Re: [Seqan-dev] Error with samtools library

["Schulze, Jakob" <SchulzeJa@rki.de>]

Dear Hannes,
thank you very much for your reply. Changing
set (SEQAN_FIND_DEPENDENCIES ZLIB BZip2)
to
set (SEQAN_FIND_DEPENDENCIES BZip2)
in my CMakeLists.txt removed the error.

Bests and thanks again,
Jakob


-----Ursprüngliche Nachricht-----
Von: Hannes Hauswedell [mailto:hannes.hauswedell@fu-berlin.de] 
Gesendet: Mittwoch, 17. Februar 2016 14:22
An: SeqAn Development
Betreff: Re: [Seqan-dev] Error with samtools library

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/samtool
> s-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/iost
> ream_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
            Takustraße 9
            Room 019
            14195 Berlin
telephone   +49 (0)30 838-75241
fax         +49 (0)30 838-75218
e-mail      hannes.hauswedell@[molgen.mpg.de|fu-berlin.de]

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