CVE-2026-31969: HTSlib CRAM decoder has a heap buffer overflow
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 BYTEARRAYSTOP method, an out-by-one error in the crambytearraystopdecodechar() 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.
Affected Software
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Event History
Frequently Asked Questions
What is the severity of CVE-2026-31969?
CVE-2026-31969 has been rated as a high-severity vulnerability due to the potential for remote code execution stemming from a heap buffer overflow.
How do I fix CVE-2026-31969?
To mitigate CVE-2026-31969, users should upgrade to HTSlib version 1.23.2 or later, which addresses the heap buffer overflow vulnerability.
What versions of HTSlib are affected by CVE-2026-31969?
CVE-2026-31969 affects HTSlib versions up to and including 1.23.1 and versions below 1.22.2.
What is the nature of the vulnerability in CVE-2026-31969?
CVE-2026-31969 involves a heap buffer overflow that occurs when reading CRAM files encoded with the BYTE_ARRAY_STOP method.
Can CVE-2026-31969 lead to data loss?
Yes, CVE-2026-31969 can potentially lead to data loss or corruption if exploited, as it allows for memory manipulation.