{"id":"UBUNTU-CVE-2026-31965","details":"HTSlib is a library for reading and writing bioinformatics file formats. CRAM is a compressed format which stores DNA sequence alignment data. In the `cram_decode_slice()` function called while reading CRAM records, validation of the reference id field occurred too late, allowing two out of bounds reads to occur before the invalid data was detected. The bug does allow two values to be leaked to the caller, however as the function reports an error it may be difficult to exploit them. It is also possible that the program will crash due to trying 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.","modified":"2026-05-20T16:25:18.888025745Z","published":"2026-03-18T19:16:00Z","upstream":["CVE-2026-31965"],"references":[{"type":"REPORT","url":"https://ubuntu.com/security/CVE-2026-31965"},{"type":"REPORT","url":"https://www.cve.org/CVERecord?id=CVE-2026-31965"},{"type":"REPORT","url":"https://github.com/samtools/htslib/security/advisories/GHSA-mqm2-v645-3qhr"},{"type":"REPORT","url":"https://github.com/samtools/htslib/commit/9cefb46453ad471e933b8212d4f45920524d3357"}],"affected":[{"package":{"name":"htslib","ecosystem":"Ubuntu:Pro:14.04:LTS","purl":"pkg:deb/ubuntu/htslib?arch=source&distro=esm-infra-legacy%2Ftrusty"},"ranges":[{"type":"ECOSYSTEM","events":[{"introduced":"0"}]}],"versions":["0.2.0~rc3-1","0.2.0~rc3-1ubuntu0.1~esm1"],"ecosystem_specific":{"binaries":[{"binary_version":"0.2.0~rc3-1ubuntu0.1~esm1","binary_name":"htslib-test"},{"binary_version":"0.2.0~rc3-1ubuntu0.1~esm1","binary_name":"libhts0"}]},"database_specific":{"source":"https://github.com/canonical/ubuntu-security-notices/blob/main/osv/cve/2026/UBUNTU-CVE-2026-31965.json"}},{"package":{"name":"htslib","ecosystem":"Ubuntu:Pro:16.04:LTS","purl":"pkg:deb/ubuntu/htslib?arch=source&distro=esm-apps%2Fxenial"},"ranges":[{"type":"ECOSYSTEM","events":[{"introduced":"0"}]}],"versions":["1.2.1-1","1.2.1-2","1.2.1-2ubuntu1","1.2.1-2ubuntu1+esm1"],"ecosystem_specific":{"binaries":[{"binary_name":"htslib-test","binary_version":"1.2.1-2ubuntu1+esm1"},{"binary_name":"libhts1","binary_version":"1.2.1-2ubuntu1+esm1"},{"binary_name":"tabix","binary_version":"1.2.1-2ubuntu1+esm1"}]},"database_specific":{"source":"https://github.com/canonical/ubuntu-security-notices/blob/main/osv/cve/2026/UBUNTU-CVE-2026-31965.json"}},{"package":{"name":"htslib","ecosystem":"Ubuntu:Pro:18.04:LTS","purl":"pkg:deb/ubuntu/htslib?arch=source&distro=esm-apps%2Fbionic"},"ranges":[{"type":"ECOSYSTEM","events":[{"introduced":"0"}]}],"versions":["1.5-1","1.5-4ubuntu1","1.6-3ubuntu1","1.6-4","1.6-4build1","1.7-2","1.7-2ubuntu0.1~esm1"],"ecosystem_specific":{"binaries":[{"binary_version":"1.7-2ubuntu0.1~esm1","binary_name":"htslib-test"},{"binary_name":"libhts2","binary_version":"1.7-2ubuntu0.1~esm1"},{"binary_version":"1.7-2ubuntu0.1~esm1","binary_name":"tabix"}]},"database_specific":{"source":"https://github.com/canonical/ubuntu-security-notices/blob/main/osv/cve/2026/UBUNTU-CVE-2026-31965.json"}},{"package":{"name":"htslib","ecosystem":"Ubuntu:20.04:LTS","purl":"pkg:deb/ubuntu/htslib?arch=source&distro=focal"},"ranges":[{"type":"ECOSYSTEM","events":[{"introduced":"0"}]}],"versions":["1.9-10","1.9-11","1.9-12","1.10.2-2ubuntu1","1.10.2-2ubuntu2","1.10.2-3","1.10.2-3ubuntu0.1"],"ecosystem_specific":{"binaries":[{"binary_version":"1.10.2-3ubuntu0.1","binary_name":"htslib-test"},{"binary_name":"libhts3","binary_version":"1.10.2-3ubuntu0.1"},{"binary_version":"1.10.2-3ubuntu0.1","binary_name":"tabix"}]},"database_specific":{"source":"https://github.com/canonical/ubuntu-security-notices/blob/main/osv/cve/2026/UBUNTU-CVE-2026-31965.json"}},{"package":{"name":"htslib","ecosystem":"Ubuntu:22.04:LTS","purl":"pkg:deb/ubuntu/htslib?arch=source&distro=jammy"},"ranges":[{"type":"ECOSYSTEM","events":[{"introduced":"0"}]}],"versions":["1.13+ds-2","1.13+ds-2build1"],"ecosystem_specific":{"binaries":[{"binary_name":"htslib-test","binary_version":"1.13+ds-2build1"},{"binary_name":"libhts3","binary_version":"1.13+ds-2build1"},{"binary_name":"tabix","binary_version":"1.13+ds-2build1"}]},"database_specific":{"source":"https://github.com/canonical/ubuntu-security-notices/blob/main/osv/cve/2026/UBUNTU-CVE-2026-31965.json"}},{"package":{"name":"htslib","ecosystem":"Ubuntu:24.04:LTS","purl":"pkg:deb/ubuntu/htslib?arch=source&distro=noble"},"ranges":[{"type":"ECOSYSTEM","events":[{"introduced":"0"}]}],"versions":["1.17+ds-1","1.18+ds-1","1.19+ds-1.1build2","1.19+ds-1.1build3"],"ecosystem_specific":{"binaries":[{"binary_name":"htslib-test","binary_version":"1.19+ds-1.1build3"},{"binary_name":"libhts3t64","binary_version":"1.19+ds-1.1build3"},{"binary_name":"tabix","binary_version":"1.19+ds-1.1build3"}]},"database_specific":{"source":"https://github.com/canonical/ubuntu-security-notices/blob/main/osv/cve/2026/UBUNTU-CVE-2026-31965.json"}},{"package":{"name":"htslib","ecosystem":"Ubuntu:25.10","purl":"pkg:deb/ubuntu/htslib?arch=source&distro=questing"},"ranges":[{"type":"ECOSYSTEM","events":[{"introduced":"0"}]}],"versions":["1.21+ds-1"],"ecosystem_specific":{"binaries":[{"binary_name":"htslib-test","binary_version":"1.21+ds-1"},{"binary_name":"libhts3t64","binary_version":"1.21+ds-1"},{"binary_name":"tabix","binary_version":"1.21+ds-1"}]},"database_specific":{"source":"https://github.com/canonical/ubuntu-security-notices/blob/main/osv/cve/2026/UBUNTU-CVE-2026-31965.json"}},{"package":{"name":"htslib","ecosystem":"Ubuntu:26.04:LTS","purl":"pkg:deb/ubuntu/htslib?arch=source&distro=resolute"},"ranges":[{"type":"ECOSYSTEM","events":[{"introduced":"0"}]}],"versions":["1.21+ds-1","1.22.1+ds2-1"],"ecosystem_specific":{"binaries":[{"binary_name":"htslib-test","binary_version":"1.22.1+ds2-1"},{"binary_name":"libhts3t64","binary_version":"1.22.1+ds2-1"},{"binary_name":"tabix","binary_version":"1.22.1+ds2-1"}]},"database_specific":{"source":"https://github.com/canonical/ubuntu-security-notices/blob/main/osv/cve/2026/UBUNTU-CVE-2026-31965.json"}}],"schema_version":"1.7.5","severity":[{"type":"CVSS_V4","score":"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"},{"type":"CVSS_V3","score":"CVSS:3.1/AV:N/AC:L/PR:N/UI:N/S:U/C:L/I:N/A:H"},{"type":"Ubuntu","score":"medium"}]}