ubuntu-cve-2026-31964
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 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.

Severity
6.9 (Medium)
CVSS:4.0/AV:N/AC:L/AT:N/PR:N/UI:N/VC:N/VI:L/VA:L/SC:N/SI:N/SA:N
7.5 (High)
CVSS:3.1/AV:N/AC:L/PR:N/UI:N/S:U/C:N/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 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.",
  "id": "UBUNTU-CVE-2026-31964",
  "modified": "2026-05-20T15:27:20Z",
  "published": "2026-03-18T19:16:00Z",
  "references": [
    {
      "type": "REPORT",
      "url": "https://ubuntu.com/security/CVE-2026-31964"
    },
    {
      "type": "REPORT",
      "url": "https://www.cve.org/CVERecord?id=CVE-2026-31964"
    },
    {
      "type": "REPORT",
      "url": "https://github.com/samtools/htslib/security/advisories/GHSA-5w97-85gf-86rm"
    },
    {
      "type": "REPORT",
      "url": "https://github.com/samtools/htslib/commit/e64e68da567d2309509d059ace016d5d7fc7514f"
    }
  ],
  "related": [],
  "schema_version": "1.7.0",
  "severity": [
    {
      "score": "CVSS:4.0/AV:N/AC:L/AT:N/PR:N/UI:N/VC:N/VI:L/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:N/I:N/A:H",
      "type": "CVSS_V3"
    },
    {
      "score": "medium",
      "type": "Ubuntu"
    }
  ],
  "upstream": [
    "CVE-2026-31964"
  ]
}



Log in or create an account to share your comment.




Tags
Taxonomy of the tags.





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.