Samtools
Monthly
HTSlib, a widely-used bioinformatics library for reading and writing sequence alignment formats, contains a critical buffer overflow vulnerability in its CRAM format decoder. The vulnerability exists in the `cram_byte_array_len_decode()` function which fails to validate that unpacked data matches the output buffer size, affecting HTSlib versions prior to 1.23.1, 1.22.2, and 1.21.1. An attacker can craft a malicious CRAM file that, when opened by a user, triggers either a heap or stack overflow with attacker-controlled bytes, potentially leading to arbitrary code execution, program crash, or memory corruption.
HTSlib versions prior to 1.23.1, 1.22.2, and 1.21.1 contain a heap buffer overflow vulnerability in the GZI index loading function `bgzf_index_load_hfile()`. An integer overflow during buffer allocation allows attackers to craft malicious `.gzi` files that trigger heap memory corruption, potentially leading to denial of service, data corruption, or remote code execution when a user opens the compromised file. No evidence of active exploitation in the wild has been reported, but the vulnerability is demonstrable and patch availability is confirmed.
HTSlib versions prior to 1.21.1, 1.22.2, and 1.23.1 contain an out-by-one error in the CRAM decoder's `cram_byte_array_stop_decode_char()` function that allows a single attacker-controlled byte to be written beyond the end of a heap allocation. This heap buffer overflow (CWE-122) affects bioinformatics applications using HTSlib to process CRAM-formatted DNA sequence alignment files, and could enable arbitrary code execution if exploited. No public exploit code or KEV status is currently documented, but patch availability exists for multiple stable release branches.
HTSlib contains a buffer overflow vulnerability in its CRAM format decoder affecting the VARINT and CONST encoding handlers, where incomplete context validation allows writes of up to eight bytes beyond heap allocation boundaries or into stack-allocated single-byte variables. This vulnerability affects HTSlib versions prior to 1.23.1, 1.22.2, and 1.21.1, and impacts any application using the library to process CRAM-formatted bioinformatics data files. An attacker can craft a malicious CRAM file to trigger heap or stack overflow conditions, potentially leading to denial of service, memory corruption, or arbitrary code execution when processed by a vulnerable application.
HTSlib contains a heap buffer overflow vulnerability in its CRAM decoder caused by an out-by-one error when validating feature boundaries. When a user opens a maliciously crafted CRAM file, an attacker can write one controlled byte beyond the end of a heap buffer, potentially causing application crashes, data corruption, or arbitrary code execution. Versions 1.23.1, 1.22.2, and 1.21.1 include fixes, and patches are available via the official GitHub repository.
HTSlib versions prior to 1.23.1, 1.22.2, and 1.21.1 contain a heap buffer overflow vulnerability in the cram_decode_seq() function when processing CRAM-formatted bioinformatics files with omitted sequence and quality data. An attacker can craft a malicious CRAM file that triggers an out-of-bounds read followed by an attacker-controlled single-byte write to heap memory, potentially enabling arbitrary code execution, data corruption, or denial of service when a user opens the file. No public exploit proof-of-concept has been identified, but the vulnerability is confirmed and patched by the HTSlib project.
SAMtools versions 1.17 and later contain a null pointer dereference vulnerability in the cram-size command due to missing error handling for the cram_decode_compression_header() function. When this function fails and returns an error, the code does not properly validate the return value before dereferencing the pointer, allowing an attacker to crash the application by providing a malformed CRAM file. This is a denial-of-service vulnerability with no active exploitation reported in the wild, though patches are available in versions 1.23.1, 1.22.2, and 1.21.1.
SAMtools mpileup command contains a use-after-free vulnerability in reference data management that can leak sensitive program state information or trigger application crashes when processing aligned DNA sequences. The vulnerability affects versions prior to 1.2 and requires no authentication or user interaction to exploit, though a patch is not yet available. An attacker could leverage this to obtain information disclosure or cause denial of service against systems processing bioinformatics data with vulnerable SAMtools versions.
HTSlib versions prior to 1.23.1, 1.22.2, and 1.21.1 contain an out-of-bounds read vulnerability in the CRAM file parser where the mate reference ID field is not validated during decoding. An attacker can craft a malicious CRAM file that, when processed by affected applications (particularly those converting CRAM to SAM format), triggers out-of-bounds array access that may leak sensitive information about program state or cause a denial of service through memory access violations. No public exploit has been reported, but no workaround exists, making patching essential.
HTSlib versions prior to 1.21.1, 1.22.2, and 1.23.1 contain a buffer over-read vulnerability in the CRAM decoder's cram_decode_seq() function that fails to properly validate feature data offsets. An attacker can craft malicious CRAM files to read arbitrary data from memory adjacent to reference sequence buffers, leading to information disclosure of program state or denial of service through memory access violations. No active exploitation has been documented, but patches are available from the vendor.
HTSlib contains an out-of-bounds read vulnerability in the cram_decode_slice() function that fails to validate the reference ID field early enough during CRAM file parsing, allowing two separate out-of-bounds reads before error detection. The vulnerability affects HTSlib versions prior to 1.23.1, 1.22.2, and 1.21.1, and can result in information disclosure through leaked memory values or application crashes when processing malicious or corrupted CRAM bioinformatics files. While the function reports an error after the reads occur, the window for exploitation exists and the practical impact depends on memory layout and application context.
HTSlib, a bioinformatics library for reading and writing sequence alignment formats, contains a null pointer dereference vulnerability in its CRAM format decoder affecting versions before 1.23.1, 1.22.2, and 1.21.1. The vulnerability exists in the CONST, XPACK, and XRLE encodings which fail to properly handle CRAM records with omitted sequence or quality data, causing attempts to write to NULL pointers when these records are decoded. An attacker can exploit this by providing a malformed CRAM file to any application using vulnerable HTSlib versions, resulting in denial of service through application crash, with no known active exploitation or public proof-of-concept at this time.
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. Rated high severity (CVSS 7.8), this vulnerability is low attack complexity. Public exploit code available.
HTSlib, a widely-used bioinformatics library for reading and writing sequence alignment formats, contains a critical buffer overflow vulnerability in its CRAM format decoder. The vulnerability exists in the `cram_byte_array_len_decode()` function which fails to validate that unpacked data matches the output buffer size, affecting HTSlib versions prior to 1.23.1, 1.22.2, and 1.21.1. An attacker can craft a malicious CRAM file that, when opened by a user, triggers either a heap or stack overflow with attacker-controlled bytes, potentially leading to arbitrary code execution, program crash, or memory corruption.
HTSlib versions prior to 1.23.1, 1.22.2, and 1.21.1 contain a heap buffer overflow vulnerability in the GZI index loading function `bgzf_index_load_hfile()`. An integer overflow during buffer allocation allows attackers to craft malicious `.gzi` files that trigger heap memory corruption, potentially leading to denial of service, data corruption, or remote code execution when a user opens the compromised file. No evidence of active exploitation in the wild has been reported, but the vulnerability is demonstrable and patch availability is confirmed.
HTSlib versions prior to 1.21.1, 1.22.2, and 1.23.1 contain an out-by-one error in the CRAM decoder's `cram_byte_array_stop_decode_char()` function that allows a single attacker-controlled byte to be written beyond the end of a heap allocation. This heap buffer overflow (CWE-122) affects bioinformatics applications using HTSlib to process CRAM-formatted DNA sequence alignment files, and could enable arbitrary code execution if exploited. No public exploit code or KEV status is currently documented, but patch availability exists for multiple stable release branches.
HTSlib contains a buffer overflow vulnerability in its CRAM format decoder affecting the VARINT and CONST encoding handlers, where incomplete context validation allows writes of up to eight bytes beyond heap allocation boundaries or into stack-allocated single-byte variables. This vulnerability affects HTSlib versions prior to 1.23.1, 1.22.2, and 1.21.1, and impacts any application using the library to process CRAM-formatted bioinformatics data files. An attacker can craft a malicious CRAM file to trigger heap or stack overflow conditions, potentially leading to denial of service, memory corruption, or arbitrary code execution when processed by a vulnerable application.
HTSlib contains a heap buffer overflow vulnerability in its CRAM decoder caused by an out-by-one error when validating feature boundaries. When a user opens a maliciously crafted CRAM file, an attacker can write one controlled byte beyond the end of a heap buffer, potentially causing application crashes, data corruption, or arbitrary code execution. Versions 1.23.1, 1.22.2, and 1.21.1 include fixes, and patches are available via the official GitHub repository.
HTSlib versions prior to 1.23.1, 1.22.2, and 1.21.1 contain a heap buffer overflow vulnerability in the cram_decode_seq() function when processing CRAM-formatted bioinformatics files with omitted sequence and quality data. An attacker can craft a malicious CRAM file that triggers an out-of-bounds read followed by an attacker-controlled single-byte write to heap memory, potentially enabling arbitrary code execution, data corruption, or denial of service when a user opens the file. No public exploit proof-of-concept has been identified, but the vulnerability is confirmed and patched by the HTSlib project.
SAMtools versions 1.17 and later contain a null pointer dereference vulnerability in the cram-size command due to missing error handling for the cram_decode_compression_header() function. When this function fails and returns an error, the code does not properly validate the return value before dereferencing the pointer, allowing an attacker to crash the application by providing a malformed CRAM file. This is a denial-of-service vulnerability with no active exploitation reported in the wild, though patches are available in versions 1.23.1, 1.22.2, and 1.21.1.
SAMtools mpileup command contains a use-after-free vulnerability in reference data management that can leak sensitive program state information or trigger application crashes when processing aligned DNA sequences. The vulnerability affects versions prior to 1.2 and requires no authentication or user interaction to exploit, though a patch is not yet available. An attacker could leverage this to obtain information disclosure or cause denial of service against systems processing bioinformatics data with vulnerable SAMtools versions.
HTSlib versions prior to 1.23.1, 1.22.2, and 1.21.1 contain an out-of-bounds read vulnerability in the CRAM file parser where the mate reference ID field is not validated during decoding. An attacker can craft a malicious CRAM file that, when processed by affected applications (particularly those converting CRAM to SAM format), triggers out-of-bounds array access that may leak sensitive information about program state or cause a denial of service through memory access violations. No public exploit has been reported, but no workaround exists, making patching essential.
HTSlib versions prior to 1.21.1, 1.22.2, and 1.23.1 contain a buffer over-read vulnerability in the CRAM decoder's cram_decode_seq() function that fails to properly validate feature data offsets. An attacker can craft malicious CRAM files to read arbitrary data from memory adjacent to reference sequence buffers, leading to information disclosure of program state or denial of service through memory access violations. No active exploitation has been documented, but patches are available from the vendor.
HTSlib contains an out-of-bounds read vulnerability in the cram_decode_slice() function that fails to validate the reference ID field early enough during CRAM file parsing, allowing two separate out-of-bounds reads before error detection. The vulnerability affects HTSlib versions prior to 1.23.1, 1.22.2, and 1.21.1, and can result in information disclosure through leaked memory values or application crashes when processing malicious or corrupted CRAM bioinformatics files. While the function reports an error after the reads occur, the window for exploitation exists and the practical impact depends on memory layout and application context.
HTSlib, a bioinformatics library for reading and writing sequence alignment formats, contains a null pointer dereference vulnerability in its CRAM format decoder affecting versions before 1.23.1, 1.22.2, and 1.21.1. The vulnerability exists in the CONST, XPACK, and XRLE encodings which fail to properly handle CRAM records with omitted sequence or quality data, causing attempts to write to NULL pointers when these records are decoded. An attacker can exploit this by providing a malformed CRAM file to any application using vulnerable HTSlib versions, resulting in denial of service through application crash, with no known active exploitation or public proof-of-concept at this time.
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. Rated high severity (CVSS 7.8), this vulnerability is low attack complexity. Public exploit code available.