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CVE-2026-31967

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

Medium6.9EPSS 0.47%
Published
Updated
Reserved
Assigned by
GitHub_M

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.

Scores

CVSS scores of CVE-2026-31967, by who scored it
Scored byCVSSScoreVector
GitHub_MCNA (assigner)4.0Medium6.9CVSS:4.0/AV:N/AC:L/AT:N/PR:N/UI:N/VC:L/VI:N/VA:L/SC:N/SI:N/SA:N
NVDNVD · Analyzed4.0Medium6.9CVSS:4.0/AV:N/AC:L/AT:N/PR:N/UI:N/VC:L/VI:N/VA:L/SC:N/SI:N/SA:N/E:X/CR:X/IR:X/AR:X/MAV:X/MAC:X/MAT:X/MPR:X/MUI:X/MVC:X/MVI:X/MVA:X/MSC:X/MSI:X/MSA:X/S:X/AU:X/R:X/V:X/RE:X/U:X
EPSS (exploitation in 30 days)
0.47% · top 59% of all CVEs (6 Nov 2026)
CISA SSVC
Exploitation: none · Automatable: yes · Technical impact: partial
Loading the EPSS history…

The list uses the assigner's score when there is one, then CISA's, then NVD's: Medium 6.9.

Weakness

Affected products

  • samtools · htslib

    • affected < 1.21.1
    • affected >= 1.22, < 1.22.2
    • affected = 1.23

References (2)

Sources

The same CVE in the primary databases and aggregators, to check against.

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Record last updated .