Quick answer
Direct answer
Risk scores
| CVSS metric | What it means |
|---|---|
| Attack vector (AV:N) | Network: reachable remotely |
| Attack complexity (AC:L) | Low complexity |
| Attack requirements (AT:N) | No attack requirements |
| Privileges required (PR:N) | No privileges required |
| User interaction (UI:P) | Passive user interaction |
| Confidentiality (VC:N) | No confidentiality impact |
| Integrity (VI:H) | High integrity impact |
| Availability (VA:L) | Low availability impact |
CVSS:4.0/AV:N/AC:L/AT:N/PR:N/UI:P/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
About Htslib
CVE-2026-31970 affects Htslib, a product from Htslib. Before acting, confirm where Htslib runs in your estate, who owns it and whether it is reachable from the internet, because exposure decides real risk more than the score alone.
What the flaw is
In plain terms: HTSlib is a library for reading and writing bioinformatics file formats. GZI files are used to index block-compressed GZIP [BGZF] files. In the GZI loading function, `bgzf_index_load_hfile()`, it was possible to trigger an integer overflow, leading to an under- or zero-sized buffer being allocated to store the index. Sixteen zero bytes would then be written to this buffer, and, depending on the result of the overflow the rest of the file may also be loaded into the buffer as well. If the function did attempt to load the data, it would eventually fail due to not reading the expected number of records, and then try to free the overflowed 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. The easiest work-around is to discard any `.gzi` index files from untrusted sources, and use the `bgzip -r` option to recreate them.
The weakness class is Heap Buffer Overflow. A write past the end of a heap buffer corrupts nearby memory.
Based on its CVSS vector, the flaw can be reached over the network, needs no login, and relies on a user taking an action. Apply the vendor fix and confirm exposure on internet facing and business critical assets first.
Affected versions and timeline
| Field | Detail |
|---|---|
| Product | Htslib |
| Affected versions | Htslib before 1.21; Htslib from 1.22 before 1.22.2; Htslib 1.23 |
| Published | Mar 18, 2026 |
| Last modified | Jun 17, 2026 |
| Added to CISA KEV | Not listed |
| Assigning CNA | security-advisories@github.com |
How to detect it
- Inventory every instance of Htslib and record the running version against the affected range above.
- Check external attack surface scans for internet facing instances of the component.
- Review logs on affected systems for unusual requests, errors or new processes around the vulnerable function.
- Confirm with an authenticated vulnerability scan once your scanner has a check for this CVE.
How to fix it
- Apply the fixed version of Htslib named in the vendor advisory.
- If patching must wait, restrict network access to the affected service and put it behind authentication or a web application firewall rule.
- Rescan after the change to prove the exposure is gone, then close the ticket.
CTEM action plan
| CTEM stage | What to do for this CVE |
|---|---|
| Scope | Add every business service that depends on Htslib to the current CTEM cycle. |
| Discover | Find all instances, including shadow and cloud deployments, and record versions and exposure. |
| Prioritize | Rank using EPSS and CVSS together with asset exposure and business impact. |
| Validate | Confirm the flaw is reachable and exploitable in your environment and that compensating controls work. |
| Mobilize | Assign the fix to the asset owner with a due date matched to the priority, then verify closure. |
CWE References
- CWE-122: Heap Buffer Overflow More CVEs with this weakness
- CWE-131 More CVEs with this weakness
- CWE-190: Integer Overflow More CVEs with this weakness
- CWE-787: Out of Bounds Write More CVEs with this weakness
Technical References
Frequently asked questions
Related CVEs
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. When reading data encoded using the `BYTE_ARRAY_LEN` method, the `cram_byte_array_len_decode()` failed to validate that the amount of data being unpacked matched the size of the output buffer where it was to be stored. Depending on the data series being read, this could result either in a heap or a stack overflow with attacker-controlled bytes. Depending on the data stream this could result either in a heap buffer overflow or a stack overflow. If a user opens a file crafted to exploit this issue it could lead to the program crashing, overwriting of data structures on the heap or stack in ways not expected by the program, or changing the control flow of 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.
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. When reading data encoded using the `BYTE_ARRAY_STOP` method, an out-by-one error in the `cram_byte_array_stop_decode_char()` function check for a full output buffer could result in a single attacker-controlled byte being written beyond the end of a heap allocation. 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.
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. For the `VARINT` and `CONST` encodings, incomplete validation of the context in which the encodings were used could result in up to eight bytes being written beyond the end of a heap allocation, or up to eight bytes being written to the location of a one byte variable on the stack, possibly causing the values to adjacent variables to change unexpectedly. Depending on the data stream this could result either in a heap buffer overflow or a stack overflow. If a user opens a file crafted to exploit this issue it could lead to the program crashing, overwriting of data structures on the heap or stack in ways not expected by the program, or changing the control flow of 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.
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.
HTSlib is a library for reading and writing bioinformatics file formats. CRAM is a compressed format which stores DNA sequence alignment data. 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 actually store data that needs to be consumed and then discarded. Unfortunately the `cram_decode_seq()` did not handle this correctly in some cases. Where this happened it could result in reading a single byte from beyond the end of a heap allocation, followed by writing a single attacker-controlled byte to the same location. 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.
Out-of-bounds write vulnerability in the WEB module.Impact: Successful exploitation of this vulnerability will affect availability and confidentiality.
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