cause a heap buffer overflow. This vulnerability allows an attacker to craft a malicious CRAM file which, when opened by a user, could lead to a program crash, data corruption, or potentially arbitrary code execution.
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Bug Depends On: 2448837, 2448838, 2448839, 2448840, 2448841, 2448842    
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Description OSIDB Bzimport 2026-03-18 19:03:26 UTC 
HTSlib is a library for reading and writing bioinformatics file formats. CRAM is a compressed format which stores DNA sequence alignment data. As one method of removing redundant data, CRAM uses reference-based compression so that instead of storing the full sequence for each alignment record it stores a location in an external reference sequence along with a list of differences to the reference at that location as a sequence of "features". When decoding these features, an out-by-one error in a test for CRAM features that appear beyond the extent of the CRAM record sequence could result in an invalid write of one attacker-controlled byte beyond the end of a heap buffer. 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.