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4 vulnerabilities found for samtools by samtools
CVE-2026-31973 (GCVE-0-2026-31973)
Vulnerability from nvd – Published: 2026-03-18 20:34 – Updated: 2026-03-19 16:14
VLAI
Title
NULL pointer dereference in samtools cram-size
Summary
SAMtools is a program for reading, manipulating and writing bioinformatics file formats. Starting in version 1.17, in the cram-size command, used to write information about how well CRAM files are compressed, a check to see if the `cram_decode_compression_header()` was missing. If the function returned an error, this could lead to a NULL pointer dereference. Exploiting this bug causes a NULL pointer dereference. Typically this will cause the program to crash. Versions 1.23.1, 1.22.2 and 1.21.1 include fixes for this issue. There is no workaround for this issue.
Severity
SSVC
Exploitation: none
Automatable: no
Technical Impact: partial
CISA Coordinator (v2.0.3)
CWE
- CWE-476 - NULL Pointer Dereference
Assigner
References
3 references
| URL | Tags |
|---|---|
| https://github.com/samtools/samtools/security/adv… | x_refsource_CONFIRM |
| https://github.com/samtools/samtools/commit/06fc2… | x_refsource_MISC |
| http://www.openwall.com/lists/oss-security/2026/0… |
Impacted products
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CVE-2026-31972 (GCVE-0-2026-31972)
Vulnerability from nvd – Published: 2026-03-18 20:32 – Updated: 2026-03-19 14:22
VLAI
Title
samtools mpileup has use-after-free leading to an invalid read
Summary
SAMtools is a program for reading, manipulating and writing bioinformatics file formats. The `mpileup` command outputs DNA sequences that have been aligned against a known reference. On each output line it writes the reference position, optionally the reference DNA base at that position (obtained from a separate file) and all of the DNA bases that aligned to that position. As the output is ordered by position, reference data that is no longer needed is discarded once it has been printed out. Under certain conditions the data could be discarded too early, leading to an attempt to read from a pointer to freed memory. This bug may allow information about program state to be leaked. It may also cause a program crash through an attempt to access invalid memory. This bug is fixed in versions 1.21.1 and 1.22. There is no workaround for this issue.
Severity
SSVC
Exploitation: none
Automatable: yes
Technical Impact: partial
CISA Coordinator (v2.0.3)
CWE
- CWE-416 - Use After Free
Assigner
References
3 references
| URL | Tags |
|---|---|
| https://github.com/samtools/samtools/security/adv… | x_refsource_CONFIRM |
| https://github.com/samtools/samtools/commit/3036e… | x_refsource_MISC |
| http://www.openwall.com/lists/oss-security/2026/0… |
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CVE-2026-31973 (GCVE-0-2026-31973)
Vulnerability from cvelistv5 – Published: 2026-03-18 20:34 – Updated: 2026-03-19 16:14
VLAI
Title
NULL pointer dereference in samtools cram-size
Summary
SAMtools is a program for reading, manipulating and writing bioinformatics file formats. Starting in version 1.17, in the cram-size command, used to write information about how well CRAM files are compressed, a check to see if the `cram_decode_compression_header()` was missing. If the function returned an error, this could lead to a NULL pointer dereference. Exploiting this bug causes a NULL pointer dereference. Typically this will cause the program to crash. Versions 1.23.1, 1.22.2 and 1.21.1 include fixes for this issue. There is no workaround for this issue.
Severity
SSVC
Exploitation: none
Automatable: no
Technical Impact: partial
CISA Coordinator (v2.0.3)
CWE
- CWE-476 - NULL Pointer Dereference
Assigner
References
3 references
| URL | Tags |
|---|---|
| https://github.com/samtools/samtools/security/adv… | x_refsource_CONFIRM |
| https://github.com/samtools/samtools/commit/06fc2… | x_refsource_MISC |
| http://www.openwall.com/lists/oss-security/2026/0… |
Impacted products
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CVE-2026-31972 (GCVE-0-2026-31972)
Vulnerability from cvelistv5 – Published: 2026-03-18 20:32 – Updated: 2026-03-19 14:22
VLAI
Title
samtools mpileup has use-after-free leading to an invalid read
Summary
SAMtools is a program for reading, manipulating and writing bioinformatics file formats. The `mpileup` command outputs DNA sequences that have been aligned against a known reference. On each output line it writes the reference position, optionally the reference DNA base at that position (obtained from a separate file) and all of the DNA bases that aligned to that position. As the output is ordered by position, reference data that is no longer needed is discarded once it has been printed out. Under certain conditions the data could be discarded too early, leading to an attempt to read from a pointer to freed memory. This bug may allow information about program state to be leaked. It may also cause a program crash through an attempt to access invalid memory. This bug is fixed in versions 1.21.1 and 1.22. There is no workaround for this issue.
Severity
SSVC
Exploitation: none
Automatable: yes
Technical Impact: partial
CISA Coordinator (v2.0.3)
CWE
- CWE-416 - Use After Free
Assigner
References
3 references
| URL | Tags |
|---|---|
| https://github.com/samtools/samtools/security/adv… | x_refsource_CONFIRM |
| https://github.com/samtools/samtools/commit/3036e… | x_refsource_MISC |
| http://www.openwall.com/lists/oss-security/2026/0… |
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