CVE-2026-31968

Summary

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. For the VARINT and CONST encodings, incomplete validation of the context in which the encodings were used could result in up to eight bytes being written beyond the end of a heap allocation, or up to eight bytes being written to the location of a one byte variable on the stack, possibly causing the values to adjacent variables to change unexpectedly. 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.

Affected Software

VendorProductVersion RangeStatus
samtoolshtslib< 1.21.1affected
samtoolshtslib>= 1.22, < 1.22.2affected
samtoolshtslib= 1.23affected

Weaknesses

  • CWE-121: CWE-121: Stack-based Buffer Overflow
  • CWE-122: CWE-122: Heap-based Buffer Overflow
  • CWE-787: CWE-787: Out-of-bounds Write
  • CWE-843: CWE-843: Access of Resource Using Incompatible Type ('Type Confusion')

ADP Enrichment

CISA ADP Vulnrichment

  • SSVC:
  • Exploitation: none
    • Automatable: yes
    • Technical Impact: partial

References