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:
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...