CVE-2026-116742
HTSlib through 1.24 Heap Out-of-Bounds Write via Truncated .gzi Index Count
HTSlib through 1.24 contains a heap out-of-bounds write and read vulnerability in bgzf_index_load_hfile() in bgzf.c that allows attackers to corrupt heap memory by supplying a crafted .gzi index entry count. A count of 0xFFFFFFFF truncates noffs to zero, causing writes past a malloc(0) buffer and an offs[-1] read in bgzf_useek(), resulting in heap corruption or crashes in tools like samtools and bcftools.
Attack profile
How easy it is to exploit
- Attack vector
- Local
- Complexity
- Low
- Privileges needed
- None
- User interaction
- Passive
What an attacker can affect
- Confidentiality
- None
- Integrity
- Low
- Availability
- Low
Exploit likelihood
What each source reports
CVE List Score used
4.8
HTSlib through 1.24 Heap Out-of-Bounds Write via Truncated .gzi Index Count
HTSlib through 1.24 contains a heap out-of-bounds write and read vulnerability in bgzf_index_load_hfile() in bgzf.c that allows attackers to corrupt heap memory by supplying a crafted .gzi index entry count. A count of 0xFFFFFFFF truncates noffs to zero, causing writes past a malloc(0) buffer and an offs[-1] read in bgzf_useek(), resulting in heap corruption or crashes in tools like samtools and bcftools.
- Record
CVE-2026-116742- CVSS 4.0
- 4.8 Medium
CVSS:4.0/AV:L/AC:L/AT:N/PR:N/UI:P/VC:N/VI:L/VA:L/SC:N/SI:N/SA:N - CVSS 3.1
- 4.4 Medium
CVSS:3.1/AV:L/AC:L/PR:N/UI:R/S:U/C:N/I:L/A:L - Weakness
- CWE-197
- Updated
- 2026-11-02
EUVDEUVD-2026-110490
4.8
HTSlib through 1.24 contains a heap out-of-bounds write and read vulnerability in bgzf_index_load_hfile() in bgzf.c that allows attackers to corrupt heap memory by supplying a crafted .gzi index entry count. A count of 0xFFFFFFFF truncates noffs to zero, causing writes past a malloc(0) buffer and an offs[-1] read in bgzf_useek(), resulting in heap corruption or crashes in tools like samtools and bcftools.
- Record
EUVD-2026-110490- CVSS 4.0
- 4.8 Medium
CVSS:4.0/AV:L/AC:L/AT:N/PR:N/UI:P/VC:N/VI:L/VA:L/SC:N/SI:N/SA:N - Updated
- 2026-11-02
GitHub AdvisoriesGHSA-r296-8jjg-794r
4.8
HTSlib through 1.24 contains a heap out-of-bounds write and read vulnerability in...
HTSlib through 1.24 contains a heap out-of-bounds write and read vulnerability in bgzf_index_load_hfile() in bgzf.c that allows attackers to corrupt heap memory by supplying a crafted .gzi index entry count. A count of 0xFFFFFFFF truncates noffs to zero, causing writes past a malloc(0) buffer and an offs[-1] read in bgzf_useek(), resulting in heap corruption or crashes in tools like samtools and bcftools.
- Record
GHSA-r296-8jjg-794r- CVSS 4.0
- 4.8 Medium
CVSS:4.0/AV:L/AC:L/AT:N/PR:N/UI:P/VC:N/VI:L/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 - CVSS 3.1
- 4.4 Medium
CVSS:3.1/AV:L/AC:L/PR:N/UI:R/S:U/C:N/I:L/A:L - Weakness
- CWE-197
- Updated
- 2026-11-02
NVD
4.8
HTSlib through 1.24 contains a heap out-of-bounds write and read vulnerability in bgzf_index_load_hfile() in bgzf.c that allows attackers to corrupt heap memory by supplying a crafted .gzi index entry count. A count of 0xFFFFFFFF truncates noffs to zero, causing writes past a malloc(0) buffer and an offs[-1] read in bgzf_useek(), resulting in heap corruption or crashes in tools like samtools and bcftools.
- Record
CVE-2026-116742- CVSS 4.0
- 4.8 Medium
CVSS:4.0/AV:L/AC:L/AT:N/PR:N/UI:P/VC:N/VI:L/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 - CVSS 3.1
- 4.4 Medium
CVSS:3.1/AV:L/AC:L/PR:N/UI:R/S:U/C:N/I:L/A:L - Weakness
- CWE-197
- Updated
- 2026-11-02
OSV
4.8
HTSlib through 1.24 Heap Out-of-Bounds Write via Truncated .gzi Index Count
HTSlib through 1.24 contains a heap out-of-bounds write and read vulnerability in bgzf_index_load_hfile() in bgzf.c that allows attackers to corrupt heap memory by supplying a crafted .gzi index entry count. A count of 0xFFFFFFFF truncates noffs to zero, causing writes past a malloc(0) buffer and an offs[-1] read in bgzf_useek(), resulting in heap corruption or crashes in tools like samtools and bcftools.
- Record
CVE-2026-116742- CVSS 4.0
- 4.8 Medium
CVSS:4.0/AV:L/AC:L/AT:N/PR:N/UI:P/VC:N/VI:L/VA:L/SC:N/SI:N/SA:N - Weakness
- CWE-197
- Updated
- 2026-11-02
OSVDEBIAN-CVE-2026-116742
4.8
HTSlib through 1.24 contains a heap out-of-bounds write and read vulnerability in bgzf_index_load_hfile() in bgzf.c that allows attackers to corrupt heap memory by supplying a crafted .gzi index entry count. A count of 0xFFFFFFFF truncates noffs to zero, causing writes past a malloc(0) buffer and an offs[-1] read in bgzf_useek(), resulting in heap corruption or crashes in tools like samtools and bcftools.
- Record
DEBIAN-CVE-2026-116742- CVSS 4.0
- 4.8 Medium
CVSS:4.0/AV:L/AC:L/AT:N/PR:N/UI:P/VC:N/VI:L/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 - Updated
- 2026-11-02
OSVUBUNTU-CVE-2026-116742
4.8
HTSlib through 1.24 contains a heap out-of-bounds write and read vulnerability in bgzf_index_load_hfile() in bgzf.c that allows attackers to corrupt heap memory by supplying a crafted .gzi index entry count. A count of 0xFFFFFFFF truncates noffs to zero, causing writes past a malloc(0) buffer and an offs[-1] read in bgzf_useek(), resulting in heap corruption or crashes in tools like samtools and bcftools.
- Record
UBUNTU-CVE-2026-116742- CVSS 4.0
- 4.8 Medium
CVSS:4.0/AV:L/AC:L/AT:N/PR:N/UI:P/VC:N/VI:L/VA:L/SC:N/SI:N/SA:N - CVSS 3.1
- 4.4 Medium
CVSS:3.1/AV:L/AC:L/PR:N/UI:R/S:U/C:N/I:L/A:L - Updated
- 2026-11-02
Affected products
Affected packages
| Package | Affected | Fixed |
|---|---|---|
htslibDebian:12 |
All versions, plus listed versions 1.16+ds-31.17+ds-0+exp11.17+ds-11.18+ds-0+exp11.18+ds-1 Show 15 moreShow less1.19+ds-0+exp01.19+ds-11.19+ds-1+exp11.19+ds-1.11.20+ds-11.20+ds-21.21+ds-0+exp11.21+ds-0+exp21.21+ds-11.22.1+ds-11.22.1+ds-21.22.1+ds2-11.24-11.24-21.24-3 |
None known |
htslibDebian:13 |
All versions, plus listed versions 1.21+ds-11.22.1+ds-11.22.1+ds-21.22.1+ds2-11.24-11.24-21.24-3 |
None known |
htslibDebian:14 |
All versions, plus listed versions 1.21+ds-11.22.1+ds-11.22.1+ds-21.22.1+ds2-11.24-11.24-21.24-3 |
None known |
htslibUbuntu:Pro:14.04:LTS |
All versions, plus listed versions 0.2.0~rc3-10.2.0~rc3-1ubuntu0.1~esm1 |
None known |
htslibUbuntu:Pro:16.04:LTS |
All versions, plus listed versions 1.2.1-11.2.1-21.2.1-2ubuntu11.2.1-2ubuntu1+esm1 |
None known |
htslibUbuntu:Pro:18.04:LTS |
All versions, plus listed versions 1.5-11.5-4ubuntu11.6-3ubuntu11.6-41.6-4build11.7-21.7-2ubuntu0.1~esm1 |
None known |
htslibUbuntu:20.04:LTS |
All versions, plus listed versions 1.9-101.9-111.9-121.10.2-2ubuntu11.10.2-2ubuntu21.10.2-31.10.2-3ubuntu0.1 |
None known |
htslibUbuntu:22.04:LTS |
All versions, plus listed versions 1.13+ds-21.13+ds-2build1 |
None known |
htslibUbuntu:24.04:LTS |
All versions, plus listed versions 1.17+ds-11.18+ds-11.19+ds-1.1build21.19+ds-1.1build3 |
None known |
htslibUbuntu:26.10 |
All versions, plus listed versions 1.22.1+ds2-11.22.1+ds2-1build1 |
None known |
htslibUbuntu:26.04:LTS |
All versions, plus listed versions 1.21+ds-11.22.1+ds2-1 |
None known |
History
| Recorded | Changed | Sources |
|---|---|---|
| first indexed | CVE List, EUVD, GitHub Advisories, NVD, OSV |
Dates are when Every CVE recorded each change. Upstream dates may differ.
In short
CVE-2026-116742 is a medium vulnerability (CVSS 4.8) in Samtools Htslib, published October 26, 2026. No source lists public exploit code. EPSS puts the chance of exploitation in the next 30 days at 0.12%, the 2nd percentile. No source names a fixed version.
References
github.com/samtools/htslib/pull/2057
github.com/samtools/htslib/commit/18dddf02bb2c0053b32acec427723555a24b2873
github.com/samtools/htslib
github.com/samtools/htslib/blob/1.24/bgzf.c
hackmd.io/@haindpwn/htslib-bgzf-gzi-int-truncation-oob
github.com/samtools/htslib/issues/2113
Show 9 moreShow less
vulncheck.com/advisories/htslib-through-1.24-heap-out-of-bounds-write-via-truncated-gzi-index-count
nvd.nist.gov/vuln/detail/CVE-2026-116742
github.com/advisories/GHSA-r296-8jjg-794r
github.com/CVEProject/cvelistV5/tree/main/cves/2026/116xxx/CVE-2026-116742.json
security-tracker.debian.org/tracker/CVE-2026-116742
ubuntu.com/security/CVE-2026-116742
cve.org/CVERecord?id=CVE-2026-116742
github.com/cveproject/cvelistv5/tree/main/cves/2026/116xxx/cve-2026-116742.json
nvd.nist.gov/vuln/detail/cve-2026-116742