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Re: [Seqan-dev] Error with samtools library

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Dear Jakob,


Am Montag, 15. Februar 2016, 15:34:21 schrieb Schulze, Jakob:
> Hi everyone,
> I came across some code which uses the samtools library. Together with seqan
> there is an error which seems to come from samtools but I do not know why.
> Since I am not the author of the samtools include I cannot say much about
> the corresponding lines in the CMakeLists.txt But since commenting out
> seqan from the main.cpp solves the error, I imagined this has something to
> do with seqan.

> [...]

> /home/schulzeja/masterthesis/workDir/seqanTestForReport2/build/samtools-1.2
> /htslib-1.2.1/htslib/bgzf.h:38:29: error: expected unqualified-id before
> numeric constant #define BGZF_MAX_BLOCK_SIZE 0x10000
>                              ^
> /home/schulzeja/masterthesis/tools/seqan-src/include/seqan/stream/iostream_b
> gzf.h:25:16: note: in expansion of macro ‘BGZF_MAX_BLOCK_SIZE’ const
> unsigned BGZF_MAX_BLOCK_SIZE = 64 * 1024;


that is unfortunate. It seems like both libraries use BGZF_MAX_BLOCK_SIZE. We 
will discuss whether we can change this internally, but that won't help you 
right now.
If you use the new SeqAn release you could *not look* for the compression 
libraries, i.e. do not call find_package(zlib). This should deactivate our 
bgzf code and then it should compile.

Best regards,
-- 
Hannes Hauswedell

PhD student
Max Planck Institute for Molecular Genetics / Freie Universität Berlin

address     Institut für Informatik
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telephone   +49 (0)30 838-75241
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e-mail      hannes.hauswedell@[molgen.mpg.de|fu-berlin.de]
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