HTSlib CRAM reader has out-of-bounds read due to improper validation of input
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. If the array value obtained also happened to be a valid pointer, it would be interpreted as a string and an attempt would be made to write the data as part of the SAM record. This bug may allow information about program state to be leaked. It may also cause a program crash through an attempt to access invalid memory. Versions 1.23.1, 1.22.2 and 1.21.1 include fixes for this issue. There is no workaround for this issue.
- Published
- Mar 18, 2026
- Updated
- Jun 17, 2026
- EPSS
- 0.5% · 43th percentile
- CWE
- CWE-125
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Report tools
Action score
27
Monitor
Low priority for now.
- CVSS
- 27 / 40 · 6.9 / 10
- CISA KEV
- 0 / 30 · Not listed
- EPSS
- 0 / 30 · 0.5%
CISA SSVC decision
- Exploitation
- none
- Automatable
- yes
- Technical impact
- partial
Vulnrichment: CISA's decision-tree inputs.
CNA vs NVD score
- NVD
- —
- CNA · GitHub_M
- 6.9
- NVD has not scored this yet; the score shown is the CNA’s.
CVSS:4.0/AV:N/AC:L/AT:N/PR:N/UI:N/VC:L/VI:N/VA:L/SC:N/SI:N/SA:N
The score given by the assigning authority versus NVD’s independent score. A gap means the severity is contested.
Affected systems
| Vendor | Product | CPE |
|---|---|---|
| htslib | htslib | cpe:2.3:a:htslib:htslib |
Affected versions
NVD version ranges (for catalog products). Add the product to your stack with a version and matching uses these.
- htslib htslibbefore 1.21.1
- htslib htslib1.22 and later · before 1.22.2
- htslib htslib1.23
Versions reported by the vendor
Affected version ranges reported by the assigning authority (GitHub_M). Independent of NVD's CPE analysis and usually ahead of it.
samtools htslib
- < 1.21.1, >= 1.22, < 1.22.2, = 1.23affected
Package-level exposure
OSV and GitHub Advisory data: ecosystem, package and range. SBOM matching uses this table.
| Ecosystem | Package | Affected range | Fix |
|---|---|---|---|
| Debian:12 | htslib | all versions | — |
Same product
htslib: all recordsOther highest-scoring records for the same primary product.
- CVE-2017-1000206samtools htslib library version 1.4.0 and earlier is vulnerable to buffer overflow in the CRAM rANS codec resulting in potential arbitrary c40Plan
- CVE-2018-13845An issue has been found in HTSlib 1.8.39Monitor
- CVE-2026-31968HTSlib CRAM decoder vulnerable to buffer overflow35Monitor
- CVE-2026-31963HTSlib CRAM reader has heap buffer overflow due to improper validation of input35Monitor
- CVE-2026-31962HTSlib CRAM reader has heap buffer overflow due to improper validation of input35Monitor
- CVE-2020-36403HTSlib through 1.10.2 allows out-of-bounds write access in vcf_parse_format (called from vcf_parse and vcf_read).35Monitor
Remediation
Which version to upgrade to
Fix versions compiled from the vendor, package registries and Microsoft. Verify the vendor's note before upgrading.
No fix version is recorded for this entry. Check the references for vendor advisories.
Exploit status
No known public exploit
No public exploit has been observed yet. That doesn't mean you're safe, only that the bar is a little higher.
Research context
For pentesters and researchers: attack profile, score disagreement, timeline, patch commits, credits, variant and chain candidates, bug bounty scope. All derived from existing data; no exploit code.
Timeline
From publication to today: proof of concept, Metasploit module, CISA KEV and fix record. Dates are as reported by the sources.
No dated events beyond publication.
FIRST EPSS daily score; only changes of 0.01 or more are recorded (step chart).
Patch and commit links
Commit, PR and diff links among the references. A starting point for patch-diffing and variant hunting; fixes, not exploits.
Credits
All researchersFinders, reporters and analysts named in the CNA record. Click a name for that researcher’s other records.
No credits in the CNA record.
Variant candidates
Same product, same weakness class, within 18 months. If the patch missed the root cause, the sibling bug is here.
- CVE-2026-319650 days apartHTSlib CRAM reader has out-of-bounds reads due to improper validation of input27Monitor
- CVE-2026-319660 days apartHTSlib CRAM reader has out-of-bounds read due to improper validation of input27Monitor
Chain candidates
An authentication bypass and a privilege-requiring bug in the same product, published close together: combined they may become an unauthenticated path.
—
Bug bounty scope
No known public program.
Source: bounty-targets-data (public HackerOne, Bugcrowd, Intigriti, YesWeHack listings).
Technical details
Attack conditions
- Anyone who can reach it over the internet can trigger it.
- No account or password is required.
- No user action is required.
- No special conditions are required; it is repeatable.
If successful
- Confidentiality
- Integrity
- Availability
- Attack vector
- Network
- Attack complexity
- Low
- Privileges required
- None
- User interaction
- None
- Scope
- X
Weakness class (CWE)
CWE-125 · Out-of-bounds ReadCVSS vector
CVSS:4.0/AV:N/AC:L/AT:N/PR:N/UI:N/VC:L/VI:N/VA:L/SC:N/SI:N/SA:N/E:X/CR:X/IR:X/AR:X/MAV:X/MAC:X/MAT:X/MPR:X/MUI:X/MVC:X/MVI:X/MVA:X/MSC:X/MSI:X/MSA:X/S:X/AU:X/R:X/V:X/RE:X/U:X
nvd-secondary
Attack context
MITRE CAPEC attack patterns and ATT&CK techniques for this weakness class (CWE). A starting point for detection rules and threat hunting.
Attack patterns (CAPEC)
ATT&CK techniques
—
Noroxi analysis
No Noroxi analysis for this record yet
We don't hand-write analysis for all 385,000+ vulnerabilities; that wouldn't be honest. For notable, high-impact vulnerabilities our team writes the mechanism, detection and remediation steps.
We use this product, ask for helpChange log
No changes recorded on tracked fields yet. Score, KEV, exploit maturity and fix status changes appear here.
References
- github.com/samtools/htslib/commit/9cefb46453ad471e933b8212d4f45920524d3357
- github.com/samtools/htslib/security/advisories/GHSA-33x5-c6vj-8f2w
Vendor advisories and official records. Exploit/PoC links are deliberately left out.