# CVE-2026-31963: htslib: HTSlib is a library for reading and writing bioinformatics file formats

CVE-2026-31963 is fixed in 12 products on 1 platform, first by DEBIAN-CVE-2026-31963, released March 18, 2026. It is not reported as exploited. Patch Radar priority: High.

- Web page: https://patchblox.com/security/cve/CVE-2026-31963
- Priority: High
- CVSS: 8.1 (high)
- EPSS: 0.0037
- 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. 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.

## 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-2026-31963](https://patchblox.com/security/data/fix/linux/debian-cve-2026-31963.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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