Vulnerabilities in pkg:maven/com.github.samtools/htsjdk

PACKAGE
Advisory Identifier: GHSA-96vh-4rfp-c42c
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Advisory Summary

CVE-2022-21126 is a HIGH (CVSS 7.8) remote code execution vulnerability (CWE-668: Exposure of Resource to Wrong Sphere) affecting Htsjdk libraries in the Maven ecosystem. The issue involves htsjdk is vulnerable to exposure of resource(s) to the wrong sphere. Remediation is available by upgrading affected packages to version 3.0.1.

1 Known Advisory Record(s)
Package Vulnerability Intelligence

pkg:maven/com.github.samtools/htsjdk

1 Known Advisory Record(s)

Vulnerability advisories affecting package pkg:maven/com.github.samtools/htsjdk. Select an advisory below to view technical details or fixes.

Advisory ID CVE / NVD Severity Summary
GHSA-96vh-4rfp-c42c CVE-2022-21126 HIGH HTSJDK is vulnerable to exposure of resource(s) to the wrong sphere

CVE-2022-21126 at a Glance

CVE Identifier CVE-2022-21126
GHSA Identifier GHSA-96vh-4rfp-c42c
Severity HIGH
CVSS v3.1 Base Score 7.8
CWE Classification CWE-668: Exposure of Resource to Wrong Sphere
Affected Product Htsjdk
Package Ecosystem Maven
Published Date
Last Updated

Security Impact

CVSS: 7.8

The security impact metrics below are parsed directly from the CVSS v3.1 vector string (CVSS:3.1/AV:L/AC:L/PR:L/UI:N/S:U/C:H/I:H/A:H).

Attack Vector Local (AV:L)
Attack Complexity Low (AC:L)
Privileges Required Low (PR:L)
User Interaction None (UI:N)
Scope Unchanged (S:U)
Confidentiality High (C:H)
Integrity High (I:H)
Availability High (A:H)

How to Fix CVE-2022-21126

To remediate this vulnerability, upgrade all affected Htsjdk dependencies to a patched release. Both direct and transitive dependencies should be checked, as frameworks or security libraries may pull in vulnerable versions transitively.

com.github.samtools:htsjdk fixed: 3.0.1 
<dependency>
    <groupId>com.github.samtools</groupId>
    <artifactId>htsjdk</artifactId>
    <version>3.0.1</version>
</dependency>
Verify Direct and Transitive Dependencies

Run the following command in your project directory to verify that all resolved dependencies use the patched release: 

mvn dependency:tree -Dincludes=com.github.samtools

How to Check if You Are Affected

To determine whether your Java application is affected by CVE-2022-21126, inspect your build dependencies using the Maven Dependency Plugin:

mvn dependency:tree -Dincludes=com.github.samtools

Analyze the terminal output to locate any version of Htsjdk in your dependency tree. If any resolved version matches the vulnerable ranges listed in the table below (for example, versions earlier than 3.0.1), your application is affected.

Note: The mvn dependency:tree -Dincludes=com.github.samtools command inspects the resolved dependency graph declared in your project's POM files; it does not perform automated security scanning or inspect runtime dynamic classpaths. Always verify runtime container classpaths and shaded JARs.

Technical Details

Vulnerability Mechanism & Technical Analysis

This vulnerability is classified under CWE-668: Exposure of Resource to Wrong Sphere, where the product exposes a resource to the wrong control sphere, providing unintended actors with inappropriate access to the resource. In Htsjdk, software state validation or input boundaries are circumvented during processing. Review the official source advisory statement below for specific affected components, classes, and reproduction details.

Source Advisory Statement

The package com.github.samtools:htsjdk before 3.0.1 are vulnerable to Creation of Temporary File in Directory with Insecure Permissions due to the createTempDir() function in util/IOUtil.java not checking for the existence of the temporary directory before attempting to create it.

CVE-2022-21126 Affected Htsjdk Versions

1 component(s)
Fixed Versions:
3.0.1
Product / Package Ecosystem Affected Versions Fixed Version
com.github.samtools:htsjdk
maven/com.github.samtools/htsjdk
Maven
< 3.0.1
3.0.1

References

NVD — CVE-2022-21126 NVD
https://nvd.nist.gov/vuln/detail/CVE-2022-21126
Htsjdk Source Repository REPOSITORY
https://github.com/samtools/htsjdk/pull/1617
Security Fix Commit FIX COMMIT
https://github.com/samtools/htsjdk/commit/4a4024a97ee3e87096df6ad9b22c8260bd527772
Htsjdk Source Repository REPOSITORY
https://github.com/samtools/htsjdk
Htsjdk Security Information SECURITY
https://security.snyk.io/vuln/SNYK-JAVA-COMGITHUBSAMTOOLS-3149901

Frequently Asked Questions

What is CVE-2022-21126?
CVE-2022-21126 is a security vulnerability in Htsjdk involving HTSJDK is vulnerable to exposure of resource(s) to the wrong sphere under CWE-668: Exposure of Resource to Wrong Sphere.
Which Htsjdk versions are affected?
Affected versions include releases prior to 3.0.1 across affected packages: com.github.samtools:htsjdk.
What version fixes CVE-2022-21126?
Upgrading to 3.0.1 (or the latest patched release for your respective branch) resolves the vulnerability.
Is htsjdk affected?
Yes, com.github.samtools:htsjdk is affected in releases prior to 3.0.1. Upgrade your dependency to 3.0.1 or later.
What is the CVSS score of CVE-2022-21126?
CVE-2022-21126 has a CVSS v3.1 base score of 7.8 (HIGH) with vector string CVSS:3.1/AV:L/AC:L/PR:L/UI:N/S:U/C:H/I:H/A:H.
What CWE is associated with CVE-2022-21126?
CVE-2022-21126 is classified under CWE-668: Exposure of Resource to Wrong Sphere (The product exposes a resource to the wrong control sphere, providing unintended actors with inappropriate access to the resource.).
How can I check Maven dependencies for CVE-2022-21126?
Run the dependency tree command: 'mvn dependency:tree -Dincludes=com.github.samtools'. This command lists direct and transitive dependencies in your build configuration so you can verify if a vulnerable version is resolved.
Machine-readable OSV JSON OSV v1.5 Schema
Normalized schema output
View Raw JSON 
{
  "schema_version" : "1.4.0",
  "id" : "GHSA-96vh-4rfp-c42c",
  "modified" : "2022-12-02T22:21:13Z",
  "published" : "2022-11-29T18:30:18Z",
  "aliases" : [ "CVE-2022-21126" ],
  "summary" : "HTSJDK is vulnerable to exposure of resource(s) to the wrong sphere",
  "details" : "The package com.github.samtools:htsjdk before 3.0.1 are vulnerable to Creation of Temporary File in Directory with Insecure Permissions due to the createTempDir() function in util/IOUtil.java not checking for the existence of the temporary directory before attempting to create it.",
  "severity" : [ {
    "type" : "CVSS_V3",
    "score" : "CVSS:3.1/AV:L/AC:L/PR:L/UI:N/S:U/C:H/I:H/A:H"
  } ],
  "affected" : [ {
    "package" : {
      "ecosystem" : "Maven",
      "name" : "com.github.samtools:htsjdk"
    },
    "ranges" : [ {
      "type" : "ECOSYSTEM",
      "events" : [ {
        "introduced" : "0"
      }, {
        "fixed" : "3.0.1"
      } ]
    } ]
  } ],
  "references" : [ {
    "type" : "ADVISORY",
    "url" : "https://nvd.nist.gov/vuln/detail/CVE-2022-21126"
  }, {
    "type" : "WEB",
    "url" : "https://github.com/samtools/htsjdk/pull/1617"
  }, {
    "type" : "WEB",
    "url" : "https://github.com/samtools/htsjdk/commit/4a4024a97ee3e87096df6ad9b22c8260bd527772"
  }, {
    "type" : "PACKAGE",
    "url" : "https://github.com/samtools/htsjdk"
  }, {
    "type" : "WEB",
    "url" : "https://security.snyk.io/vuln/SNYK-JAVA-COMGITHUBSAMTOOLS-3149901"
  } ],
  "database_specific" : {
    "cwe_ids" : [ "CWE-668" ],
    "severity" : "HIGH",
    "github_reviewed" : true,
    "github_reviewed_at" : "2022-12-02T22:21:13Z",
    "nvd_published_at" : "2022-11-29T17:15:00Z"
  }
}