CVE-2026-31969
Received
Received - Intake
Heap Buffer Overflow in HTSlib CRAM BYTE_ARRAY_STOP Decoder
Publication date: 2026-03-18
Last updated on: 2026-03-19
Assigner: GitHub, Inc.
Description
Description
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.
CVSS Scores
EPSS Scores
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Meta Information
Affected Vendors & Products
| Vendor | Product | Version / Range |
|---|---|---|
| htslib | htslib | to 1.21.1 (exc) |
| htslib | htslib | From 1.22 (inc) to 1.22.2 (exc) |
| htslib | htslib | 1.23 |
Helpful Resources
Exploitability
CWE
KEV
| CWE ID | Description |
|---|---|
| CWE-787 | The product writes data past the end, or before the beginning, of the intended buffer. |
| CWE-122 | A heap overflow condition is a buffer overflow, where the buffer that can be overwritten is allocated in the heap portion of memory, generally meaning that the buffer was allocated using a routine such as malloc(). |
