CVE-2026-31971

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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_LEN` method, the `cram_byte_array_len_decode()` failed to validate that the amount of data being unpacked matched the size of the output buffer where it was to be stored. Depending on the data series being read, this could result either in a heap or a stack overflow with attacker-controlled bytes. Depending on the data stream this could result either in a heap buffer overflow or a stack overflow. If a user opens a file crafted to exploit this issue it could lead to the program crashing, overwriting of data structures on the heap or stack in ways not expected by the program, or changing the control flow of 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."}, {"lang": "es", "value": "HTSlib es una biblioteca para leer y escribir formatos de archivo de bioinform\u00e1tica. 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. Al leer datos codificados utilizando el m\u00e9todo 'BYTE_ARRAY_LEN', la funci\u00f3n 'cram_byte_array_len_decode()' no valid\u00f3 que la cantidad de datos que se estaban desempaquetando coincidiera con el tama\u00f1o del b\u00fafer de salida donde se iba a almacenar. Dependiendo de la serie de datos que se leyera, esto podr\u00eda resultar en un desbordamiento de mont\u00f3n o un desbordamiento de pila con bytes controlados por el atacante. Dependiendo del flujo de datos, esto podr\u00eda resultar en un desbordamiento de b\u00fafer en el mont\u00f3n o un desbordamiento de pila. Si un usuario abre un archivo dise\u00f1ado para explotar este problema, podr\u00eda provocar el bloqueo del programa, la sobrescritura de estructuras de datos en el mont\u00f3n o la pila de maneras no esperadas por el programa, o el cambio del flujo de control del programa. Podr\u00eda ser posible usar esto para obtener ejecuci\u00f3n de c\u00f3digo arbitrario. 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-2026-31971", "lastModified": "2026-06-17T10:34:52.020", "metrics": {"cvssMetricV31": [{"cvssData": {"attackComplexity": "LOW", "attackVector": "NETWORK", "availabilityImpact": "HIGH", "baseScore": 8.1, "baseSeverity": "HIGH", "confidentialityImpact": "NONE", "integrityImpact": "HIGH", "privilegesRequired": "NONE", "scope": "UNCHANGED", "userInteraction": "REQUIRED", "vectorString": "CVSS:3.1/AV:N/AC:L/PR:N/UI:R/S:U/C:N/I:H/A:H", "version": "3.1"}, "exploitabilityScore": 2.8, "impactScore": 5.2, "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": 7.1, "baseSeverity": "HIGH", "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": "PASSIVE", "valueDensity": "NOT_DEFINED", "vectorString": "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/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": "HIGH", "vulnerabilityResponseEffort": "NOT_DEFINED"}, "source": "security-advisories@github.com", "type": "Secondary"}], "ssvcV203": [{"source": "134c704f-9b21-4f2e-91b3-4a467353bcc0", "ssvcData": {"id": "CVE-2026-31971", "options": [{"exploitation": "none"}, {"automatable": "no"}, {"technicalImpact": "partial"}], "role": "CISA Coordinator", "timestamp": "2026-03-18T20:15:12.038273Z", "version": "2.0.3"}}]}, "published": "2026-03-18T20:16:22.243", "references": [{"source": "security-advisories@github.com", "tags": ["Patch"], "url": "https://github.com/samtools/htslib/commit/01cd003b46fa2ebea4d9be5475b11217eb4c11be"}, {"source": "security-advisories@github.com", "tags": ["Patch", "Vendor Advisory"], "url": "https://github.com/samtools/htslib/security/advisories/GHSA-jvx4-4wq7-6fmh"}], "sourceIdentifier": "security-advisories@github.com", "vulnStatus": "Analyzed", "weaknesses": [{"description": [{"lang": "en", "value": "CWE-121"}, {"lang": "en", "value": "CWE-122"}, {"lang": "en", "value": "CWE-787"}, {"lang": "en", "value": "CWE-1284"}], "source": "security-advisories@github.com", "type": "Secondary"}]}

{}

{"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": "2026-03-19T15:56:21.681876+00:00", "value": {"mitigation_remediation": ["Update the HTSlib library to version 1.23.1 or newer, which includes the buffer\u2011overflow fix.", "Verify that your bioinformatics pipelines are linked against the updated library and re\u2011compile if necessary.", "Re\u2011scan or re\u2011validate any CRAM files that were previously processed with older versions to ensure no corruption occurred."], "summary": {"action": "Patch ASAP", "impact": "Remote Code Execution"}, "threat_synthesis": {"affected_systems": "The issue affects the samtools/htslib library on versions prior to 1.23.1, 1.22.2, and 1.21.1. Versions listed in the KNOWN_CPES or the vendor patch notes indicate that these releases include the fix. Any deployment that uses these libraries to process CRAM files is therefore affected, especially in bioinformatics pipelines that open untrusted data.", "description_and_impact": "HTSlib is a bioinformatics library that reads and writes CRAM files. The vulnerability resides in cram_byte_array_len_decode() when decoding data serialized with the BYTE_ARRAY_LEN method. The function fails to validate that the amount of data being unpacked matches the size of the output buffer, allowing an attacker to supply crafted CRAM data that causes either a heap or a stack overflow. This overflow can corrupt program data structures or hijack control flow, potentially leading to arbitrary code execution. The weakness is a classic buffer overflow (CWE\u2011121, CWE\u2011122, CWE\u2011787, CWE\u20111284) and may be exploited by any user who opens a malicious file.", "risk_and_exploitability": "The CVSS base score is 7.1, indicating a moderate to high severity. The EPSS score is less than 1%, suggesting a low probability of current exploitation, and the vulnerability is not listed in the CISA KEV catalog. Nevertheless, because the flaw can lead to remote code execution on the host that runs the library, it is considered a critical risk for systems that ingest untrusted CRAM files. An attacker would need to supply a malicious CRAM file to the vulnerable parser; no additional privileges are required for the attacker to trigger the overflow."}}}}, "created": "2026-03-19T08:55:36.839921+00:00", "updated": "2026-03-25T11:52:18.709450+00:00", "vendors": ["samtools", "samtools$PRODUCT$htslib"]}