[Seqan-dev] i am lost again
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
