CVE-2026-31967: HTSlib is a library for reading and writing bioinformatics file formats

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CRITICAL 9.1REMOTEUPGRADE

CVE-2026-31967 is a critical-severity flaw (CVSS 9.1) 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. 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. I

Why this priority

Critical severity
Remotely exploitable, no login, no user action

A fixed release or distro patch exists.

Risk facts

CVSS score	9.1 (Critical)
Attack vector	Network (remote)
Attack complexity	Low
Privileges needed	None
User interaction	None
EPSS exploit chance	0.5% (top 60%)
CISA exploited list	No
Weakness	CWE-125, CWE-129
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-2026-31967?

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

Is CVE-2026-31967 being exploited?

CVE-2026-31967 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-2026-31967 affect?

CVE-2026-31967 affects htslib. Severity is critical (CVSS 9.1). 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 re

How urgent is CVE-2026-31967?

Priority 47/100. Critical 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-2026-31966 CRITICAL 9.1 UPGRADE HTSlib is a library for reading and writing bioinformatics file formats

References

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