CVE-2017-1000206 in samtools htslib Library
Summary
by MITRE
samtools htslib library version 1.4.0 and earlier is vulnerable to buffer overflow in the CRAM rANS codec resulting in potential arbitrary code execution
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Analysis
by VulDB Data Team • 12/08/2019
The vulnerability identified as CVE-2017-1000206 affects the samtools htslib library version 1.4.0 and earlier, presenting a critical buffer overflow condition within the CRAM rANS codec implementation. This flaw resides in the decompression routine of the CRAM file format processing component, which is widely used in genomic data analysis workflows. The issue manifests when the library processes malformed CRAM files that contain specially crafted data structures designed to trigger the buffer overflow during decompression operations.
The technical exploitation of this vulnerability occurs through improper bounds checking within the rANS (range ANS) compression algorithm implementation. The flaw specifically targets the decoding process where the library fails to validate input data sizes against allocated buffer boundaries. When processing CRAM files with maliciously constructed compressed data, the decompression routine can overwrite adjacent memory regions, potentially allowing attackers to execute arbitrary code with the privileges of the process running the affected library. This represents a classic buffer overflow vulnerability that can be leveraged for remote code execution in environments where untrusted CRAM files are processed automatically.
The operational impact of this vulnerability extends across various genomic analysis platforms and bioinformatics workflows that rely on samtools for processing CRAM formatted sequence data. Organizations utilizing next-generation sequencing data processing pipelines, genomic databases, and research computing environments are particularly at risk. The vulnerability can be exploited through multiple attack vectors including web-based file uploads, automated processing of genomic datasets, and collaborative research environments where data sharing occurs. The potential for arbitrary code execution makes this a critical concern for any system handling genomic data, as attackers could gain complete control over computational resources processing sensitive biological information.
Mitigation strategies for CVE-2017-1000206 primarily focus on immediate software updates and deployment of patched versions of the samtools htslib library. Organizations should prioritize upgrading to version 1.5 or later where the buffer overflow has been addressed through proper bounds checking and input validation. Additional defensive measures include implementing strict file validation procedures for CRAM inputs, deploying automated scanning systems to identify potentially malicious files, and establishing network segmentation to limit the impact of potential exploitation. Security monitoring should include detection of unusual processing patterns and memory access violations during CRAM file handling operations. The vulnerability aligns with CWE-121, which describes stack-based buffer overflow conditions, and maps to ATT&CK technique T1059.007 for execution through command and scripting interpreter. Organizations should also consider implementing sandboxing mechanisms for processing untrusted genomic data and maintaining comprehensive backup procedures to ensure rapid recovery from potential exploitation incidents.