CVE-2026-31969— HTSlib CRAM decoder has a heap buffer overflow
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I. Basic Information for CVE-2026-31969
Vulnerability Information
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Vulnerability Title
HTSlib CRAM decoder has a heap buffer overflow
Source: NVD (National Vulnerability Database)
Vulnerability Description
HTSlib is a library for reading and writing bioinformatics file formats. CRAM is a compressed format which stores DNA sequence alignment data using a variety of encodings and compression methods. When reading data encoded using the `BYTE_ARRAY_STOP` method, an out-by-one error in the `cram_byte_array_stop_decode_char()` function check for a full output buffer could result in a single attacker-controlled byte being written beyond the end of a heap allocation. 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.
Source: NVD (National Vulnerability Database)
CVSS Information
N/A
Source: NVD (National Vulnerability Database)
Vulnerability Type
堆缓冲区溢出
Source: NVD (National Vulnerability Database)
Vulnerability Title
HTSlib 缓冲区错误漏洞
Source: CNNVD (China National Vulnerability Database)
Vulnerability Description
HTSlib是samtools开源的一个C语言的库文件。 HTSlib 1.23.1之前版本、1.22.2之前版本和1.21.1之前版本存在缓冲区错误漏洞，该漏洞源于cram_byte_array_stop_decode_char函数存在差一错误，可能导致堆缓冲区溢出。
Source: CNNVD (China National Vulnerability Database)
CVSS Information
N/A
Source: CNNVD (China National Vulnerability Database)
Vulnerability Type
N/A
Source: CNNVD (China National Vulnerability Database)
Affected Products
II. Public POCs for CVE-2026-31969
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Same Patch Batch · samtools · 2026-03-18 · 12 CVEs total
| CVE-2026-31962 | HTSlib CRAM reader has heap buffer overflow due to improper validation of input | |
| CVE-2026-31964 | HTSlib CRAM decoder has a NULL Pointer Dereference | |
| CVE-2026-31963 | HTSlib CRAM reader has heap buffer overflow due to improper validation of input | |
| CVE-2026-31965 | HTSlib CRAM reader has out-of-bounds reads due to improper validation of input | |
| CVE-2026-31966 | HTSlib CRAM reader has out-of-bounds read due to improper validation of input | |
| CVE-2026-31967 | HTSlib CRAM reader has out-of-bounds read due to improper validation of input | |
| CVE-2026-31968 | HTSlib CRAM decoder vulnerable to buffer overflow | |
| CVE-2026-31971 | HTSlib CRAM decoder vulnerable to buffer overflow | |
| CVE-2026-31970 | HTSlib BGZF index file reader has a heap buffer overflow | |
| CVE-2026-31973 | NULL pointer dereference in samtools cram-size | |
| CVE-2026-31972 | samtools mpileup has use-after-free leading to an invalid read |
IV. Related Vulnerabilities
Same product: htslib
- CVE-2026-31971
HTSlib CRAM decoder vulnerable to buffer overflow - CVE-2026-31970
HTSlib BGZF index file reader has a heap buffer overflow - CVE-2026-31968
HTSlib CRAM decoder vulnerable to buffer overflow - CVE-2026-31967
HTSlib CRAM reader has out-of-bounds read due to improper va - CVE-2026-31966
HTSlib CRAM reader has out-of-bounds read due to improper va
Same vendor: samtools
- CVE-2026-31973
NULL pointer dereference in samtools cram-size - CVE-2026-31972
samtools mpileup has use-after-free leading to an invalid re - CVE-2026-31971
HTSlib CRAM decoder vulnerable to buffer overflow - CVE-2026-31970
HTSlib BGZF index file reader has a heap buffer overflow - CVE-2026-31968
HTSlib CRAM decoder vulnerable to buffer overflow
Same weakness: CWE-122
- CVE-2026-8261
Squirrel sqobject.cpp Load heap-based overflow - CVE-2026-8213
OSGeo gdal Grid File GDapi.c GDSDfldsrch heap-based overflow - CVE-2026-8212
OSGeo gdal SWapi.c SWSDfldsrch heap-based overflow - CVE-2026-42309
Pillow: Heap buffer overflow with nested list coordinates - CVE-2026-45130
Vim: Heap Buffer Overflow in spell file loading
V. Comments for CVE-2026-31969
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