CVE intelligence and bounded remediation

CVE-2026-31964 — HTSlib is a library for reading and writing bioinformatics file formats

High CVSS 7.5

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. 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 `CONST`, `XPACK` and `XRLE` encodings did not properly implement the interface needed to do this. Trying to decode records with omitted sequence or quality data using these encodings would result in an attempt to write to a NULL pointer. Exploiting this bug causes a NULL pointer dereference. Typically this will cause the program to crash. Versions 1.23.1, 1.22.2 and 1.21.1 include fixes for this issue. There is no workaround for this issue.

Severity
High
CVSS
7.5 (3.1)
Published
2026-03-18
CISA KEV
Not currently listed
Ecosystem
software/application
Weaknesses
CWE-476

Affected products

  • htslib / htslib
  • htslib / htslib / 1.23

Showing 2 representative product identities from 3 source matches. Confirm exact affected versions with the linked vendor and NVD evidence.

Matched remediation archetype

Buffer bounds, memory safety, and memory corruption

This catalog composition supplies bounded fallback guidance. Explicitly reviewed curated workflows load with the complete record below.

Check exposure

  • Identify affected native-code versions, build flags, architectures, parsers, codecs, drivers, and input paths in all shipped artifacts.
  • Determine whether untrusted data reaches the affected routine and the process privilege, sandbox, and network exposure.
  • Confirm statically linked, vendored, firmware, and platform-provided copies, not only package-manager records.

Remediate safely

  • Apply the maintained upstream correction or replace the affected component, then rebuild every dependent artifact from clean inputs.
  • Adopt bounds-checked interfaces, validated sizes and integer conversions, clear ownership, and memory-safe components where practical.
  • Enable supported compiler and runtime hardening and add sanitized tests and fuzz regression seeds derived from non-weaponized fixtures.

Authoritative sources

Complete CVE record and remediation plan

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