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.
History

Wed, 18 Mar 2026 20:15:00 +0000

Type Values Removed Values Added
Metrics ssvc

{'options': {'Automatable': 'yes', 'Exploitation': 'none', 'Technical Impact': 'partial'}, 'version': '2.0.3'}


Wed, 18 Mar 2026 19:30:00 +0000

Type Values Removed Values Added
Description 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.
Title HTSlib CRAM reader has out-of-bounds read due to improper validation of input
Weaknesses CWE-125
CWE-129
References
Metrics cvssV4_0

{'score': 6.9, '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'}


cve-icon MITRE

Status: PUBLISHED

Assigner: GitHub_M

Published:

Updated: 2026-03-18T19:58:55.083Z

Reserved: 2026-03-10T15:40:10.485Z

Link: CVE-2026-31967

cve-icon Vulnrichment

Updated: 2026-03-18T19:58:51.581Z

cve-icon NVD

Status : Received

Published: 2026-03-18T20:16:21.280

Modified: 2026-03-18T20:16:21.280

Link: CVE-2026-31967

cve-icon Redhat

No data.

cve-icon OpenCVE Enrichment

No data.