Re: [Seqan-dev] i am lost again

[Bernd Jagla <bernd.jagla@pasteur.fr>]

Great that works. Don't know how I could have come up with this 
solution... I guess I need A LOT more C++ experience...
So beware of more of these questions....

By the way... I am now looking into how to access a character from a 
string (CharString/Dna5String) and do position based comparisons... But 
I will ask if I won't find anything on the net...

Thanks again,

Bernd

On 9/26/2011 5:38 PM, Holtgrewe, Manuel wrote:
> The offending line is:
>
> > std::ifstream fasta(options.inFile,
> > std::ios_base::in | std::ios_base::binary);
> The ifstream from the STL does not know about SeqAn Strings (which is the type of options.inFile).
>
> Try this instead:
>
> std::ifstream fasta(toCString(options.inFile), std::ios_base::in | std::ios_base::binary);
>
>
> Am 26.09.2011 um 16:30 schrieb Bernd Jagla:
>
> > Sorry for these naive questions...
> >
> > I am running into problems with a simple program to read in fastq data.
> > I am trying to use the samples/demos that you provide...
> >
> > In short I am getting the following error message:
> >
> > make readCleansing
> > Building file: ../src/readCleansing.cpp
> > Invoking: GCC C++ Compiler
> > g++ -DSEQAN_ENABLE_DEBUG=1 -DSEQAN_HAS_ZLIB=1
> > -I/pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/include
> > -I/pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/extras/include
> > -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/readCleansing.d"
> > -MT"src/readCleansing.d" -o "src/readCleansing.o" "../src/readCleansing.cpp"
> > ../src/readCleansing.cpp: In function ‘int main(int, const char**)’:
> > ../src/readCleansing.cpp:299: error: no matching function for call to
> > ‘std::basic_ifstream<char, std::char_traits<char>
> > > ::basic_ifstream(seqan::CharString&, std::_Ios_Openmode)’
> > /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/fstream:442:
> > note: candidates are: std::basic_ifstream<_CharT,
> > _Traits>::basic_ifstream(const char*, std::_Ios_Openmode) [with _CharT =
> > char, _Traits = std::char_traits<char>]
> > /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/fstream:428:
> > note: std::basic_ifstream<_CharT, _Traits>::basic_ifstream() [with
> > _CharT = char, _Traits = std::char_traits<char>]
> > /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iosfwd:89:
> > note: std::basic_ifstream<char, std::char_traits<char>
> > > ::basic_ifstream(const std::basic_ifstream<char,
> > std::char_traits<char>  >&)
> > make: *** [src/readCleansing.o] Error 1
> >
> > The offending code looks like this:
> >
> > std::ifstream fasta(options.inFile,
> > std::ios_base::in | std::ios_base::binary);
> > if (!fasta.good())
> > return 1;
> > RecordReader<std::ifstream, SinglePass<>  >  reader(fasta);
> >
> >
> > I have tried to exchange fasta with fastq, but though I believe that is
> > what I really want it is not the real problem...
> >
> > As I am a novice to C++ and I appologize for the naive questions...
> >
> > Please let me know if you need further information for identifying the
> > problem...
> >
> > PS. Other programs compile correctly
> >
> > Thanks,
> >
> > Bernd
> >
> >
> >
> >
> > _______________________________________________
> > seqan-dev mailing list
> > seqan-dev@lists.fu-berlin.de
> > https://lists.fu-berlin.de/listinfo/seqan-dev
>
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