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CVE-2026-31967

CVE-2026-31967 · HTSlib CRAM reader has out-of-bounds read 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. In the `cram_decode_slice()` function called while reading CRAM records, the value of the mate reference id field was not validated. Later use of this value, for example when converting the data to SAM format, could result in the out of bounds array reads when looking up the corresponding reference name. If the array value obtained also happened to be a valid pointer, it would be interpreted as a string and an attempt would be made to write the data as part of the SAM record. 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. There is no workaround for this issue.

CVSS 6.9 · Medium · EPSS 0.5% · 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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