Download the source code here: samtools-1.23.1.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:
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This release bundles HTSlib 1.23.1, which includes many important bug fixes. Please see htslib/NEWS for details.
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Fix incorrect variable expansion in seq_cache_populate.py (PR #2291. Thanks to Ruben Vorderman)
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Don't try to write out empty strings in threaded consensus pileup mode. (PR #2305)
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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)
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Make
samtools cram-sizeexit cleanly instead of crashing if it reads an invalid CRAM header. (CVE-2026-31973) (PR #2313)
Build changes:
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Reordered options for grep commands in tests so the input file is at the end. (PR #2311)
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Limit memory used by samtools sort in tests. (PR #2312)
Download the source code here: samtools-1.23.1.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.)