samtools mpileup has use-after-free leading to an invalid read
Summary
samtools mpileup has use-after-free leading to an invalid read
Original description
The description as published by the source.
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.
Source: OSV.dev (Open Source Vulnerabilities) NVD GitHub Advisory OSV
Fix status by distribution
Fixed packages published by each distribution for this CVE
- Debian DEBIAN-CVE-2026-31972 samtools
- Ubuntu UBUNTU-CVE-2026-31972 samtools
References
- advisory github.com
- advisory github.com
- advisory nvd.nist.gov
- patch github.com
- web openwall.com