CVE-2026-31963: HTSlib CRAM reader has heap buffer overflow due to improper validation of input
Noroxi assessment
Priority: Monitor (action score 35/100)
- The sources we track (CISA KEV, Exploit-DB, Metasploit, Nuclei, GitHub) show no public exploit code or exploitation in the wild.
- Probability of exploitation in the next 30 days: 0.36% (FIRST EPSS).
- 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.
- According to CISA the attack is automatable: targets can be found by mass scanning.
- Fixed version: htslib (Debian:14) 1.24-2.
Low priority for now. Upgrade to htslib (Debian:14) 1.24-2 or later.
Generated automatically from the record's data: CVSS (NVD and CNA), CISA KEV and SSVC, FIRST EPSS, exploit sources, fixed versions. How we calculate it
Primary sources: NVD · CVE.org · FIRST EPSS
HTSlib is a library for reading and writing bioinformatics file formats. CRAM is a compressed format which stores DNA sequence alignment data. As one method of removing redundant data, CRAM uses reference-based compression so that instead of storing the full sequence for each alignment record it stores a location in an external reference sequence along with a list of differences to the reference at that location as a sequence of "features". When decoding these features, an out-by-one error in a test for CRAM features that appear beyond the extent of the CRAM record sequence could result in an invalid write of one attacker-controlled byte beyond the end of a heap buffer. Exploiting this bug causes a heap buffer overflow. If a user opens a file crafted to exploit this issue, it could lead to the program crashing, or overwriting of data and heap structures in ways not expected by the program. It may be possible to use this to obtain arbitrary code execution. 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
- 0.3% · 29th percentile
- CWE
- CWE-122
Report tools
Action score
35
Monitor
Low priority for now.
- CVSS
- 35 / 40 · 8.8 / 10
- CISA KEV
- 0 / 30 · Not listed
- EPSS
- 0 / 30 · 0.3%
CISA SSVC decision
- Exploitation
- none
- Automatable
- yes
- Technical impact
- partial
Vulnrichment: CISA's decision-tree inputs.
CNA vs NVD score
- NVD
- —
- CNA · GitHub_M
- 8.8
- 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:N/VI:H/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.
Get told when this record changes
- Not in KEV: no record of exploitation in the wild
- No public exploit code on record
- A fix has been released
If any of these changes, we'll tell you in the daily email digest.
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Noroxi analysis
What does it mean in your environment?
The assessment above is generated automatically from the record's data; it doesn't know your environment. Our team verifies on your systems whether this vulnerability is actually exploitable and which mitigation is enough.
We use this product, ask for helpAffected systems
Is your version affected?
Pick the product and type the version you run. It's compared with this record's version ranges in your browser; the version isn't sent anywhere.
| 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 | from 0 | — |
| Debian:14 | htslib | before 1.24-2 | 1.24-2 |
Same product
htslib: all recordsOther highest-scoring records for the same primary product.
- CVE-2018-13845An issue has been found in HTSlib 1.8.40Plan
- 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-2026-31968HTSlib CRAM decoder vulnerable to buffer overflow35Monitor
Published before and after this one in the same product
- ← EarlierCVE-2020-36403Jun 30, 2021 · HTSlib through 1.10.2 allows out-of-bounds write access in vcf_parse_format (called from vcf_parse and vcf_read).35Monitor
- ← EarlierCVE-2026-31962Mar 18, 2026 · HTSlib CRAM reader has heap buffer overflow due to improper validation of input35Monitor
- Later →CVE-2026-31964Mar 18, 2026 · HTSlib CRAM decoder has a NULL Pointer Dereference27Monitor
Remediation
Which version to upgrade to
Fix versions compiled from the vendor, package registries and Microsoft. Verify the vendor's note before upgrading.
| Product / package | Fixed version | Source |
|---|---|---|
| debian:htslib | 1.24-2 · Debian:14 | Package registry (OSV) |
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.
No history yet (it accumulates with the daily EPSS job).
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-2026-319620 days apartHTSlib CRAM reader has heap buffer overflow due to improper validation of input35Monitor
- CVE-2026-319690 days apartHTSlib CRAM decoder has a heap buffer overflow28Monitor
- CVE-2026-319700 days apartHTSlib BGZF index file reader has a heap buffer overflow28Monitor
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-122 · Heap-based Buffer OverflowCVSS vector
CVSS:4.0/AV:N/AC:L/AT:N/PR:N/UI:N/VC:N/VI:H/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
—
Change log
- Fix✗ → ✓
For records you follow, these changes also arrive as notifications. →
References
Show all references (1 more)Show less
Vendor advisories and official records. Exploit/PoC links are deliberately left out.