ubuntu-cve-2026-31969
Vulnerability from osv_ubuntu
Published
2026-03-18 20:16
Modified
2026-05-20 15:27
Summary
Details

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_STOP method, an out-by-one error in the cram_byte_array_stop_decode_char() function check for a full output buffer could result in a single attacker-controlled byte being written beyond the end of a heap allocation. 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.

Severity
7.1 (High)
CVSS:4.0/AV:N/AC:L/AT:N/PR:N/UI:P/VC:N/VI:H/VA:L/SC:N/SI:N/SA:N
8.1 (High)
CVSS:3.1/AV:N/AC:L/PR:N/UI:R/S:U/C:N/I:H/A:H
N/A (UNKNOWN)
medium
References
To clipboard 

{
  "affected": [
    {
      "ecosystem_specific": {
        "binaries": [
          {
            "binary_name": "htslib-test",
            "binary_version": "0.2.0~rc3-1ubuntu0.1~esm1"
          },
          {
            "binary_name": "libhts0",
            "binary_version": "0.2.0~rc3-1ubuntu0.1~esm1"
          }
        ]
      },
      "package": {
        "ecosystem": "Ubuntu:Pro:14.04:LTS",
        "name": "htslib",
        "purl": "pkg:deb/ubuntu/htslib@0.2.0~rc3-1ubuntu0.1~esm1?arch=source\u0026distro=esm-infra-legacy/trusty"
      },
      "ranges": [
        {
          "events": [
            {
              "introduced": "0"
            }
          ],
          "type": "ECOSYSTEM"
        }
      ],
      "versions": [
        "0.2.0~rc3-1",
        "0.2.0~rc3-1ubuntu0.1~esm1"
      ]
    },
    {
      "ecosystem_specific": {
        "binaries": [
          {
            "binary_name": "htslib-test",
            "binary_version": "1.2.1-2ubuntu1+esm1"
          },
          {
            "binary_name": "libhts1",
            "binary_version": "1.2.1-2ubuntu1+esm1"
          },
          {
            "binary_name": "tabix",
            "binary_version": "1.2.1-2ubuntu1+esm1"
          }
        ]
      },
      "package": {
        "ecosystem": "Ubuntu:Pro:16.04:LTS",
        "name": "htslib",
        "purl": "pkg:deb/ubuntu/htslib@1.2.1-2ubuntu1+esm1?arch=source\u0026distro=esm-apps/xenial"
      },
      "ranges": [
        {
          "events": [
            {
              "introduced": "0"
            }
          ],
          "type": "ECOSYSTEM"
        }
      ],
      "versions": [
        "1.2.1-1",
        "1.2.1-2",
        "1.2.1-2ubuntu1",
        "1.2.1-2ubuntu1+esm1"
      ]
    },
    {
      "ecosystem_specific": {
        "binaries": [
          {
            "binary_name": "htslib-test",
            "binary_version": "1.7-2ubuntu0.1~esm1"
          },
          {
            "binary_name": "libhts2",
            "binary_version": "1.7-2ubuntu0.1~esm1"
          },
          {
            "binary_name": "tabix",
            "binary_version": "1.7-2ubuntu0.1~esm1"
          }
        ]
      },
      "package": {
        "ecosystem": "Ubuntu:Pro:18.04:LTS",
        "name": "htslib",
        "purl": "pkg:deb/ubuntu/htslib@1.7-2ubuntu0.1~esm1?arch=source\u0026distro=esm-apps/bionic"
      },
      "ranges": [
        {
          "events": [
            {
              "introduced": "0"
            }
          ],
          "type": "ECOSYSTEM"
        }
      ],
      "versions": [
        "1.5-1",
        "1.5-4ubuntu1",
        "1.6-3ubuntu1",
        "1.6-4",
        "1.6-4build1",
        "1.7-2",
        "1.7-2ubuntu0.1~esm1"
      ]
    },
    {
      "ecosystem_specific": {
        "binaries": [
          {
            "binary_name": "htslib-test",
            "binary_version": "1.10.2-3ubuntu0.1"
          },
          {
            "binary_name": "libhts3",
            "binary_version": "1.10.2-3ubuntu0.1"
          },
          {
            "binary_name": "tabix",
            "binary_version": "1.10.2-3ubuntu0.1"
          }
        ]
      },
      "package": {
        "ecosystem": "Ubuntu:20.04:LTS",
        "name": "htslib",
        "purl": "pkg:deb/ubuntu/htslib@1.10.2-3ubuntu0.1?arch=source\u0026distro=focal"
      },
      "ranges": [
        {
          "events": [
            {
              "introduced": "0"
            }
          ],
          "type": "ECOSYSTEM"
        }
      ],
      "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"
      ]
    },
    {
      "ecosystem_specific": {
        "binaries": [
          {
            "binary_name": "htslib-test",
            "binary_version": "1.13+ds-2build1"
          },
          {
            "binary_name": "libhts3",
            "binary_version": "1.13+ds-2build1"
          },
          {
            "binary_name": "tabix",
            "binary_version": "1.13+ds-2build1"
          }
        ]
      },
      "package": {
        "ecosystem": "Ubuntu:22.04:LTS",
        "name": "htslib",
        "purl": "pkg:deb/ubuntu/htslib@1.13+ds-2build1?arch=source\u0026distro=jammy"
      },
      "ranges": [
        {
          "events": [
            {
              "introduced": "0"
            }
          ],
          "type": "ECOSYSTEM"
        }
      ],
      "versions": [
        "1.13+ds-2",
        "1.13+ds-2build1"
      ]
    },
    {
      "ecosystem_specific": {
        "binaries": [
          {
            "binary_name": "htslib-test",
            "binary_version": "1.19+ds-1.1build3"
          },
          {
            "binary_name": "libhts3t64",
            "binary_version": "1.19+ds-1.1build3"
          },
          {
            "binary_name": "tabix",
            "binary_version": "1.19+ds-1.1build3"
          }
        ]
      },
      "package": {
        "ecosystem": "Ubuntu:24.04:LTS",
        "name": "htslib",
        "purl": "pkg:deb/ubuntu/htslib@1.19+ds-1.1build3?arch=source\u0026distro=noble"
      },
      "ranges": [
        {
          "events": [
            {
              "introduced": "0"
            }
          ],
          "type": "ECOSYSTEM"
        }
      ],
      "versions": [
        "1.17+ds-1",
        "1.18+ds-1",
        "1.19+ds-1.1build2",
        "1.19+ds-1.1build3"
      ]
    },
    {
      "ecosystem_specific": {
        "binaries": [
          {
            "binary_name": "htslib-test",
            "binary_version": "1.21+ds-1"
          },
          {
            "binary_name": "libhts3t64",
            "binary_version": "1.21+ds-1"
          },
          {
            "binary_name": "tabix",
            "binary_version": "1.21+ds-1"
          }
        ]
      },
      "package": {
        "ecosystem": "Ubuntu:25.10",
        "name": "htslib",
        "purl": "pkg:deb/ubuntu/htslib@1.21+ds-1?arch=source\u0026distro=questing"
      },
      "ranges": [
        {
          "events": [
            {
              "introduced": "0"
            }
          ],
          "type": "ECOSYSTEM"
        }
      ],
      "versions": [
        "1.21+ds-1"
      ]
    },
    {
      "ecosystem_specific": {
        "binaries": [
          {
            "binary_name": "htslib-test",
            "binary_version": "1.22.1+ds2-1"
          },
          {
            "binary_name": "libhts3t64",
            "binary_version": "1.22.1+ds2-1"
          },
          {
            "binary_name": "tabix",
            "binary_version": "1.22.1+ds2-1"
          }
        ]
      },
      "package": {
        "ecosystem": "Ubuntu:26.04:LTS",
        "name": "htslib",
        "purl": "pkg:deb/ubuntu/htslib@1.22.1+ds2-1?arch=source\u0026distro=resolute"
      },
      "ranges": [
        {
          "events": [
            {
              "introduced": "0"
            }
          ],
          "type": "ECOSYSTEM"
        }
      ],
      "versions": [
        "1.21+ds-1",
        "1.22.1+ds2-1"
      ]
    }
  ],
  "aliases": [],
  "details": "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_STOP` method, an out-by-one error in the `cram_byte_array_stop_decode_char()` function check for a full output buffer could result in a single attacker-controlled byte being written beyond the end of a heap allocation. 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.",
  "id": "UBUNTU-CVE-2026-31969",
  "modified": "2026-05-20T15:27:20Z",
  "published": "2026-03-18T20:16:00Z",
  "references": [
    {
      "type": "REPORT",
      "url": "https://ubuntu.com/security/CVE-2026-31969"
    },
    {
      "type": "REPORT",
      "url": "https://www.cve.org/CVERecord?id=CVE-2026-31969"
    },
    {
      "type": "REPORT",
      "url": "https://github.com/samtools/htslib/security/advisories/GHSA-q4cj-f4h5-fqgc"
    },
    {
      "type": "REPORT",
      "url": "https://github.com/samtools/htslib/commit/88cdf69e4b83bb550ab4f6f7134892c2ad1978f4"
    }
  ],
  "related": [],
  "schema_version": "1.7.0",
  "severity": [
    {
      "score": "CVSS:4.0/AV:N/AC:L/AT:N/PR:N/UI:P/VC:N/VI:H/VA:L/SC:N/SI:N/SA:N",
      "type": "CVSS_V4"
    },
    {
      "score": "CVSS:3.1/AV:N/AC:L/PR:N/UI:R/S:U/C:N/I:H/A:H",
      "type": "CVSS_V3"
    },
    {
      "score": "medium",
      "type": "Ubuntu"
    }
  ],
  "upstream": [
    "CVE-2026-31969"
  ]
}



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Forecast uses a logistic model when the trend is rising, or an exponential decay model when the trend is falling. Fitted via linearized least squares.

Sightings

Author Source Type Date Other

Nomenclature

  • Seen: The vulnerability was mentioned, discussed, or observed by the user.
  • Confirmed: The vulnerability has been validated from an analyst's perspective.
  • Published Proof of Concept: A public proof of concept is available for this vulnerability.
  • Exploited: The vulnerability was observed as exploited by the user who reported the sighting.
  • Patched: The vulnerability was observed as successfully patched by the user who reported the sighting.
  • Not exploited: The vulnerability was not observed as exploited by the user who reported the sighting.
  • Not confirmed: The user expressed doubt about the validity of the vulnerability.
  • Not patched: The vulnerability was not observed as successfully patched by the user who reported the sighting.


Detection rules are retrieved from Rulezet.