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

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HIGH 8.2REMOTEUPGRADE

CVE-2026-31965 is a high-severity flaw (CVSS 8.2) 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, 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

Why this priority

  • High severity
  • Remotely exploitable, no login, no user action

A fixed release or distro patch exists.

Risk facts

CVSS score8.2 (High)
Attack vectorNetwork (remote)
Attack complexityLow
Privileges neededNone
User interactionNone
EPSS exploit chance0.4% (top 67%)
CISA exploited listNo
WeaknessCWE-125, CWE-129
Published2026-03-18
Last modified2026-06-17
Publisher (CNA): GitHub, Inc. · Vendor: htslib

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

Am I affected?

Timeline

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-2026-31965?

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

Is CVE-2026-31965 being exploited?

CVE-2026-31965 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-2026-31965 affect?

CVE-2026-31965 affects htslib. Severity is high (CVSS 8.2). 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 refere

How urgent is CVE-2026-31965?

Priority 42/100. High severity; Remotely exploitable, no login, no user action

Related CVEs

References

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