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CVE-2026-31971

CVE-2026-31971 · HTSlib CRAM decoder vulnerable to buffer overflow

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 using a variety of encodings and compression methods. When reading data encoded using the `BYTE_ARRAY_LEN` method, the `cram_byte_array_len_decode()` failed to validate that the amount of data being unpacked matched the size of the output buffer where it was to be stored. Depending on the data series being read, this could result either in a heap or a stack overflow with attacker-controlled bytes. Depending on the data stream this could result either in a heap buffer overflow or a stack overflow. If a user opens a file crafted to exploit this issue it could lead to the program crashing, overwriting of data structures on the heap or stack in ways not expected by the program, or changing the control flow of 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 7.1 · High · EPSS 0.3% · 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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