High
htslib — security advisory
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.
- Products
- htslib
- Affected versions
- 0.2.0~rc3-1, 0.2.0~rc3-1ubuntu0.1~esm1, 1.10.2-2ubuntu1, 1.10.2-2ubuntu2, 1.10.2-3, 1.10.2-3ubuntu0.1, 1.13+ds-2, 1.13+ds-2build1, 1.17+ds-1, 1.18+ds-1, 1.19+ds-1.1build2, 1.19+ds-1.1build3, 1.2.1-1, 1.2.1-2, 1.2.1-2ubuntu1, 1.2.1-2ubuntu1+esm1, 1.21+ds-1, 1.22.1+ds2-1, 1.22.1+ds2-1build1, 1.5-1, 1.5-4ubuntu1, 1.6-3ubuntu1, 1.6-4, 1.6-4build1, 1.7-2, 1.7-2ubuntu0.1~esm1, 1.9-10, 1.9-11, 1.9-12
- Fixed versions
- Not specified
- CVEs
- CVE-2026-31963
- Confirmed fixed CVEs
- Not specified
- Updated in this feed
- 31 Oct 2026, 02:07 UTC · Revision 1
Source evidence
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.
osv:UBUNTU-CVE-2026-31963
htslib
Fixed versions: Not specified
htslib
Fixed versions: Not specified
htslib
Fixed versions: Not specified
htslib
Fixed versions: Not specified
htslib
Fixed versions: Not specified
htslib
Fixed versions: Not specified
htslib
Fixed versions: Not specified
htslib
Fixed versions: Not specified
htslib
Fixed versions: Not specified
Complete source record
{
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"url": "https://osv.dev/vulnerability/UBUNTU-CVE-2026-31963",
"method": "structured",
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"modified": "2026-10-17T12:58:09.035365900Z",
"provider": "osv",
"upstream": [
"CVE-2026-31963"
],
"references": [
"https://ubuntu.com/security/CVE-2026-31963",
"https://www.cve.org/CVERecord?id=CVE-2026-31963",
"https://github.com/samtools/htslib/security/advisories/GHSA-qgqh-h2q9-7w3c",
"https://github.com/samtools/htslib/commit/8bcc9907be0f945ddc31796d64f078fa05456acd"
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"value": "CVE-2026-31963",
"evidence": "/upstream"
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],
"security_relevant": true,
"severity_evidence": "/severity/0/score"
},
"source_id": "core-osv",
"document_id": 358230,
"published_at": "2026-03-18T19:16:00+00:00"
}