CVE-2026-31969: HTSlib is a library for reading and writing bioinformatics file formats

Routine

HIGH 8.1UPGRADE

CVE-2026-31969 is a high-severity flaw (CVSS 8.1) affecting htslib. Below: why it ranks where it does, which versions are affected, what to do, and the exact commands.

HTSlib is a library for reading and writing bioinformatics file formats. CRAM is a compressed format which stores DNA sequence alignment data using a variety of encodings and compression methods. When reading data encoded using the `BYTE_ARRAY_STOP` method, an out-by-one error in the `cram_byte_array_stop_decode_char()` function check for a full output buffer could result in a single attacker-controlled byte being written beyond the end of a hea

Why this priority

High severity

A fixed release or distro patch exists.

Risk facts

CVSS score	8.1 (High)
Attack vector	Network (remote)
Attack complexity	Low
Privileges needed	None
User interaction	Required
EPSS exploit chance	0.3% (top 72%)
CISA exploited list	No
Weakness	CWE-122, CWE-787
Published	2026-03-18
Last modified	2026-06-17

Publisher (CNA): GitHub, Inc. · Vendor: htslib

Last updated 2026-06-17 · Sources: CVE Program, NVD, CISA KEV, EPSS and vendor advisories · How we score

Am I affected?

Timeline

2026-03-18 20:16 UTCPublished CVE record published
2026-06-17 10:34 UTCUpdated Record last modified

htslib htslib UPGRADE

Affected: < 1.21.1 · >= 1.22 and < 1.22.2 · 1.23

Fixed in: 1.21.1, 1.22.2

Safe to downgrade to: a release before 1.22

1. Check installed version

apt-cache policy htslib || rpm -q htslib || htslib --version

2. UPGRADE to 1.21.1 (Debian / Ubuntu)

sudo apt update && sudo apt install --only-upgrade htslib

2. UPGRADE (RHEL / Amazon Linux / Fedora)

sudo dnf upgrade htslib

Note

Distros often backport fixes without changing the version number. Confirm with the distro advisory or changelog.

3. If no update is available yet, DOWNGRADE to a release before 1.22 (Debian / Ubuntu)

apt-cache madison htslib sudo apt install htslib=<VERSION_BEFORE_1.22> sudo apt-mark hold htslib

3. If no update is available yet, DOWNGRADE (RHEL / Amazon Linux / Fedora)

dnf --showduplicates list htslib sudo dnf downgrade htslib-<VERSION_BEFORE_1.22> sudo dnf versionlock add htslib

Downgrade risk

Downgrading can break dependent software and may reopen older bugs. Read the distro advisory first and test on a non-production host.

After downgrade

Restart the service, and keep the package held until a fixed release ships.

Verify at the official source NVD · CVE Program · Report a problem with this page
Scores and fixes here are computed automatically from those and other public sources. Confirm with the vendor advisory before changing production systems.

Quick answers

How do I fix CVE-2026-31969?

htslib: upgrade to 1.21.1, 1.22.2. Exact commands for each OS are on this page.

Is CVE-2026-31969 being exploited?

CVE-2026-31969 is not on the CISA Known Exploited Vulnerabilities list at the time of the last update. Check again, as this can change.

What does CVE-2026-31969 affect?

CVE-2026-31969 affects htslib. Severity is high (CVSS 8.1). HTSlib is a library for reading and writing bioinformatics file formats. CRAM is a compressed format which stores DNA sequence alignment data using a variety of encodings and compression methods. When reading data encoded using the `BYTE_A

How urgent is CVE-2026-31969?

Priority 35/100. High severity

Related CVEs

CVE-2026-31971 HIGH 8.1 UPGRADE HTSlib is a library for reading and writing bioinformatics file formats
CVE-2026-31970 HIGH 8.1 UPGRADE HTSlib is a library for reading and writing bioinformatics file formats
CVE-2026-31968 HIGH 8.1 UPGRADE HTSlib is a library for reading and writing bioinformatics file formats
CVE-2026-31967 CRITICAL 9.1 UPGRADE HTSlib is a library for reading and writing bioinformatics file formats
CVE-2026-31966 CRITICAL 9.1 UPGRADE HTSlib is a library for reading and writing bioinformatics file formats

References

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