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CVE-2026-31964

CVE-2026-31964 · HTSlib CRAM decoder has a NULL Pointer Dereference

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. 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.

CVSS 6.9 · Medium · 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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