On Fri, 2 Nov 2018, Remik Ziemlinski wrote:
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.
This rather pessimistic message comes from bamtk.c. It should really be
removed as the Windows build gets tested regularly by Appveyor so it
should be fairly reliable, albeit less battle-tested than on Linux.
Could you tell me what issues to expect? Are these bugs reproducible?
There may be some lurking issues with paths that get split on ':', which
plays badly with Windows drive letters. If you spot problems with this or
anything else, please raise an issue in GitHub so it can be fixed.
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.
We usually build and test with mingw64 (via msys2). What version did you
build, and how did you get it to work with msvc? I didn't think that was
possible...
Rob Davies r...@sanger.ac.uk
The Sanger Institute http://www.sanger.ac.uk/
Hinxton, Cambs.,
CB10 1SA, U.K.
--
The Wellcome Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2742969, whose registered
office is 215 Euston Road, London, NW1 2BE.
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