Bug 2448771 (CVE-2026-31969)

Summary: CVE-2026-31969 htslib: HTSlib: CRAM decoder has a heap buffer overflow
Product: [Other] Security Response Reporter: OSIDB Bzimport <bzimport>
Component: vulnerabilityAssignee: Product Security DevOps Team <prodsec-dev>
Status: NEW --- QA Contact:
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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 used for bioinformatics file formats. A remote attacker could exploit an out-by-one error when processing a specially crafted CRAM (Compressed Reference-oriented Alignment Map) file. This vulnerability can lead to a heap buffer overflow, potentially allowing for arbitrary code execution, data corruption, or causing the program to crash. This poses a significant risk to the integrity and availability of systems handling bioinformatics data.
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Bug Depends On: 2448882, 2448889, 2448886    
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Description OSIDB Bzimport 2026-03-18 20:01:50 UTC 
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.