CVE-2026-31967CWE-125CWE-129

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

Medium · published March 18, 2026

CVSS v4.0
6.9
EPSS
1%
Percentile
45.8
In the wild
Unconfirmed
What it is

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, the value of the mate reference id field was not validated. Later use of this value, for example when converting the data to SAM format, could result in the out of bounds array reads when looking up the corresponding reference name. If the array value obtained also happened to be a valid pointer, it would be interpreted as a string and an attempt would be made to write the data as part of the SAM record. This bug may allow information about program state to be leaked. It may also cause a program crash through an attempt 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.

The record
Technical detail
CVSS v4.0
6.9 · MEDIUM
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
EPSS
0.00559 · 45.8th percentile
Weaknesses
CWE-125 · Out-of-bounds Read; CWE-129 · Improper Validation of Array Index
Published
2026-03-18T19:15Z
EPSS history
Timeline
  • 18 MAR 19:15Z
    HTSlib CRAM reader has out-of-bounds read due to improper validation of input
    cvelistv5