Re: [Seqan-dev] Trouble using SequenceStream

["Holtgrewe, Manuel" <manuel.holtgrewe@fu-berlin.de>]

Hi Theo,

I think this is related to a bug that was just fixed.

Could you try to update your SeqAn SVN checkout and recompile your program?

HTH,
Manuel
________________________________________
From: Theodore Omtzigt [theo@stillwater-sc.com]
Sent: Thursday, January 24, 2013 6:42 PM
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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