CVE-2026-31963: high-severity vulnerability in samtools htslib
HTSlib CRAM reader has heap buffer overflow due to improper validation of input
Published
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21Vexday Risk Score
No sign of exploitation. No public exploitation artifact known so far.
ssvc Trackcvss 8.8epss 0.4%
HTSlib is a library for reading and writing bioinformatics file formats. CRAM is a compressed format which stores DNA sequence alignment data. As one method of removing redundant data, CRAM uses reference-based compression so that instead of storing the full sequence for each alignment record it stores a location in an external reference sequence along with a list of differences to the reference at that location as a sequence of "features". When decoding these features, an out-by-one error in a test for CRAM features that appear beyond the extent of the CRAM record sequence could result in an invalid write of one attacker-controlled byte beyond the end of a heap buffer. 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.
CVSS:4.0/AV:N/AC:L/AT:N/PR:N/UI:N/VC:N/VI:H/VA:L/SC:N/SI:N/SA:N
Affected products
samtools · htslibRelated CVEs — samtools htslib
In the same product, most dangerous first.
CVE-2026-31966MEDIUMHTSlib CRAM reader has out-of-bounds read due to improper validation of inputEPSS 0.5%CVE-2026-31970HIGHHTSlib BGZF index file reader has a heap buffer overflowEPSS 0.5%CVE-2026-31967MEDIUMHTSlib CRAM reader has out-of-bounds read due to improper validation of inputEPSS 0.5%CVE-2026-31968HIGHHTSlib CRAM decoder vulnerable to buffer overflowEPSS 0.4%CVE-2026-31965MEDIUMHTSlib CRAM reader has out-of-bounds reads due to improper validation of inputEPSS 0.4%CVE-2026-31962HIGHHTSlib CRAM reader has heap buffer overflow due to improper validation of inputEPSS 0.4%