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, the value of the mate reference id field was not validated. Later use of this value, for example when converting the data to SAM format, could result in the out of bounds array reads when looking up the corresponding reference name. If the array value obtained also happened to be a valid pointer, it would be interpreted as a string and an attempt would be made to write the data as part of the SAM record. 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
| 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 | — |