Re: [Seqan-dev] seqan-dev Digest, Vol 32, Issue 8

[Raymond Wan <rwan@cuhk.edu.hk>]

Hi Neil,


On Thursday, May 31, 2012 12:12 PM, Neil Justice wrote:
> error C3861: 'Bam': identifier not
> found	c:\Seqan\seqan-trunk\extras\demos\bam_library_size.cpp	244
> error C2665: 'open' : none of the 8 overloads could convert all the
> argument types	c:\Seqan\seqan-trunk\extras\demos\bam_library_size.cpp	238
> error C2079: 'inBamStream' uses undefined class
> 'seqan::Stream'	c:\Seqan\seqan-trunk\extras\demos\bam_library_size.cpp	237
> error C2065: 'Bgzf' : undeclared
> identifier	c:\Seqan\seqan-trunk\extras\demos\bam_library_size.cpp	237


I think this is a problem with building the demos -- it doesn't 
necessarily mean that you have a problem with your Seqan installation...


> Assuming these errors are resolved by obtaining zlib/bzlib: link
> https://trac.seqan.de/wiki/HowTo/InstallContribsWindows leads to a
> login/password prompt for FU Berlin for which I have no login or
> password. Is there another link to zlib/bzlib?


zlib and bzlib are public.  Try digging around:

http://zlib.net/
http://www.bzip.org/

for library versions that are suitable for Windows.  After you install 
them, you should check that CMake can indeed find them.  That's 
unrelated to Seqan -- for example, skim over this message about getting 
Zlib to work under Windows with CMake:

http://www.cmake.org/pipermail/cmake/2006-October/011466.html


> Also, which files contain the most performance-sensitive code?


Quite frankly, if there was a section of code that was 
performance-sensitive and they knew about it, I think the Seqan 
developers (which, BTW, is not me) would have spotted it and fixed it.  :-D

On the other hand, they may have something on their to-do list that they 
never got around to fixing...

Ray