CVE intelligence and bounded remediation

CVE-2026-31966 — HTSlib is a library for reading and writing bioinformatics file formats

Critical CVSS 9.1

HTSlib is a library for reading and writing bioinformatics file formats. CRAM is a compressed format which stores DNA sequence alignment data. As one method of removing redundant data, CRAM uses reference-based compression so that instead of storing the full sequence for each alignment record it stores a location in an external reference sequence along with a list of differences to the reference at that location as a sequence of "features". When decoding CRAM records, the reference data is stored in a char array, and parts matching the alignment record sequence are copied over as necessary. Due to insufficient validation of the feature data series, it was possible to make the `cram_decode_seq()` function copy data from either before the start, or after the end of the stored reference either into the buffer used to store the output sequence for the cram record, or into the buffer used to build the SAM `MD` tag. This allowed arbitrary data to be leaked to the calling function. 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.…

Severity
Critical
CVSS
9.1 (3.1)
Published
2026-03-18
CISA KEV
Not currently listed
Ecosystem
software/application
Weaknesses
CWE-125, CWE-129

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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