ubuntu-cve-2026-31967
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. 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.

Severity
6.9 (Medium)
CVSS:4.0/AV:N/AC:L/AT:N/PR:N/UI:N/VC:L/VI:N/VA:L/SC:N/SI:N/SA:N
9.1 (Critical)
CVSS:3.1/AV:N/AC:L/PR:N/UI:N/S:U/C:H/I:N/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. 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.",
  "id": "UBUNTU-CVE-2026-31967",
  "modified": "2026-05-20T15:27:20Z",
  "published": "2026-03-18T20:16:00Z",
  "references": [
    {
      "type": "REPORT",
      "url": "https://ubuntu.com/security/CVE-2026-31967"
    },
    {
      "type": "REPORT",
      "url": "https://www.cve.org/CVERecord?id=CVE-2026-31967"
    },
    {
      "type": "REPORT",
      "url": "https://github.com/samtools/htslib/security/advisories/GHSA-33x5-c6vj-8f2w"
    },
    {
      "type": "REPORT",
      "url": "https://github.com/samtools/htslib/commit/9cefb46453ad471e933b8212d4f45920524d3357"
    }
  ],
  "related": [],
  "schema_version": "1.7.0",
  "severity": [
    {
      "score": "CVSS:4.0/AV:N/AC:L/AT:N/PR:N/UI:N/VC:L/VI:N/VA:L/SC:N/SI:N/SA:N",
      "type": "CVSS_V4"
    },
    {
      "score": "CVSS:3.1/AV:N/AC:L/PR:N/UI:N/S:U/C:H/I:N/A:H",
      "type": "CVSS_V3"
    },
    {
      "score": "medium",
      "type": "Ubuntu"
    }
  ],
  "upstream": [
    "CVE-2026-31967"
  ]
}



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Nomenclature

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