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 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.
Affected products
| Vendor | Product | Affected | Fixed |
|---|---|---|---|
| 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.
Debian
Security tracker ↗| Release | Package | Fixed in | Advisory |
|---|---|---|---|
| Debian 14 | htslib | 1.24-2 | — |
| Debian 13 | htslib | No fix yet | — |
| Debian 12 | htslib | No fix yet | — |
Ubuntu
Security tracker ↗| Release | Package | Fixed in | Advisory |
|---|---|---|---|
| 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)Fewer releases
| Release | Package | Fixed in | Advisory |
|---|---|---|---|
| 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 | — |