CVE-2018-13844 in HTSlib
Summary
by MITRE
An issue has been found in HTSlib 1.8. It is a memory leak in fai_read in faidx.c.
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Analysis
by VulDB Data Team • 08/05/2024
The vulnerability identified as CVE-2018-13844 represents a critical memory management flaw within HTSlib version 1.8, specifically affecting the fai_read function located in the faidx.c source file. This issue manifests as a memory leak that occurs during the processing of sequence index files, which are commonly used in bioinformatics applications for rapid access to genomic sequences. The flaw impacts the library's ability to properly release allocated memory resources, leading to progressive memory consumption over time. HTSlib serves as a fundamental component in numerous genomic analysis tools and pipelines, making this vulnerability particularly concerning for research institutions and bioinformatics workflows that rely heavily on efficient memory management.
The technical root cause of this memory leak stems from improper memory deallocation within the fai_read function, which is responsible for reading and parsing sequence index files used in FASTA file access. When processing large genomic datasets or running long-running applications that repeatedly access indexed sequences, the function fails to properly free previously allocated memory blocks, resulting in cumulative memory consumption. This behavior aligns with CWE-401, which categorizes memory leaks as a common weakness in software systems where allocated memory is not properly released. The vulnerability is particularly insidious because it does not immediately crash applications but rather causes gradual performance degradation, making it difficult to detect during routine testing and monitoring.
The operational impact of this memory leak extends beyond simple resource consumption, affecting the reliability and scalability of bioinformatics applications that depend on HTSlib. Systems running applications such as samtools, bcftools, or various genomic analysis pipelines may experience progressive slowdowns, increased memory pressure, and potential system instability when processing large datasets over extended periods. This vulnerability is particularly dangerous in high-throughput sequencing environments where applications may run for hours or days, as the cumulative effect of memory leaks can eventually lead to system resource exhaustion and application failures. The flaw also impacts the broader bioinformatics ecosystem since many downstream tools and workflows depend on HTSlib's functionality, potentially creating cascading effects across multiple applications and research projects.
Mitigation strategies for CVE-2018-13844 primarily involve upgrading to HTSlib version 1.9 or later, where the memory leak has been addressed through proper memory management practices in the fai_read function. System administrators and bioinformatics pipeline developers should prioritize updating their HTSlib installations and verify that all dependent applications are using patched versions. Additionally, monitoring applications for unusual memory consumption patterns and implementing regular memory profiling can help detect the early signs of this vulnerability in environments where immediate upgrades are not feasible. Organizations should also consider implementing automated patch management processes to ensure timely deployment of security updates across their bioinformatics infrastructure. The ATT&CK framework categorizes this type of vulnerability under software supply chain compromises, as it represents an exploitable weakness in a widely-used open-source library that affects numerous downstream applications.