Description
HTSlib is a library for reading and writing bioinformatics file formats. GZI files are used to index block-compressed GZIP [BGZF] files. In the GZI loading function, `bgzf_index_load_hfile()`, it was possible to trigger an integer overflow, leading to an under- or zero-sized buffer being allocated to store the index. Sixteen zero bytes would then be written to this buffer, and, depending on the result of the overflow the rest of the file may also be loaded into the buffer as well. If the function did attempt to load the data, it would eventually fail due to not reading the expected number of records, and then try to free the overflowed 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. The easiest work-around is to discard any `.gzi` index files from untrusted sources, and use the `bgzip -r` option to recreate them.
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 | — |