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TI-2026-24513 Aliases CVE-2026-31969

HTSlib CRAM decoder has a heap buffer overflow

Priority LOW 31CWE-122Published · Updated

Key facts

Attack vector
Network
Privileges required
None
User interaction
Passive
Attack complexity
Low
Attack requirements
None
Impact type
—
Confidentiality · integrity · availability
None · High · Low
Fix status
Fixed

Attack profile from CVSS 4.0 · CNA. Fix status from CNA.

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. When reading data encoded using the `BYTE_ARRAY_STOP` method, an out-by-one error in the `cram_byte_array_stop_decode_char()` function check for a full output buffer could result in a single attacker-controlled byte being written beyond the end of a heap allocation. Exploiting this bug causes a heap buffer overflow. If a user opens a file crafted to exploit this issue, it could lead to the program crashing, or overwriting of data and heap structures in ways not expected by 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.

Why it matters now

Exploitation None reported CISA SSVC · not in CISA KEV
EPSS 0.00357 29th percentileScored 2026-11-07
Fix Fixed htslib (samtools): 1.21.1, 1.22.2

SSVC decision points

CISA ADP · SSVC 2.0.3

Exploitation
None
Automatable
No
Technical impact
Partial

The decision (Track, Attend, Act) also depends on your mission and well-being impact; see CISA's SSVC guide.

Affected products

VendorProductAffected versionsFixed inStatusSource
samtoolshtslibbefore 1.21.1; 1.22 to before 1.22.2; = 1.231.21.1, 1.22.2Patch availableCNA
  • htslib Vendorsamtools Affected before 1.21.1; 1.22 to before 1.22.2; = 1.23 Fixed in 1.21.1, 1.22.2 Patch available CNA

CPE configurations NVD · 2

CPEVersionsRoleVendor
cpe:2.3:a:htslib:htslib:*:*:*:*:*:*:*:*before 1.21.1; 1.22 to before 1.22.2VulnerableHtslib
cpe:2.3:a:htslib:htslib:1.23:*:*:*:*:*:*:*1.23VulnerableHtslib
  • cpe:2.3:a:htslib:htslib:*:*:*:*:*:*:*:* Versions before 1.21.1; 1.22 to before 1.22.2 Vulnerable ·Htslib
  • cpe:2.3:a:htslib:htslib:1.23:*:*:*:*:*:*:* Versions 1.23 Vulnerable ·Htslib

Remediation

  • Fix · CNA htslib (samtools) Fixed in 1.21.1, 1.22.2

Vendor assessments

Red Hat

Red Hat's page for this CVE →

Not affected: 1 product
  • Red Hat

Timeline

  1. 2026-10-02 Threatist record created from CVE-2026-31969

References

Patch 2

  • TI-2022-05532 Creation of Temporary File in Directory with Insecure Permissions CVSS 3.1HIGH 7.8
  • TI-2026-24512 HTSlib CRAM decoder vulnerable to buffer overflow CVSS 4.0HIGH 8.8
  • TI-2026-24507 HTSlib CRAM reader has heap buffer overflow due to improper validation of input CVSS 4.0HIGH 8.8
  • TI-2026-24506 HTSlib CRAM reader has heap buffer overflow due to improper validation of input CVSS 4.0HIGH 8.8
  • TI-2026-24516 samtools mpileup has use-after-free leading to an invalid read CVSS 4.0MEDIUM 6.9
  • TI-2026-24511 HTSlib CRAM reader has out-of-bounds read due to improper validation of input CVSS 4.0MEDIUM 6.9
See all 13 →

Sources

This product uses the NVD API but is not endorsed or certified by the NVD. Sources and licences