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OpenAdvisories
Medium · 6.9 CVE-2026-31965 EUVD-2026-12934

HTSlib CRAM reader has out-of-bounds reads due to improper validation of input

Published Mar 18, 2026 · Updated Mar 19, 2026 · Assigned by GitHub_M

Description

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.

Affected products

VendorProductAffectedFixed
samtools htslib < 1.21.1, >= 1.22, < 1.22.2, = 1.23 —

Fixed in Linux distributions

Distributions backport fixes, so the version that fixes this vulnerability differs per release — upgrade to at least the version shown. From the distributions' security trackers and advisories.

ReleasePackageFixed inAdvisory
Debian 14 htslib 1.24-2 —
Debian 13 htslib No fix yet —
Debian 12 htslib No fix yet —
ReleasePackageFixed inAdvisory
Ubuntu 26.10 htslib No fix yet —
Ubuntu 26.04 LTS htslib No fix yet —
Ubuntu 25.10 htslib No fix yet —
Ubuntu 24.04 LTS htslib No fix yet —
Ubuntu 22.04 LTS htslib No fix yet —
Show 4 more (older releases, extended support, other products)
ReleasePackageFixed inAdvisory
Ubuntu 20.04 LTS htslib No fix yet —
Ubuntu Pro 18.04 LTS htslib No fix yet —
Ubuntu Pro 16.04 LTS htslib No fix yet —
Ubuntu Pro 14.04 LTS htslib No fix yet —

References