Re: [Seqan-dev] Trouble using SequenceStream

["zhoutianliangwen@genomics.org.cn" <zhoutianliangwen@genomics.org.cn>]

seqan::SequenceStream seqIO(argv[1]);

 

if( !isGood(seqIO) )

{

std::cout <<" file type or format error!\n";

exit(-1);

}

Program will be quit if your file format is unvalid.

 

---

 

 

From: Theodore Omtzigt

Date: 2013-01-25 01:42

To: seqan-dev@lists.fu-berlin.de

Subject: [Seqan-dev] Trouble using SequenceStream

I am getting stuck on the simplest of tasks, reading an uncompressed

fastq file. This statement:

          seqan::SequenceStream seqIO(argv[1]);

 

returns a FILE_FORMAT_ERROR on a valid fastq text file. In

sequence_stream.h in the function _checkFormat, checkStreamFormat

returns false,

 

    // Guess file format, given the record reader.

    template <typename TStream, typename TSpec>

    SeqIOFileFormat_::Type _checkFormat(RecordReader<TStream, TSpec> &

recordReader)

    {

        AutoSeqStreamFormat formatTag;

        if (!checkStreamFormat(recordReader, formatTag))

            return SeqIOFileFormat_::FILE_FORMAT_ERROR;

 

The recursion in checkStreamFormat in guess_stream_format.h is confusing

me so I can't figure out what specific failure it is tripping over. I am

trying to debug this but need some help deciphering the recursion

architecture of the guessFormat code.

 

How do I know it is a valid fastq file? The file provided has been a

test file for non seqan code, and I have been able to use it in seqan

with the FragmentStore without trouble.

 

 

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