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Medium · 6.9 CVE-2026-31966 EUVD-2026-12936

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

Published Mar 18, 2026 · Updated Mar 18, 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. 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 CRAM records, the reference data is stored in a char array, and parts matching the alignment record sequence are copied over as necessary. Due to insufficient validation of the feature data series, it was possible to make the `cram_decode_seq()` function copy data from either before the start, or after the end of the stored reference either into the buffer used to store the output sequence for the cram record, or into the buffer used to build the SAM `MD` tag. This allowed arbitrary data to be leaked to the calling function. This bug may allow information about program state to be leaked. It may also cause a program crash through an attempt 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