Bug 2448773 (CVE-2026-31971)

Summary: CVE-2026-31971 htslib: HTSlib: CRAM decoder vulnerable to 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. When reading CRAM (Compressed Reference-oriented Alignment Map) files, the `cram_byte_array_len_decode()` function did not properly validate the size of incoming data against the allocated buffer. This memory corruption vulnerability allows a remote attacker to cause a heap or stack overflow by tricking a user into opening a specially crafted CRAM file. Successful exploitation could lead to arbitrary code execution, program crashes, or data corruption.
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Bug Depends On: 2448880, 2448884, 2448888, 2448892    
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Description OSIDB Bzimport 2026-03-18 20:02:03 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_LEN` method, the `cram_byte_array_len_decode()` failed to validate that the amount of data being unpacked matched the size of the output buffer where it was to be stored. Depending on the data series being read, this could result either in a heap or a stack overflow with attacker-controlled bytes. Depending on the data stream this could result either in a heap buffer overflow or a stack overflow. If a user opens a file crafted to exploit this issue it could lead to the program crashing, overwriting of data structures on the heap or stack in ways not expected by the program, or changing the control flow of 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.