CVE-2026-31965 PUBLISHED

HTSlib CRAM reader has out-of-bounds reads due to improper validation of input

Assigner: GitHub_M
Reserved: 10.03.2026 Published: 18.03.2026 Updated: 19.03.2026

HTSlib is a library for reading and writing bioinformatics file formats. CRAM is a compressed format which stores DNA sequence alignment data. In the cram_decode_slice() function called while reading CRAM records, validation of the reference id field occurred too late, allowing two out of bounds reads to occur before the invalid data was detected. The bug does allow two values to be leaked to the caller, however as the function reports an error it may be difficult to exploit them. It is also possible that the program will crash due to trying to access invalid memory. Versions 1.23.1, 1.22.2 and 1.21.1 include fixes for this issue. There is no workaround for this issue.

Metrics

CVSS Vector: CVSS:4.0/AV:N/AC:L/AT:N/PR:N/UI:N/VC:L/VI:N/VA:L/SC:N/SI:N/SA:N
CVSS Score: 6.9

Product Status

Vendor samtools
Product htslib
Versions
  • Version < 1.21.1 is affected
  • Version >= 1.22, < 1.22.2 is affected
  • Version = 1.23 is affected

References

Problem Types

  • CWE-125: Out-of-bounds Read CWE
  • CWE-129: Improper Validation of Array Index CWE