CVE-2026-31969 | samtools htslib up to 1.21.0/1.22.1/1.23 cram_byte_array_stop_decode_char heap-based overflow (GHSA-q4cj-f4h5-fqgc)

VDB-351624 · CVE-2026-31969 · GHSA-Q4CJ-F4H5-FQGC SAMTOOLS HTSLIB UP TO 1.21.0/1.22.1/1.23 CRAM_BYTE_ARRAY_STOP_DECODE_CHAR HEAP-BASED OVERFLOW HISTORYDIFFRELATEJSONXMLCTI CVSS Meta Temp Score Current Exploit Price (≈) CTI Interest Score 6.0 $0-$5k 0.56+ Summaryinfo A vulnerability classified as critical was found in samtools htslib up to 1.21.0/1.22.1/1.23. This impacts the function cram_byte_array_stop_decode_char. The manipulation results in heap-based overflow. This vulnerability is cataloged as CVE-2026-31969. The attack may be launched remotely. There is no exploit available. Upgrading the affected component is advised. Detailsinfo A vulnerability, which was classified as critical, was found in samtools htslib up to 1.21.0/1.22.1/1.23. Affected is the function cram_byte_array_stop_decode_char. The manipulation with an unknown input leads to a heap-based overflow vulnerability. CWE is classifying the issue as 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(). This is going to have an impact on confidentiality, integrity, and availability. CVE summarizes: 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. The advisory is shared for download at github.com. This vulnerability is traded as CVE-2026-31969 since 03/10/2026. The exploitability is told to be easy. It is possible to launch the attack remotely. The exploitation doesn't require any form of authentication. Successful exploitation requires user interaction by the victim. There are known technical details, but no exploit is available. Upgrading to version 1.21.1 or 1.22.2 eliminates this vulnerability. Applying the patch 88cdf69e4b83bb550ab4f6f7134892c2ad1978f4 is able to eliminate this problem. The bugfix is ready for download at github.com. The best possible mitigation is suggested to be upgrading to the latest version. Productinfo Vendor samtools Name htslib Version 1.0 1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8 1.9 1.10 1.11 1.12 1.13 1.14 1.15 1.16 1.17 1.18 1.19 1.20 1.21 1.21.0 1.22 1.22.0 1.22.1 1.23 License open-source Website Product: https://github.com/samtools/htslib/ CPE 2.3info 🔒 🔒 🔒 CPE 2.2info 🔒 🔒 🔒 CVSSv4info VulDB Vector: 🔒 VulDB Reliability: 🔍 CNA CVSS-B Score: 🔒 CNA CVSS-BT Score: 🔒 CNA Vector: 🔒 CVSSv3info VulDB Meta Base Score: 6.3 VulDB Meta Temp Score: 6.0 VulDB Base Score: 6.3 VulDB Temp Score: 6.0 VulDB Vector: 🔒 VulDB Reliability: 🔍 CVSSv2info Vector Complexity Authentication Confidentiality Integrity Availability Unlock Unlock Unlock Unlock Unlock Unlock Unlock Unlock Unlock Unlock Unlock Unlock Unlock Unlock Unlock Unlock Unlock Unlock VulDB Base Score: 🔒 VulDB Temp Score: 🔒 VulDB Reliability: 🔍 Exploitinginfo Class: Heap-based overflow CWE: CWE-122 / CWE-119 CAPEC: 🔒 ATT&CK: 🔒 Physical: No Local: No Remote: Yes Availability: 🔒 Status: Not defined Price Prediction: 🔍 Current Price Estimation: 🔒 0-Day Unlock Unlock Unlock Unlock Today Unlock Unlock Unlock Unlock Threat Intelligenceinfo Interest: 🔍 Active Actors: 🔍 Active APT Groups: 🔍 Countermeasuresinfo Recommended: Upgrade Status: 🔍 0-Day Time: 🔒 Upgrade: htslib 1.21.1/1.22.2 Patch: 88cdf69e4b83bb550ab4f6f7134892c2ad1978f4 Timelineinfo 03/10/2026 CVE reserved 03/18/2026 +8 days Advisory disclosed 03/18/2026 +0 days VulDB entry created 03/19/2026 +0 days VulDB entry last update Sourcesinfo Product: github.com Advisory: GHSA-q4cj-f4h5-fqgc Status: Confirmed CVE: CVE-2026-31969 (🔒) GCVE (CVE): GCVE-0-2026-31969 GCVE (VulDB): GCVE-100-351624 Entryinfo Created: 03/19/2026 00:00 Changes: 03/19/2026 00:00 (70) Complete: 🔍 Cache ID: 99:F72:101 Discussion No comments yet. Languages: en. Please log in to comment. ◂ PreviousOverviewNext ▸