Hello, I just ran samtools for the first time on Windows and I saw this
warning at the end of its command-line usage:
Note: The Windows version of SAMtools is mainly designed for read-only
operations, such as viewing the alignments and generating the
pileup.
Binary files generated by the Windows version may be buggy.
Could you tell me what issues to expect? Are these bugs reproducible?
I built htslib and samtools natively with the Visual Studio (msvc)
toolchain and I wonder if this could provide more stability than a mingw
build, unless these are logical or functional bugs rather than
library/api bugs.
Remik
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