CVE-2026-31964

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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."}, {"lang": "es", "value": "HTSlib es una biblioteca para leer y escribir formatos de archivo bioinform\u00e1ticos. CRAM es un formato comprimido que almacena datos de alineaci\u00f3n de secuencias de ADN utilizando una variedad de codificaciones y m\u00e9todos de compresi\u00f3n. Aunque la mayor\u00eda de los registros de alineaci\u00f3n almacenan valores de secuencia de ADN y de calidad, el formato tambi\u00e9n permite omitir estos datos en ciertos casos para ahorrar espacio. Debido a algunas peculiaridades del formato CRAM, es necesario manejar estos registros con cuidado, ya que en realidad almacenar\u00e1n datos que deben ser consumidos y luego descartados. Desafortunadamente, las codificaciones CONST, XPACK y XRLE no implementaron correctamente la interfaz necesaria para hacer esto. Intentar decodificar registros con datos de secuencia o calidad omitidos utilizando estas codificaciones resultar\u00eda en un intento de escribir en un puntero NULL. Explotar este error causa una desreferencia de puntero NULL. T\u00edpicamente, esto har\u00e1 que el programa falle. Las versiones 1.23.1, 1.22.2 y 1.21.1 incluyen correcciones para este problema. No hay una soluci\u00f3n alternativa para este problema."}], "id": "CVE-2026-31964", "lastModified": "2026-06-17T10:34:51.160", "metrics": {"cvssMetricV31": [{"cvssData": {"attackComplexity": "LOW", "attackVector": "NETWORK", "availabilityImpact": "HIGH", "baseScore": 7.5, "baseSeverity": "HIGH", "confidentialityImpact": "NONE", "integrityImpact": "NONE", "privilegesRequired": "NONE", "scope": "UNCHANGED", "userInteraction": "NONE", "vectorString": "CVSS:3.1/AV:N/AC:L/PR:N/UI:N/S:U/C:N/I:N/A:H", "version": "3.1"}, "exploitabilityScore": 3.9, "impactScore": 3.6, "source": "nvd@nist.gov", "type": "Primary"}], "cvssMetricV40": [{"cvssData": {"Automatable": "NOT_DEFINED", "Recovery": "NOT_DEFINED", "Safety": "NOT_DEFINED", "attackComplexity": "LOW", "attackRequirements": "NONE", "attackVector": "NETWORK", "availabilityRequirement": "NOT_DEFINED", "baseScore": 6.9, "baseSeverity": "MEDIUM", "confidentialityRequirement": "NOT_DEFINED", "exploitMaturity": "NOT_DEFINED", "integrityRequirement": "NOT_DEFINED", "modifiedAttackComplexity": "NOT_DEFINED", "modifiedAttackRequirements": "NOT_DEFINED", "modifiedAttackVector": "NOT_DEFINED", "modifiedPrivilegesRequired": "NOT_DEFINED", "modifiedSubAvailabilityImpact": "NOT_DEFINED", "modifiedSubConfidentialityImpact": "NOT_DEFINED", "modifiedSubIntegrityImpact": "NOT_DEFINED", "modifiedUserInteraction": "NOT_DEFINED", "modifiedVulnAvailabilityImpact": "NOT_DEFINED", "modifiedVulnConfidentialityImpact": "NOT_DEFINED", "modifiedVulnIntegrityImpact": "NOT_DEFINED", "privilegesRequired": "NONE", "providerUrgency": "NOT_DEFINED", "subAvailabilityImpact": "NONE", "subConfidentialityImpact": "NONE", "subIntegrityImpact": "NONE", "userInteraction": "NONE", "valueDensity": "NOT_DEFINED", "vectorString": "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/E:X/CR:X/IR:X/AR:X/MAV:X/MAC:X/MAT:X/MPR:X/MUI:X/MVC:X/MVI:X/MVA:X/MSC:X/MSI:X/MSA:X/S:X/AU:X/R:X/V:X/RE:X/U:X", "version": "4.0", "vulnAvailabilityImpact": "LOW", "vulnConfidentialityImpact": "NONE", "vulnIntegrityImpact": "LOW", "vulnerabilityResponseEffort": "NOT_DEFINED"}, "source": "security-advisories@github.com", "type": "Secondary"}], "ssvcV203": [{"source": "134c704f-9b21-4f2e-91b3-4a467353bcc0", "ssvcData": {"id": "CVE-2026-31964", "options": [{"exploitation": "none"}, {"automatable": "yes"}, {"technicalImpact": "partial"}], "role": "CISA Coordinator", "timestamp": "2026-03-18T18:46:07.706478Z", "version": "2.0.3"}}]}, "published": "2026-03-18T19:16:04.633", "references": [{"source": "security-advisories@github.com", "tags": ["Patch"], "url": "https://github.com/samtools/htslib/commit/e64e68da567d2309509d059ace016d5d7fc7514f"}, {"source": "security-advisories@github.com", "tags": ["Patch", "Vendor Advisory"], "url": "https://github.com/samtools/htslib/security/advisories/GHSA-5w97-85gf-86rm"}], "sourceIdentifier": "security-advisories@github.com", "vulnStatus": "Analyzed", "weaknesses": [{"description": [{"lang": "en", "value": "CWE-476"}], "source": "security-advisories@github.com", "type": "Secondary"}]}

{"bugzilla": {"description": "htslib: HTSlib: Denial of Service via NULL pointer dereference in CRAM decoding", "id": "2448756", "url": "https://bugzilla.redhat.com/show_bug.cgi?id=2448756"}, "csaw": false, "cvss3": {"cvss3_base_score": "5.0", "cvss3_scoring_vector": "CVSS:3.1/AV:L/AC:L/PR:L/UI:R/S:U/C:N/I:N/A:H", "status": "draft"}, "cwe": "CWE-476", "details": ["A flaw was found in HTSlib, a library for reading and writing bioinformatics file formats. When processing specially crafted CRAM (Compressed Reference-aligned Alignment Map) data, specifically records that omit sequence or quality data using the CONST, XPACK, or XRLE encodings, the library attempts to write to a NULL pointer. This NULL pointer dereference can cause the program to crash, leading to a Denial of Service (DoS)."], "name": "CVE-2026-31964", "public_date": "2026-03-18T18:27:26Z", "references": ["https://www.cve.org/CVERecord?id=CVE-2026-31964\nhttps://nvd.nist.gov/vuln/detail/CVE-2026-31964\nhttps://github.com/samtools/htslib/commit/e64e68da567d2309509d059ace016d5d7fc7514f\nhttps://github.com/samtools/htslib/security/advisories/GHSA-5w97-85gf-86rm"], "statement": "This MODERATE NULL pointer dereference in HTSlib's CRAM decoder affects the CONST, XPACK, and XRLE encodings when processing records with omitted data. Exploitation requires local access and user interaction. Impact is limited to availability (crash/DoS) with no confidentiality or integrity impact. Affects htslib and python-pysam in EPEL and Fedora. Fixed in versions 1.23.1, 1.22.2, and 1.21.1.", "threat_severity": "Moderate"}

{"affected": [{"configurations": [{"platform": null, "status": "affected", "versions": {"scheme": "semver", "value": "[0,1.21.1)"}}, {"platform": null, "status": "affected", "versions": {"scheme": "generic", "value": "[1.22,1.22.2)"}}, {"platform": null, "status": "affected", "versions": {"scheme": "generic", "value": "1.23"}}], "enrichment": {"confidence": 100.0, "confidence_source": "cna", "scores": [{"score": 100.0, "source": "cna"}]}, "product": "htslib", "vendor": "samtools"}], "analysis": {"en": {"generated_at": "2026-03-19T16:51:05.407009+00:00", "value": {"mitigation_remediation": ["Upgrade HTSlib to version 1.23.1, 1.22.2, or 1.21.1, or later, as these releases contain the bug fix.", "Verify that any applications using HTSlib are linked against the patched library; if an upgrade cannot be performed immediately, avoid processing CRAM files that omit sequence or quality data until the fix is applied."], "summary": {"action": "Patch", "impact": "Null pointer dereference causing program crash (DoS)"}, "threat_synthesis": {"affected_systems": "The affected product is samtools:htslib. All releases of HTSlib that predates the specific patched versions are vulnerable. The CVE notes that versions 1.23.1, 1.22.2, and 1.21.1 contain the fix; therefore any older version (including 1.23.0, 1.22.1, 1.21.0, etc.) is considered vulnerable.", "description_and_impact": "HTSlib is a widely used library for processing bioinformatics file formats, including the compressed CRAM format. The vulnerability lies in the handling of CONST, XPACK, and XRLE encodings when a CRAM record omits sequence or quality data. Because the decoder incorrectly writes to a null pointer under these conditions, the resulting crash is a classic NULL Pointer Dereference (CWE\u2011476). The impact is a denial\u2011of\u2011service condition; no direct data exfiltration or code execution is provided by the flaw itself.", "risk_and_exploitability": "The CVSS score of 6.9 indicates moderate severity, while the EPSS score of less than 1\u202f% suggests a low likelihood of widespread exploitation in the near term. The vulnerability is not listed in CISA\u2019s KEV catalog. The most plausible attack vector is the delivery of a malicious CRAM file that triggers the faulty decoder during normal processing, which could occur via a local user or a remote user submitting data to an application that incorporates HTSlib. The exploit will cause the consuming process to crash, leading to service interruption but not compromising other system components."}}}}, "created": "2026-03-19T08:55:43.622807+00:00", "updated": "2026-03-25T11:52:26.294689+00:00", "vendors": ["samtools", "samtools$PRODUCT$htslib"]}