CVE-2026-31971 | samtools htslib up to 1.21.0/1.22.1/1.23 cram_byte_array_len_decode stack-based overflow (GHSA-jvx4-4wq7-6fmh)

VDB-351625 · CVE-2026-31971 · GHSA-JVX4-4WQ7-6FMH SAMTOOLS HTSLIB UP TO 1.21.0/1.22.1/1.23 CRAM_BYTE_ARRAY_LEN_DECODE STACK-BASED OVERFLOW HISTORYDIFFRELATEJSONXMLCTI CVSS Meta Temp Score Current Exploit Price (≈) CTI Interest Score 6.0 $0-$5k 0.46+ Summaryinfo A vulnerability, which was classified as critical, has been found in samtools htslib up to 1.21.0/1.22.1/1.23. Affected is the function cram_byte_array_len_decode. This manipulation causes stack-based overflow. This vulnerability is registered as CVE-2026-31971. Remote exploitation of the attack is possible. No exploit is available. It is advisable to upgrade the affected component. Detailsinfo A vulnerability has been found in samtools htslib up to 1.21.0/1.22.1/1.23 and classified as critical. Affected by this vulnerability is the function cram_byte_array_len_decode. The manipulation with an unknown input leads to a stack-based overflow vulnerability. The CWE definition for the vulnerability is CWE-121. A stack-based buffer overflow condition is a condition where the buffer being overwritten is allocated on the stack (i.e., is a local variable or, rarely, a parameter to a function). As an impact it is known to affect confidentiality, integrity, and availability. The summary by CVE is: 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. The advisory is shared at github.com. This vulnerability is known as CVE-2026-31971 since 03/10/2026. The exploitation appears to be easy. The attack can be launched remotely. The exploitation doesn't need any form of authentication. It demands that the victim is doing some kind of user interaction. Technical details are known, but no exploit is available. Upgrading to version 1.21.1 or 1.22.2 eliminates this vulnerability. Applying the patch 01cd003b46fa2ebea4d9be5475b11217eb4c11be 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: Stack-based overflow CWE: CWE-121 / 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: 01cd003b46fa2ebea4d9be5475b11217eb4c11be 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-jvx4-4wq7-6fmh Status: Confirmed CVE: CVE-2026-31971 (🔒) GCVE (CVE): GCVE-0-2026-31971 GCVE (VulDB): GCVE-100-351625 Entryinfo Created: 03/19/2026 00:00 Changes: 03/19/2026 00:00 (70) Complete: 🔍 Cache ID: 99:167:101 Discussion No comments yet. Languages: en. Please log in to comment. ◂ PreviousOverviewNext ▸