samtools/samtools 1.21.1

on GitHub

Download the source code here: samtools-1.21.1.tar.bz2.(The "Source code" downloads are generated by GitHub and are incomplete as they don't bundle HTSlib and are missing some generated files.)

Bug fixes:

• This release bundles HTSlib 1.21.1, which includes many important bug fixes. Please see htslib/NEWS for details.

• Fix use-after-free bug in samtools mpileup -a due to reference sequences being discarded too early. This could happen when the -a option was used, and all the alignments for one of the references started at the same position. This caused mpileup to try to load the next reference before it had finished writing data for the previous one out. (CVE-2026-31972) (PR #2229, fixes #2227. Reported by Pouya Kheradpour)

• Fix samtools fastq -i to force CRAM aux tag decoding. (PR #2155, fixes #2154. Reported by Alex Leonard)

• Improve plot-bamstats quality plots. (PR #2143 combined with PR #2116. Thanks to James Gilbert)

• Fix depth counts when overlap removal is enabled. (PR #2171, fixes #2170. Reported by Yangqi Su)

• Protect against merging CRAM files with different headers. (PR#2220, fixes #2218. Reported by Kevin Lewis)

• Prevent samtools coverage from printing a coverage table on failure. (PR #2247, fixes #2242. Reported by Georges Kanaan)

• Remove deprecated line style commands from plot-bamstats. (PR #2251, fixes #2243. Reported by Suhas Srinivasan)

• Check for file close errors in samtools addreplacerg. (PR #2254. Thanks to Martin Pollard)

• Add missing sam_global_args_free calls to address memory leaks. (PR #2274)

• Wrap ctype.h functions to avoid array subscript warnings, and add casts to prevent sign extension where arrays are indexed with char values. (PR #2306)

• Make samtools cram-size exit cleanly instead of crashing if it reads an invalid CRAM header. (CVE-2026-31973) (PR #2313)
  Build changes:

• Fix broken tests due to MSYS2 changes. Due to changes in how MSYS2 perl reported the identity of the OS it was built for, our tests were failing to adapt to the Windows style file locations. (PR #2196)

• Added settings to limit memory used by samtools sort when running tests. (PR #2226)

• Ensure test files are cleaned up. (PR #2241. Thanks to John Marshall)

• Reordered options for grep commands in tests so the input file is at the end. (PR #2311)

Download the source code here: samtools-1.21.1.tar.bz2.(The "Source code" downloads are generated by GitHub and are incomplete as they don't bundle HTSlib and are missing some generated files.)