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13 vulnerabilities by samtools
CVE-2026-31973 (GCVE-0-2026-31973)
Vulnerability from cvelistv5 – Published: 2026-03-18 20:34 – Updated: 2026-03-18 23:08
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 ?
CWE
- CWE-476 - NULL Pointer Dereference
Assigner
References
| URL | Tags | |||||||
|---|---|---|---|---|---|---|---|---|
|
||||||||
Impacted products
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CVE-2026-31972 (GCVE-0-2026-31972)
Vulnerability from cvelistv5 – Published: 2026-03-18 20:32 – Updated: 2026-03-18 23:08
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 ?
CWE
- CWE-416 - Use After Free
Assigner
References
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|---|---|---|---|---|---|---|---|---|
|
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CVE-2026-31971 (GCVE-0-2026-31971)
Vulnerability from cvelistv5 – Published: 2026-03-18 19:55 – Updated: 2026-03-18 20:15
VLAI?
Title
HTSlib CRAM decoder vulnerable to buffer overflow
Summary
HTSlib is a library for reading and writing bioinformatics file formats. CRAM is a compressed format which stores DNA sequence alignment data using a variety of encodings and compression methods. When reading data encoded using the `BYTE_ARRAY_LEN` method, the `cram_byte_array_len_decode()` failed to validate that the amount of data being unpacked matched the size of the output buffer where it was to be stored. Depending on the data series being read, this could result either in a heap or a stack overflow with attacker-controlled bytes. Depending on the data stream this could result either in a heap buffer overflow or a stack overflow. If a user opens a file crafted to exploit this issue it could lead to the program crashing, overwriting of data structures on the heap or stack in ways not expected by the program, or changing the control flow of 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.
Severity ?
CWE
Assigner
References
| URL | Tags | |||||||
|---|---|---|---|---|---|---|---|---|
|
||||||||
Impacted products
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CVE-2026-31970 (GCVE-0-2026-31970)
Vulnerability from cvelistv5 – Published: 2026-03-18 19:53 – Updated: 2026-03-18 23:08
VLAI?
Title
HTSlib BGZF index file reader has a heap buffer overflow
Summary
HTSlib is a library for reading and writing bioinformatics file formats. GZI files are used to index block-compressed GZIP [BGZF] files. In the GZI loading function, `bgzf_index_load_hfile()`, it was possible to trigger an integer overflow, leading to an under- or zero-sized buffer being allocated to store the index. Sixteen zero bytes would then be written to this buffer, and, depending on the result of the overflow the rest of the file may also be loaded into the buffer as well. If the function did attempt to load the data, it would eventually fail due to not reading the expected number of records, and then try to free the overflowed 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. The easiest work-around is to discard any `.gzi` index files from untrusted sources, and use the `bgzip -r` option to recreate them.
Severity ?
CWE
Assigner
References
| URL | Tags | |||||||
|---|---|---|---|---|---|---|---|---|
|
||||||||
Impacted products
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CVE-2026-31969 (GCVE-0-2026-31969)
Vulnerability from cvelistv5 – Published: 2026-03-18 19:47 – Updated: 2026-03-18 20:12
VLAI?
Title
HTSlib CRAM decoder has a heap buffer overflow
Summary
HTSlib is a library for reading and writing bioinformatics file formats. CRAM is a compressed format which stores DNA sequence alignment data using a variety of encodings and compression methods. When reading data encoded using the `BYTE_ARRAY_STOP` method, an out-by-one error in the `cram_byte_array_stop_decode_char()` function check for a full output buffer could result in a single attacker-controlled byte being written beyond the end of a heap allocation. 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.
Severity ?
Assigner
References
| URL | Tags | |||||||
|---|---|---|---|---|---|---|---|---|
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Impacted products
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CVE-2026-31968 (GCVE-0-2026-31968)
Vulnerability from cvelistv5 – Published: 2026-03-18 19:38 – Updated: 2026-03-18 19:57
VLAI?
Title
HTSlib CRAM decoder vulnerable to buffer overflow
Summary
HTSlib is a library for reading and writing bioinformatics file formats. CRAM is a compressed format which stores DNA sequence alignment data using a variety of encodings and compression methods. For the `VARINT` and `CONST` encodings, incomplete validation of the context in which the encodings were used could result in up to eight bytes being written beyond the end of a heap allocation, or up to eight bytes being written to the location of a one byte variable on the stack, possibly causing the values to adjacent variables to change unexpectedly. Depending on the data stream this could result either in a heap buffer overflow or a stack overflow. If a user opens a file crafted to exploit this issue it could lead to the program crashing, overwriting of data structures on the heap or stack in ways not expected by the program, or changing the control flow of 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.
Severity ?
CWE
Assigner
References
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|---|---|---|---|---|---|---|---|---|
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CVE-2026-31967 (GCVE-0-2026-31967)
Vulnerability from cvelistv5 – Published: 2026-03-18 19:15 – Updated: 2026-03-18 19:58
VLAI?
Title
HTSlib CRAM reader has out-of-bounds read due to improper validation of input
Summary
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, the value of the mate reference id field was not validated. Later use of this value, for example when converting the data to SAM format, could result in the out of bounds array reads when looking up the corresponding reference name. If the array value obtained also happened to be a valid pointer, it would be interpreted as a string and an attempt would be made to write the data as part of the SAM record. 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. Versions 1.23.1, 1.22.2 and 1.21.1 include fixes for this issue. There is no workaround for this issue.
Severity ?
Assigner
References
| URL | Tags | |||||||
|---|---|---|---|---|---|---|---|---|
|
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Impacted products
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CVE-2026-31966 (GCVE-0-2026-31966)
Vulnerability from cvelistv5 – Published: 2026-03-18 18:58 – Updated: 2026-03-18 19:58
VLAI?
Title
HTSlib CRAM reader has out-of-bounds read due to improper validation of input
Summary
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 CRAM records, the reference data is stored in a char array, and parts matching the alignment record sequence are copied over as necessary. Due to insufficient validation of the feature data series, it was possible to make the `cram_decode_seq()` function copy data from either before the start, or after the end of the stored reference either into the buffer used to store the output sequence for the cram record, or into the buffer used to build the SAM `MD` tag. This allowed arbitrary data to be leaked to the calling function. 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. Versions 1.23.1, 1.22.2 and 1.21.1 include fixes for this issue. There is no workaround for this issue.
Severity ?
Assigner
References
| URL | Tags | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Impacted products
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CVE-2026-31965 (GCVE-0-2026-31965)
Vulnerability from cvelistv5 – Published: 2026-03-18 18:50 – Updated: 2026-03-18 18:50
VLAI?
Title
HTSlib CRAM reader has out-of-bounds reads due to improper validation of input
Summary
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.
Severity ?
Assigner
References
| URL | Tags | |||||||
|---|---|---|---|---|---|---|---|---|
|
||||||||
Impacted products
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CVE-2026-31964 (GCVE-0-2026-31964)
Vulnerability from cvelistv5 – Published: 2026-03-18 18:27 – Updated: 2026-03-18 18:46
VLAI?
Title
HTSlib CRAM decoder has a NULL Pointer Dereference
Summary
HTSlib is a library for reading and writing bioinformatics file formats. CRAM is a compressed format which stores DNA sequence alignment data using a variety of encodings and compression methods. While most alignment records store DNA sequence and quality values, the format also allows them to omit this data in certain cases to save space. Due to some quirks of the CRAM format, it is necessary to handle these records carefully as they will actually store data that needs to be consumed and then discarded. Unfortunately the `CONST`, `XPACK` and `XRLE` encodings did not properly implement the interface needed to do this. Trying to decode records with omitted sequence or quality data using these encodings would result in an attempt to write to a NULL pointer. 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 ?
CWE
- CWE-476 - NULL Pointer Dereference
Assigner
References
| URL | Tags | |||||||
|---|---|---|---|---|---|---|---|---|
|
||||||||
Impacted products
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CVE-2026-31963 (GCVE-0-2026-31963)
Vulnerability from cvelistv5 – Published: 2026-03-18 18:22 – Updated: 2026-03-18 18:52
VLAI?
Title
HTSlib CRAM reader has heap buffer overflow due to improper validation of input
Summary
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.
Severity ?
CWE
Assigner
References
| URL | Tags | |||||||
|---|---|---|---|---|---|---|---|---|
|
||||||||
Impacted products
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CVE-2026-31962 (GCVE-0-2026-31962)
Vulnerability from cvelistv5 – Published: 2026-03-18 18:08 – Updated: 2026-03-18 18:37
VLAI?
Title
HTSlib CRAM reader has heap buffer overflow due to improper validation of input
Summary
HTSlib is a library for reading and writing bioinformatics file formats. CRAM is a compressed format which stores DNA sequence alignment data. While most alignment records store DNA sequence and quality values, the format also allows them to omit this data in certain cases to save space. Due to some quirks of the CRAM format, it is necessary to handle these records carefully as they will actually store data that needs to be consumed and then discarded. Unfortunately the `cram_decode_seq()` did not handle this correctly in some cases. Where this happened it could result in reading a single byte from beyond the end of a heap allocation, followed by writing a single attacker-controlled byte to the same location. 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.
Severity ?
CWE
Assigner
References
| URL | Tags | |||||||
|---|---|---|---|---|---|---|---|---|
|
||||||||
Impacted products
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CVE-2022-21126 (GCVE-0-2022-21126)
Vulnerability from cvelistv5 – Published: 2022-11-29 16:50 – Updated: 2025-04-24 18:34
VLAI?
Title
Creation of Temporary File in Directory with Insecure Permissions
Summary
The package com.github.samtools:htsjdk before 3.0.1 are vulnerable to Creation of Temporary File in Directory with Insecure Permissions due to the createTempDir() function in util/IOUtil.java not checking for the existence of the temporary directory before attempting to create it.
Severity ?
7.3 (High)
CWE
- Creation of Temporary File in Directory with Insecure Permissions
Assigner
References
Impacted products
| Vendor | Product | Version | ||
|---|---|---|---|---|
| n/a | com.github.samtools:htsjdk |
Affected:
unspecified , < 3.0.1
(custom)
|
Date Public ?
2022-11-29 00:00
Credits
Jonathan Leitschuh
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