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CVE-2026-31963

CVE-2026-31963 · HTSlib CRAM reader has heap buffer overflow due to improper validation of input

This page contains facts from public vulnerability sources. Check the original advisory before updating.

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 these features, an out-by-one error in a test for CRAM features that appear beyond the extent of the CRAM record sequence could result in an invalid write of one attacker-controlled byte beyond the end of a heap buffer. 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.

CVSS 8.8 · High · EPSS 0.4% · Fix available

Published
Updated

Stack: system

Affected products and versions

  • htslib

    Versions
    • < 1.21.1: Affected
    • >= 1.22, < 1.22.2: Affected
    • = 1.23: Affected

    No fix published

  • htslib Debian:12

    Versions
    • 1.16+ds-3
    • 1.17+ds-0+exp1
    • 1.17+ds-1
    • 1.18+ds-0+exp1
    • 1.18+ds-1
    • 1.19+ds-0+exp0
    • 1.19+ds-1
    • 1.19+ds-1+exp1
    • 1.19+ds-1.1
    • 1.20+ds-1
    • 1.20+ds-2
    • 1.21+ds-0+exp1
    • 1.21+ds-0+exp2
    • 1.21+ds-1
    • 1.22.1+ds-1
    • 1.22.1+ds-2
    • 1.22.1+ds2-1
    • 1.24-1
    • 1.24-2
    • 1.24-3
    Affected ranges
    • ECOSYSTEM: (−∞, +∞)

    No fix published

  • htslib Debian:13

    Versions
    • 1.21+ds-1
    • 1.22.1+ds-1
    • 1.22.1+ds-2
    • 1.22.1+ds2-1
    • 1.24-1
    • 1.24-2
    • 1.24-3
    Affected ranges
    • ECOSYSTEM: (−∞, +∞)

    No fix published

  • htslib Debian:14

    Versions
    • 1.21+ds-1
    • 1.22.1+ds-1
    • 1.22.1+ds-2
    • 1.22.1+ds2-1
    • 1.24-1
    Affected ranges
    • ECOSYSTEM: < 1.24-2

    Update to 1.24-2

  • htslib Ubuntu:Pro:14.04:LTS

    Versions
    • 0.2.0~rc3-1
    • 0.2.0~rc3-1ubuntu0.1~esm1
    Affected ranges
    • ECOSYSTEM: (−∞, +∞)

    No fix published

  • htslib Ubuntu:Pro:16.04:LTS

    Versions
    • 1.2.1-1
    • 1.2.1-2
    • 1.2.1-2ubuntu1
    • 1.2.1-2ubuntu1+esm1
    Affected ranges
    • ECOSYSTEM: (−∞, +∞)

    No fix published

  • htslib Ubuntu:Pro:18.04:LTS

    Versions
    • 1.5-1
    • 1.5-4ubuntu1
    • 1.6-3ubuntu1
    • 1.6-4
    • 1.6-4build1
    • 1.7-2
    • 1.7-2ubuntu0.1~esm1
    Affected ranges
    • ECOSYSTEM: (−∞, +∞)

    No fix published

  • htslib Ubuntu:20.04:LTS

    Versions
    • 1.9-10
    • 1.9-11
    • 1.9-12
    • 1.10.2-2ubuntu1
    • 1.10.2-2ubuntu2
    • 1.10.2-3
    • 1.10.2-3ubuntu0.1
    Affected ranges
    • ECOSYSTEM: (−∞, +∞)

    No fix published

  • htslib Ubuntu:22.04:LTS

    Versions
    • 1.13+ds-2
    • 1.13+ds-2build1
    Affected ranges
    • ECOSYSTEM: (−∞, +∞)

    No fix published

  • htslib Ubuntu:24.04:LTS

    Versions
    • 1.17+ds-1
    • 1.18+ds-1
    • 1.19+ds-1.1build2
    • 1.19+ds-1.1build3
    Affected ranges
    • ECOSYSTEM: (−∞, +∞)

    No fix published

  • htslib Ubuntu:25.10

    Versions
    • 1.21+ds-1
    Affected ranges
    • ECOSYSTEM: (−∞, +∞)

    No fix published

  • htslib Ubuntu:26.10

    Versions
    • 1.22.1+ds2-1
    • 1.22.1+ds2-1build1
    Affected ranges
    • ECOSYSTEM: (−∞, +∞)

    No fix published

  • htslib Ubuntu:26.04:LTS

    Versions
    • 1.21+ds-1
    • 1.22.1+ds2-1
    Affected ranges
    • ECOSYSTEM: (−∞, +∞)

    No fix published

Original sources

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