ubuntu-cve-2026-31963
Vulnerability from osv_ubuntu
Published
2026-03-18 19:16
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. As one method of removing redundant data, CRAM uses reference-based compression so that instead of storing the full sequence for each alignment record it stores a location in an external reference sequence along with a list of differences to the reference at that location as a sequence of "features". When decoding these features, an out-by-one error in a test for CRAM features that appear beyond the extent of the CRAM record sequence could result in an invalid write of one attacker-controlled byte beyond the end of a heap buffer. 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
8.8 (High)
CVSS:4.0/AV:N/AC:L/AT:N/PR:N/UI:N/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. As one method of removing redundant data, CRAM uses reference-based compression so that instead of storing the full sequence for each alignment record it stores a location in an external reference sequence along with a list of differences to the reference at that location as a sequence of \"features\". When decoding these features, an out-by-one error in a test for CRAM features that appear beyond the extent of the CRAM record sequence could result in an invalid write of one attacker-controlled byte beyond the end of a heap buffer. 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-2026-31963",
  "modified": "2026-05-20T15:27:20Z",
  "published": "2026-03-18T19:16:00Z",
  "references": [
    {
      "type": "REPORT",
      "url": "https://ubuntu.com/security/CVE-2026-31963"
    },
    {
      "type": "REPORT",
      "url": "https://www.cve.org/CVERecord?id=CVE-2026-31963"
    },
    {
      "type": "REPORT",
      "url": "https://github.com/samtools/htslib/security/advisories/GHSA-qgqh-h2q9-7w3c"
    },
    {
      "type": "REPORT",
      "url": "https://github.com/samtools/htslib/commit/8bcc9907be0f945ddc31796d64f078fa05456acd"
    }
  ],
  "related": [],
  "schema_version": "1.7.0",
  "severity": [
    {
      "score": "CVSS:4.0/AV:N/AC:L/AT:N/PR:N/UI:N/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-2026-31963"
  ]
}



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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.