# CVE-2026-31965: htslib: HTSlib is a library for reading and writing bioinformatics file formats

CVE-2026-31965 is fixed in 12 products on 1 platform, first by DEBIAN-CVE-2026-31965, released March 18, 2026. It is not reported as exploited. Patch Radar priority: High.

- Web page: https://patchblox.com/security/cve/CVE-2026-31965
- Priority: High
- CVSS: 8.2 (high)
- EPSS: 0.0040
- CISA KEV: not listed
- Exploited (vendor report): no
- Publicly disclosed: no
- Published: Mar 18, 2026

## 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.

## Where it's fixed

| Platform | Product | Fixed in | Fix | Released |
|---|---|---|---|---|
| Linux | bcftools Fedora 43 | 1.23.1-1.fc43 | [FEDORA-2026-3B06345BF2](https://patchblox.com/security/data/fix/linux/fedora-2026-3b06345bf2.md) | Mar 19, 2026 |
| Linux | bcftools-debuginfo Fedora 43 | 1.23.1-1.fc43 | [FEDORA-2026-3B06345BF2](https://patchblox.com/security/data/fix/linux/fedora-2026-3b06345bf2.md) | Mar 19, 2026 |
| Linux | bcftools-debugsource Fedora 43 | 1.23.1-1.fc43 | [FEDORA-2026-3B06345BF2](https://patchblox.com/security/data/fix/linux/fedora-2026-3b06345bf2.md) | Mar 19, 2026 |
| Linux | htslib Debian 14 | 1.24-2 | [DEBIAN-CVE-2026-31965](https://patchblox.com/security/data/fix/linux/debian-cve-2026-31965.md) | Mar 18, 2026 |
| Linux | htslib Fedora 43 | 1.23.1-1.fc43 | [FEDORA-2026-3B06345BF2](https://patchblox.com/security/data/fix/linux/fedora-2026-3b06345bf2.md) | Mar 19, 2026 |
| Linux | htslib-debuginfo Fedora 43 | 1.23.1-1.fc43 | [FEDORA-2026-3B06345BF2](https://patchblox.com/security/data/fix/linux/fedora-2026-3b06345bf2.md) | Mar 19, 2026 |
| Linux | htslib-debugsource Fedora 43 | 1.23.1-1.fc43 | [FEDORA-2026-3B06345BF2](https://patchblox.com/security/data/fix/linux/fedora-2026-3b06345bf2.md) | Mar 19, 2026 |
| Linux | htslib-devel Fedora 43 | 1.23.1-1.fc43 | [FEDORA-2026-3B06345BF2](https://patchblox.com/security/data/fix/linux/fedora-2026-3b06345bf2.md) | Mar 19, 2026 |
| Linux | htslib-tools Fedora 43 | 1.23.1-1.fc43 | [FEDORA-2026-3B06345BF2](https://patchblox.com/security/data/fix/linux/fedora-2026-3b06345bf2.md) | Mar 19, 2026 |
| Linux | htslib-tools-debuginfo Fedora 43 | 1.23.1-1.fc43 | [FEDORA-2026-3B06345BF2](https://patchblox.com/security/data/fix/linux/fedora-2026-3b06345bf2.md) | Mar 19, 2026 |
| Linux | samtools Fedora 43 | 1.23.1-1.fc43 | [FEDORA-2026-3B06345BF2](https://patchblox.com/security/data/fix/linux/fedora-2026-3b06345bf2.md) | Mar 19, 2026 |
| Linux | samtools-debuginfo Fedora 43 | 1.23.1-1.fc43 | [FEDORA-2026-3B06345BF2](https://patchblox.com/security/data/fix/linux/fedora-2026-3b06345bf2.md) | Mar 19, 2026 |
| Linux | samtools-debugsource Fedora 43 | 1.23.1-1.fc43 | [FEDORA-2026-3B06345BF2](https://patchblox.com/security/data/fix/linux/fedora-2026-3b06345bf2.md) | Mar 19, 2026 |

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Data as of 2026-11-08T13:06:02Z UTC. Source: Patchblox Patch Radar (https://patchblox.com/security/patch-radar). Patchblox finds out-of-date software on Windows, macOS and Linux and updates it through release rings: https://patchblox.com/demo

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