CVE catalog

CVE-2026-31969

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. Whe

[CVE catalog]

Severity: High · CVSS 7.3CVSS:3.1/AV:L/AC:L/PR:N/UI:R/S:U/C:H/I:H/A:L
Published: Mar 18, 2026, 7:47:44 PM UTC
Source: [NVD] · [CVE record]
EPSS: 0.35% · Oct 25, 2026

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.

Vulnerable and fixed packages

Distribution-reported package versions and fixes. These do not depend on matching against the OpenFactory package catalog.

Distribution	Package	Release	Version	Status
Debian	htslib	sid	`1.24-3`	fixed
Debian	htslib	forky	`1.24-3`	fixed
Debian	htslib	trixie	`1.21+ds-1`	vulnerable
Debian	htslib	bookworm	`1.16+ds-3`	vulnerable
Cpe	htslib	Not reported	Not reported	vulnerable
Cpe	htslib	Not reported	Not reported	unknown

Fixed-version evidence

Distribution	Package	Type	Release	Fixed version	Urgency	Origin	Bugs
Debian	htslib	source	sid	`1.24-2`	not yet assigned	Not reported	[1131493]
Debian	htslib	source	forky	`1.24-2`	not yet assigned	Not reported	[1131493]
Debian	htslib	source	trixie	`(unfixed)`	not yet assigned	Not reported	[1131493]
Debian	htslib	source	bookworm	`(unfixed)`	not yet assigned	Not reported	[1131493]

[Debian bug #1131493]

Notes

[trixie] htslib: Minor issue [bookworm] htslib: Minor issue

OpenFactory catalog packages

[Debian 12 (Bookworm)]

[htslib-test]Affected
Source package: [htslib]
Details (2)
- 1.16+ds-3 · all · bookworm
  Affected
  nvd · htslib · debian · bookworm; nvd · htslib · debian · 12
- 1.16+ds-3 · all · bookworm
  Affected
  nvd · htslib · debian · bookworm; nvd · htslib · debian · 12
[libhts3]Affected
Source package: [htslib]
Details (2)
- 1.16+ds-3 · amd64 · bookworm
  Affected
  nvd · htslib · debian · bookworm; nvd · htslib · debian · 12
- 1.16+ds-3 · arm64 · bookworm
  Affected
  nvd · htslib · debian · bookworm; nvd · htslib · debian · 12
[libhts-dev]Affected
Source package: [htslib]
Details (2)
- 1.16+ds-3 · amd64 · bookworm
  Affected
  nvd · htslib · debian · bookworm; nvd · htslib · debian · 12
- 1.16+ds-3 · arm64 · bookworm
  Affected
  nvd · htslib · debian · bookworm; nvd · htslib · debian · 12
[tabix]Affected
Source package: [htslib]
Details (2)
- 1.16+ds-3 · amd64 · bookworm
  Affected
  nvd · htslib · debian · bookworm; nvd · htslib · debian · 12
- 1.16+ds-3 · arm64 · bookworm
  Affected
  nvd · htslib · debian · bookworm; nvd · htslib · debian · 12

[Debian 13 (Trixie)]

[htslib-test]Affected
Source package: [htslib]
Details (2)
- 1.21+ds-1 · all · trixie
  Affected
  nvd · htslib · debian · 13
- 1.21+ds-1 · all · trixie
  Affected
  nvd · htslib · debian · 13
[libhts3t64]Affected
Source package: [htslib]
Details (2)
- 1.21+ds-1 · amd64 · trixie
  Affected
  nvd · htslib · debian · 13
- 1.21+ds-1 · arm64 · trixie
  Affected
  nvd · htslib · debian · 13
[libhts-dev]Affected
Source package: [htslib]
Details (2)
- 1.21+ds-1 · amd64 · trixie
  Affected
  nvd · htslib · debian · 13
- 1.21+ds-1 · arm64 · trixie
  Affected
  nvd · htslib · debian · 13
[tabix]Affected
Source package: [htslib]
Details (2)
- 1.21+ds-1 · amd64 · trixie
  Affected
  nvd · htslib · debian · 13
- 1.21+ds-1 · arm64 · trixie
  Affected
  nvd · htslib · debian · 13

Observed: Oct 23, 2026, 10:40:20 PM UTC

References

[Debian Security Tracker] · [FIRST EPSS] · [National Vulnerability Database (NVD)] · [OSV Package Vulnerability Database] · [Red Hat security advisories and VEX]