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TI-2026-24506 Aliases CVE-2026-31962

HTSlib CRAM reader has heap buffer overflow due to improper validation of input

Priority MEDIUM 44CWE-122Published · Updated

Key facts

Attack vector
Network
Privileges required
None
User interaction
None
Attack complexity
Low
Attack requirements
None
Impact type
—
Confidentiality · integrity · availability
Low · 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. While most alignment records store DNA sequence and quality values, the format also allows them to omit this data in certain cases to save space. Due to some quirks of the CRAM format, it is necessary to handle these records carefully as they will actually store data that needs to be consumed and then discarded. Unfortunately the `cram_decode_seq()` did not handle this correctly in some cases. Where this happened it could result in reading a single byte from beyond the end of a heap allocation, followed by writing a single attacker-controlled byte to the same location. 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 0.00383 32nd 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
Yes
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-2026-31962

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-2026-24516 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
  • TI-2026-24510 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