Re: [Seqan-dev] Trouble using SequenceStream
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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