I forked and built the develop branches of htslib and samtools with the
msvc compiler v19.13.26132 that's part of VS2017 v15.6.7. The code
changes were fairly trivial. The makefile modifications were more
significant, though. I think a port to CMake would help unify the build
process. Would you agree? All the tests passed, except it wasn't clear
to me how to get test.pl to work, and I fixed a crash due to
uninitialized mutexes. Also, my requirements are non-interactive, so I
completely skirted curses/tview. Let me know if you'd be interested in
a pull request with any of the above. Thanks,
Remik
On 11/2/18 10:58 AM, Robert Davies wrote:
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.
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