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CVE-2026-116742

HTSlib through 1.24 Heap Out-of-Bounds Write via Truncated .gzi Index Count

4.8 Medium

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

0.12%Unchanged since Oct 27, 2026
90%50%10%1%

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 MediumCVSS: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 MediumCVSS: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 MediumCVSS: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 MediumCVSS: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 MediumCVSS: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 MediumCVSS: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 MediumCVSS: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 MediumCVSS: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 MediumCVSS: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 MediumCVSS: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 MediumCVSS: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

Affected packages
PackageAffectedFixed
htslib
Debian:12
All versions, plus listed versions
1.16+ds-31.17+ds-0+exp11.17+ds-11.18+ds-0+exp11.18+ds-1
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1.19+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
htslib
Debian: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
htslib
Debian: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
htslib
Ubuntu:Pro:14.04:LTS
All versions, plus listed versions
0.2.0~rc3-10.2.0~rc3-1ubuntu0.1~esm1
None known
htslib
Ubuntu: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
htslib
Ubuntu: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
htslib
Ubuntu: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
htslib
Ubuntu:22.04:LTS
All versions, plus listed versions
1.13+ds-21.13+ds-2build1
None known
htslib
Ubuntu: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
htslib
Ubuntu:26.10
All versions, plus listed versions
1.22.1+ds2-11.22.1+ds2-1build1
None known
htslib
Ubuntu:26.04:LTS
All versions, plus listed versions
1.21+ds-11.22.1+ds2-1
None known

History

History
RecordedChangedSources
first indexedCVE 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

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