HTSlib CRAM reader has out-of-bounds reads due to improper validation of input
Summary
HTSlib CRAM reader has out-of-bounds reads due to improper validation of input
Original description
The description as published by the source.
HTSlib is a library for reading and writing bioinformatics file formats. CRAM is a compressed format which stores DNA sequence alignment data. In the cram_decode_slice() function called while reading CRAM records, validation of the reference id field occurred too late, allowing two out of bounds reads to occur before the invalid data was detected. The bug does allow two values to be leaked to the caller, however as the function reports an error it may be difficult to exploit them. It is also possible that the program will crash due to trying to access invalid memory. Versions 1.23.1, 1.22.2 and 1.21.1 include fixes for this issue. There is no workaround for this issue.
Source: OSV.dev (Open Source Vulnerabilities) NVD GitHub Advisory OSV
Fix status by distribution
Fixed packages published by each distribution for this CVE
- Debian DEBIAN-CVE-2026-31965 htslib
- Ubuntu UBUNTU-CVE-2026-31965 htslib
References
- advisory github.com
- advisory github.com
- advisory nvd.nist.gov
- patch github.com