CVE-2026-31964: HTSlib is a library for reading and writing bioinformatics file formats

Routine

HIGH 7.5REMOTEUPGRADE

CVE-2026-31964 is a high-severity flaw (CVSS 7.5) 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. While most alignment records store DNA sequence and quality values, the format also allows them to omit this data in certain cases to save space. Due to some quirks of the CRAM format, it is necessary to handle these records carefully as they will actua

Why this priority

High severity
Remotely exploitable, no login, no user action

A fixed release or distro patch exists.

Risk facts

CVSS score	7.5 (High)
Attack vector	Network (remote)
Attack complexity	Low
Privileges needed	None
User interaction	None
EPSS exploit chance	0.3% (top 73%)
CISA exploited list	No
Weakness	CWE-476
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 19:16 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-2026-31964?

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

Is CVE-2026-31964 being exploited?

CVE-2026-31964 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-2026-31964 affect?

CVE-2026-31964 affects htslib. Severity is high (CVSS 7.5). 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. While most alignment records store DNA sequ

How urgent is CVE-2026-31964?

Priority 38/100. High severity; Remotely exploitable, no login, no user action

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-2026-31969 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

References

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